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WO2024238872A2 - Isoindolinone-glutarimide antibody conjugates, and uses thereof - Google Patents

Isoindolinone-glutarimide antibody conjugates, and uses thereof Download PDF

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Publication number
WO2024238872A2
WO2024238872A2 PCT/US2024/029822 US2024029822W WO2024238872A2 WO 2024238872 A2 WO2024238872 A2 WO 2024238872A2 US 2024029822 W US2024029822 W US 2024029822W WO 2024238872 A2 WO2024238872 A2 WO 2024238872A2
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alkyl
antibody conjugate
conjugate composition
aryldiyl
heteroalkyldiyl
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WO2024238872A3 (en
Inventor
Luca Arista
John A. Flygare
Freya M. HARVEY
Thomas Ryckmans
Sean Wesley Smith
Christoph C. GROHMANN
Bernhard Geierstanger
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Firefly Bio Inc
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Firefly Bio Inc
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6835—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site
    • A61K47/6851—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a determinant of a tumour cell
    • A61K47/6863—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a determinant of a tumour cell the tumour determinant being from stomach or intestines cancer cell
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6801—Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent
    • A61K47/6803—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6835—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site
    • A61K47/6851—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a determinant of a tumour cell
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6835—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site
    • A61K47/6851—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a determinant of a tumour cell
    • A61K47/6855—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a determinant of a tumour cell the tumour determinant being from breast cancer cell
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents

Definitions

  • the disclosure relates generally to antibody conjugate compositions, intermediates for their manufacture, and methods of their use.
  • the compositions are useful for facilitating intracellular degradation of target proteins.
  • the ubiquitin proteasome system can be manipulated to conduct targeted degradation of specific proteins. Promoting the targeted degradation of pathogenic proteins using small molecule degraders is a new modality in the treatment of diseases, including redirecting the activity of E3 ligases such as cereblon.
  • Proteolysis targeting chimera compounds called PROTAC (Sakamoto, K. M , et al. (2001) Proc. Natl. Acad. Sci. USA 98:8554-8559; Sun, X. et al. (2019) Signal Transduct. Target. Ther. 4:64; Schapira, M., et al (2019) Nat. Rev. Drug Discov.
  • PROTAC comprise three parts, including a ligand for binding a target protein, another ligand for recruiting an E3 ligase, and a linker to help anchor the target protein to the E3 ubiquitin ligase to promote its ubiquitination and subsequent proteasomal degradation. Similar to PROTAC, molecular glues can also cause ubiquitination and degradation of a target protein.
  • molecular glues are small molecular weight compounds that trigger a compact protein-protein interaction between a target protein and an E3 ubiquitin ligase.
  • Molecular glues are typically smaller than PROTAC and may have better pharmacological properties, higher membrane permeability, better cellular uptake, and better penetration of the blood-brain barrier.
  • Molecular glues promote the poly-ubiquitination and proteasomal degradation of various disease-associated protein targets (Chamberlain, P., et al (2019) Drug Disc. Today. Tech. 31:29-34; WO 2022/152821).
  • the molecular glue molecules bind to both the E3 ligase and the target protein, thereby mediating an alteration of the ligase surface and enabling an interaction with the target protein.
  • Examples include the IMiD (immunomodulatory imide drug) class including thalidomide, lenalidomide and pomalidomide, each approved for use in treating hematological cancers. More efficient targeting strategies are still required.
  • GSPT1 contains a well-defined degron, a peptidic motif that signals for degradation, allowing for the recruitment of the E3 ligase cereblon (CRBN) and subsequent proteasomal degradation in the presence of molecular glue degraders.
  • GSPT1 (G1 to S phase transition 1) is a translation termination factor that recognizes the termination codon by binding eRFl, forcing the proteins to dissociate from the ribosome after translation
  • Downregulation of GSPT1 can cause the abnormal expression of key proteins, inhibit proliferation or induce apoptosis in diverse tumor cells (Chauvin, C., et al. (2007) Mol. Cell. Biol. 27:5619-5629; Matyskiela, M. E., et al. (2016) Nature 535:252-257; Yang, I, et al. J. Med. Chem. (2019) 62:9471-9487).
  • Targeted therapeutic agents to treat hyperproliferative disorders like cancer, and other disease are of interest.
  • the invention is generally directed to an antibody conjugate composition
  • an antibody conjugate composition comprising an isoindolinone-glutarimide moiety covalently attached to an antibody by an antibody linker, wherein the antibody binds to a tumor-associated antigen or cell-surface receptor.
  • the antibody conjugate composition has Formula I: or a pharmaceutically acceptable salt thereof, wherein:
  • L is the antibody linker
  • IG is the isoindolinone-glutarimide moiety; and p is an integer from 1 to 12
  • Another aspect of the invention is an antibody conjugate composition selected from Formulae la and lb:
  • Another aspect of the invention is an isoindolinone-glutarimide linker compound selected from Formulae Ila and lib: lib wherein the substituents are defined herein.
  • Another aspect of the invention is the antibody conjugate composition prepared by conjugation of a cysteine amino acid of an antibody with an isoindolinone-glutarimide linker compound.
  • Another aspect of the invention is a process for preparing the antibody conjugate comprising reacting a cysteine amino acid of an antibody with an isoindolinone-glutarimide linker compound.
  • Another aspect of the invention is a pharmaceutical composition comprising a therapeutically effective amount of the antibody conjugate composition, and one or more pharmaceutically acceptable diluent, vehicle, carrier or excipient
  • Another aspect of the invention is a method for treating cancer comprising administering a therapeutically effective amount of the pharmaceutical composition to a patient in need thereof,
  • Another aspect of the invention is a use of the antibody conjugate composition in the manufacture of a medicament for the treatment of cancer in a mammal.
  • Another aspect of the invention is the antibody conjugate composition for use in a method for treating cancer.
  • Figure 1 shows a graph of in vivo tumor volume over time in the treatment of CD22+ WSU-DLCL2 syngeneic tumor bearing CB17 SCID mice with pinatuzumab, and anti-CD22 conjugates IGAC-59 and IGAC-62 (Table 3).
  • Figure 2 shows a graph of in vivo tumor volume over time in the treatment of CD22+ WSU-DLCL2 syngeneic tumor bearing CB17 SCID mice with pinatuzumab, and anti-CD22 conjugates IGAC-53, IGAC-60 and IGAC-62 (Table 3).
  • Figure 3 shows a graph of in vivo tumor volume over time in the treatment of HER2+ NCI-N87 gastric tumor xenograft bearing female BALB/c nude mice with anti-HER2 conjugates IGAC-58 and IGAC-61 (Table 3).
  • Figure 4 shows a graph of in vivo tumor volume over time in the treatment of HER2+ NCI-N87 gastric tumor xenograft bearing female BALB/c nude mice with anti-HER2 conjugates IGAC-54, IGAC-55, IGAC-56 and IGAC-57 (Table 3).
  • antibody or “antibody construct” refer to a polypeptide comprising an antigen binding region (including the complementarity determining region (CDRs)) from an immunoglobulin gene or fragments thereof.
  • antibody specifically encompasses monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e g., bispecific antibodies), and antibody fragments that exhibit the desired biological activity.
  • An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one “heavy” chain (about 50-70 kDa) connected by disulfide bonds.
  • Each chain is composed of structural domains, which are referred to as immunoglobulin domains. These domains are classified into different categories by size and function, e g., variable domains or regions on the light and heavy chains (VL and VH, respectively) and constant domains or regions on the light and heavy chains (CL and CH, respectively).
  • the N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids, referred to as the paratope, primarily responsible for antigen recognition, i.e., the antigen binding domain.
  • Light chains are classified as either kappa or lambda.
  • Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.
  • IgG antibodies are large molecules of about 150 kDa composed of four peptide chains.
  • IgG antibodies contain two identical class y heavy chains of about 50 kDa and two identical light chains of about 25 kDa, thus a tetrameric quaternary structure The two heavy chains are linked to each other and to a light chain each by disulfide bonds. The resulting tetramer has two identical halves, which together form the Y-like shape Each end of the fork contains an identical antigen binding domain.
  • IgGl IgG2
  • IgG3 IgG4
  • IgG4 IgG4
  • IgGl is the most abundant
  • the antigen binding domain of an antibody will be most critical in specificity and affinity of binding to cancer cells.
  • Bispecific antibodies are antibodies that bind two distinct epitopes to cancer (Suurs F.V. et al Pharmacology & Therapeutics 201: 103-119). Bispecific antibodies may engage immune cells to destroy tumor cells, deliver isoindolinone-glutarimide moi eties to tumors, and/or block tumor signaling pathways.
  • An antibody that targets a particular antigen includes a bispecific or multispecific antibody with at least one antigen binding region that targets the particular antigen.
  • the targeted monoclonal antibody is a bispecific antibody with at least one antigen binding region that targets tumor cells.
  • antigens include but are not limited to: mesothelin, prostate specific membrane antigen (PSMA), HER2, TROP2, CEA, CEACAM5, EGFR, 5T4, Nectin4, CCL-1, CCR7, CD19, CD20, CD22, CD30, CD33, CD70, CD79b, CD 123, CDH3, B7H3, B7H4 (also known as 08E), Integrin-beta6, protein tyrosine kinase 7 (PTK7), glypican-3, GPC-1, LIV-1, Folate receptor alpha, Claudinl8.2, RG1, fucosyl-GMl, tissue factor (CD142), cKit (CD117), Axl, , GC-C, CTLA-4, and CD44 (WO 2017/196598).
  • Other antigen binding regions of bispecific antibodies include those in the following section: ANTIBODY TARGETS.
  • the antibody construct is an antigen-binding antibody “fragment,” which comprises at least an antigen-binding region of an antibody, alone or with other components that together constitute the antibody construct.
  • antibody “fragments” are known in the art, including, for instance, (i) a Fab fragment, which is a monovalent fragment consisting of the VL, VH, CL, and CHi domains, (ii) a F(ab’)2 fragment, which is a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region, (iii) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (iv) a Fab’ fragment, which results from breaking the disulfide bridge of an F(ab’)2 fragment using mild reducing conditions, (v) a disulfide-stabilized Fv fragment (dsFv), and (vi) a single chain Fv (scFv), which is a monovalent Fab fragment.
  • the antibody or antibody fragment can be part of a larger construct, for example, a conjugate or fusion construct of the antibody fragment to additional regions.
  • the antibody fragment can be fused to an Fc region as described herein
  • the antibody fragment e.g., a Fab or scFv
  • the antibody fragment can be part of a chimeric antigen receptor or chimeric T-cell receptor, for instance, by fusing to a transmembrane domain (optionally with an intervening linker or “stalk” (e.g., hinge region)) and optional intercellular signaling domain.
  • the antibody fragment can be fused to the gamma and/or delta chains of a t-cell receptor, so as to provide a T-cell receptor like construct that binds PD-L1 .
  • the antibody fragment is part of a bispecific T-cell engager (BiTEs) comprising a CD1 or CD3 binding domain and linker.
  • BiTEs bispecific T-cell engager
  • the antibody construct comprises an Fc domain.
  • the antibody construct is a fusion protein.
  • the antigen binding domain can be a single-chain variable region fragment (scFv).
  • scFv single-chain variable region fragment
  • dsFv disulfide-stabilized variable region fragments
  • the antibody construct or antigen binding domain may comprise one or more variable regions (e.g., two variable regions) of an antigen binding domain of an antibody, each variable region comprising a CDR1, a CDR2, and a CDR3.
  • Cysteine-mutant antibody is an antibody in which one or more amino acid residues of an antibody are substituted with cysteine residues.
  • a cysteine-mutant antibody may be prepared from the parent antibody by antibody engineering methods (Junutula, J et al., (2008b) Nature Biotech., 26(8):925-932; Doman et al. (2QQ9) Blood 114(13):2721-2729; US 7521541; US 7723485; US 2012/0121615; WO 2009/052249).
  • Cysteine residues provide for site-specific conjugation of a drug moiety such as a isoindolinone-glutarimide compound to the antibody through the reactive cysteine thiol groups at the engineered cysteine sites but do not perturb immunoglobulin folding and assembly or alter antigen binding and effector functions.
  • Cysteine- mutant antibodies can be conjugated to the isoindolinone-glutarimide linker compound with uniform stoichiometry of the antibody conjugate (e.g., up to two isoindolinone-glutarimide moieties per antibody in an antibody that has a single engineered, mutant cysteine site).
  • the isoindolinone-glutarimide linker compound has a reactive electrophilic group to react specifically with the free cysteine thiol groups of the cysteine-mutant antibody.
  • Epitope means any antigenic determinant or epitopic determinant of an antigen to which an antigen binding domain binds (i.e., at the paratope of the antigen binding domain).
  • Antigenic determinants usually consist of chemically active surface groupings of molecules, such as amino acids or sugar side chains, and usually have specific three dimensional structural characteristics, as well as specific charge characteristics
  • Fc receptor refers to a receptor that binds to the Fc region of an antibody
  • FcyR which binds to IgG
  • FcaR which binds to IgA
  • FceR which binds to IgE.
  • the FcyR family includes several members, such as Fcyl (CD64), FcyRIIA (CD32A), FcyRIIB (CD32B), FcyRIIIA (CD16A), and FcyRIIIB (CD16B).
  • the Fey receptors differ in their affinity for IgG and also have different affinities for the IgG subclasses (e.g., IgGl, IgG2, IgG3, and IgG4).
  • Nucleic acid or amino acid sequence “identity,” as referenced herein, can be determined by comparing a nucleic acid or amino acid sequence of interest to a reference nucleic acid or amino acid sequence.
  • the percent identity is the number of nucleotides or amino acid residues that are the same (i.e., that are identical) as between the optimally aligned sequence of interest and the reference sequence divided by the length of the longest sequence (i.e., the length of either the sequence of interest or the reference sequence, whichever is longer). Alignment of sequences and calculation of percent identity can be performed using available software programs.
  • Such programs include CLUSTAL-W, T-Coffee, and ALIGN (for alignment of nucleic acid and amino acid sequences), BLAST programs (e g., BLAST 2.1, BL2SEQ, BLASTp, BLASTn, and the like) and FASTA programs (e.g., FASTA3x, FASTM, and S SEARCH) (for sequence alignment and sequence similarity searches). Sequence alignment algorithms also are disclosed in, for example, Altschul et al., J. Molecular Biol., 215(3): 403-410 (1990), Beigert et al., Proc. Natl. Acad. Sci. USA, 106( ⁇ Q ⁇ .
  • Percent (%) identity of sequences can be also calculated, for example, as 100 x [(identical positions)/min(TGA, TGB)], where TGA and TGB are the sum of the number of residues and internal gap positions in peptide sequences A and B in the alignment that minimizes TGA and TGB. See, e.g., Russell et al., J. Mol Biol., 244: 332-350 (1994).
  • the “antibody construct” or “binding agent” comprises Ig heavy and light chain variable region polypeptides that together form the antigen binding site.
  • Each of the heavy and light chain variable regions are polypeptides comprising three complementarity determining regions (CDR1, CDR2, and CDR3) connected by framework regions.
  • the antibody construct can be any of a variety of types of binding agents known in the art that comprise Ig heavy and light chains.
  • the binding agent can be an antibody, an antigen-binding antibody “fragment,” or a T-cell receptor.
  • Amino acid refers to any monomeric unit that can be incorporated into a peptide, polypeptide, or protein.
  • Amino acids include naturally-occurring a-amino acids and their stereoisomers, as well as unnatural (non-naturally occurring) amino acids and their stereoisomers.
  • “Stereoisomers” of a given amino acid refer to isomers having the same molecular formula and intramolecular bonds but different three-dimensional arrangements of bonds and atoms (e.g., an L-amino acid and the corresponding D-amino acid).
  • amino acids can be glycosylated (e.g., //-linked glycans, O-linked glycans, phosphoglycans, C-linked glycans, or glypication) or deglycosylated.
  • Amino acids may be referred to herein by either the commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission.
  • Naturally-occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, y-carboxyglutamate, and O-phosphoserine.
  • Naturally-occurring a-amino acids include, without limitation, alanine (Ala), cysteine (Cys), aspartic acid (Asp), glutamic acid (Glu), phenylalanine (Phe), glycine (Gly), histidine (His), isoleucine (He), arginine (Arg), lysine (Lys), leucine (Leu), methionine (Met), asparagine (Asn), proline (Pro), glutamine (Gin), serine (Ser), threonine (Thr), valine (Vai), tryptophan (Trp), tyrosine (Tyr), and combinations thereof.
  • Stereoisomers of naturally- occurring a-amino acids include, without limitation, D-alanine (D-Ala), D-cysteine (D-Cys), D-aspartic acid (D-Asp), D-glutamic acid (D-Glu), D-phenylalanine (D-Phe), D-histidine (D-His), D-isoleucine (D-Ile), D-arginine (D-Arg), D-lysine (D-Lys), D-leucine (D-Leu), D-methionine (D-Met), D-asparagine (D-Asn), D-proline (D-Pro), D-glutamine (D-Gln), D-serine (D-Ser), D-threonine (D-Thr), D-valine (D-Val), D-tryptophan (D-Trp), D-tyrosine (D-Tyr), and combinations thereof.
  • D-alanine D-
  • Naturally-occurring amino acids include those formed in proteins by post-translational modification, such as citrulline (Cit).
  • Unnatural (non-naturally occurring) amino acids include, without limitation, amino acid analogs, amino acid mimetics, synthetic amino acids, A-substituted glycines, and A-methyl amino acids in either the L- or D-configuration that function in a manner similar to the naturally- occurring amino acids.
  • amino acid analogs can be unnatural amino acids that have the same basic chemical structure as naturally-occurring amino acids (i.e., a carbon that is bonded to a hydrogen, a carboxyl group, an amino group) but have modified side-chain groups or modified peptide backbones, e.g., homoserine, norleucine, methionine sulfoxide, and methionine methyl sulfonium.
  • Amino acid mimetics refer to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally -occurring amino acid.
  • Linker refers to a functional group that covalently bonds two or more moieties in an antibody conjugate compound.
  • the linking moiety can serve to covalently bond a drug isoindolinone-glutarimide moiety to an antibody in an antibody conjugate composition.
  • Useful bonds for connecting linking moieties to proteins and other materials include, but are not limited to, amides, amines, esters, carbamates, ureas, thioethers, thiocarbamates, thiocarbonates, and thioureas.
  • Divalent refers to a chemical moiety that contains two points of attachment for linking two functional groups; polyvalent linking moieties can have additional points of attachment for linking further functional groups.
  • Divalent radicals may be denoted by the suffix “diyl”.
  • divalent linking moieties include divalent polymer moieties such as divalent poly(ethylene glycol), divalent cycloalkyl, divalent heterocycloalkyl, divalent aryl, and divalent heteroaryl group.
  • a “divalent cycloalkyl, heterocycloalkyl, aryl, or heteroaryl group” refers to a cycloalkyl, heterocycloalkyl, aryl, or heteroaryl group having two points of attachment for covalently linking two moieties in a molecule or material. Cycloalkyl, heterocycloalkyl, aryl, or heteroaryl groups can be substituted or unsubstituted. Cycloalkyl, heterocycloalkyl, aryl, or heteroaryl groups can be substituted with one or more groups selected from halo, hydroxy, amino, alkylamino, amido, acyl, nitro, cyano, alkoxy, and others.
  • a wavy line (“ ”) and one or more asterisks (*) represents a point of attachment of the specified chemical moiety to another moiety. If the specified chemical moiety has two wavy lines (“ present, it will be understood that the chemical moiety can be used bilaterally, i.e., as read from left to right or from right to left. In some embodiments, a specified moiety having two wavy lines present is considered to be used as read from left to right.
  • Alkyl refers to a straight (linear) or branched, saturated, aliphatic radical having the number of carbon atoms indicated. Alkyl can include any number of carbons, for example from one to six, one to eight, one to twelve, one to twenty, or one to forty.
  • alkyl groups include, but are not limited to, methyl (Me, -CH 3 ), ethyl (Et, -CH 2 CH 3 ), 1 -propyl (n-Pr, n- propyl, -CH 2 CH 2 CH 3 ), 2-propyl (i-Pr, i-propyl, -CH(CH 3 )2), 1 -butyl (n-Bu, n-butyl, - CH 2 CH 2 CH 2 CH 3 ), 2-m ethyl- 1 -propyl (i-Bu, i-butyl, -CH 2 CH(CH 3 )2), 2 -butyl (s-Bu, s-butyl, - CH(CH 3 )CH 2 CH 3 ), 2-methyl-2-propyl (t-Bu, t-butyl, -C(CH 3 ) 3 ), 1 -pentyl (n-pentyl, - CH 2 CH 2 CH 2 CH 2 CH 3
  • alkyldiyl refers to a divalent alkyl radical.
  • alkyldiyl groups include, but are not limited to, methylene (-CH 2 -), ethylene (-CH 2 CH 2 -), propylene (- CH 2 CH 2 CH 2 -), and the like.
  • An alkyldiyl group may also be referred to as an “alkylene” group.
  • Alkynyl refers to a straight (linear) or branched, unsaturated, aliphatic radical having the number of carbon atoms indicated and at least one carbon-carbon triple bond, sp. Alkynyl can include from two to about 12 or more carbons atoms.
  • C 2 -C 6 alkynyl includes, but is not limited to ethynyl (-CACI I), propynyl (propargyl, -CI FCUCI I), butynyl, pentynyl, hexynyl, and isomers thereof Alkynyl groups can be substituted or unsubstituted.
  • alkynylene or “alkynyldiyl” refer to a divalent alkynyl radical.
  • Heteroalkyl or “heteroalkylene” refer to a monovalent, straight or branched chain alkyl group, as defined above, comprising at least one heteroatom including but not limited to Si, N, O, P or S within the alkyl chain or at a terminus of the alkyl chain. In some embodiments, a heteroatom is within the alkyl chain. In other embodiments, a heteroatom is at a terminus of the alkylene and thus serves to join the alkyl to the remainder of the molecule. In some embodiments, a heteroalkyl group may have 1 to 12 carbon atoms (C 1 -C 12 heteroalkyl).
  • a heteroalkyl group may have 1 to 24 carbon atoms (C 1 -C24 heteroalkyl). In some embodiments, a heteroalkyl group may have 1 to 40 carbon atoms (C 1 -C40 heteroalkyl). Unless stated otherwise specifically in the specification, a heteroalkyl group is optionally substituted.
  • heteroalkyl groups can be substituted with 1 -6 fluoro (F) substituents, for example, on the carbon backbone (as -CHF- or -CF 2 -) or on terminal carbons of straight chain or branched heteroalkyls (such as -CHF2 or -CF3).
  • a terminal polyethylene glycol (PEG) moiety is a type of heteroalkyl group.
  • exemplary heteroalkyl groups also include ethylene oxide (e.g., polyethylene oxide), propylene oxide, amino acid chains (i.e., short to medium length peptides such as containing 1-15 amino acids), and alkyl chains connected via a variety of functional groups such as amides, disulfides, ketones, phosphonates, phosphates, sulfates, sulfones, sulfonamides, esters, ethers, -S-, carbamates, ureas, thioureas, anhydrides, or the like (including combinations thereof).
  • a heteroalkyl group includes a poly amino acid having 1-10 amino acids.
  • a heteroalkyl group includes a polyamin
  • Heteroalkyl groups include a solubilizing unit comprising one or more groups of polyglycine, polysarcosine, polyethyleneoxy (PEG), and a glycoside, or combinations thereof.
  • Heteroalkenyl refers to a heteroalkyl group, as defined above, that contains at least one carbon-carbon double bond.
  • Heteroalkynyl refers to a heteroalkyl group, as defined above, that contains at least one carbon-carbon triple bond.
  • Heteroalkyldiyl refers to a divalent form of a heteroalkyl group as defined above.
  • a heteroalkyldiyl group may have 1 to 12 carbon atoms (C 1 - C 12 heteroalkyl diyl).
  • a heteroalkyldiyl group may have 1 to 24 carbon atoms (C 1 -C 24 heteroalkyldiyl).
  • a heteroalkyldiyl group may have 1 to 40 carbon atoms (C 1 -C 40 heteroalkyldiyl).
  • a divalent polyethylene glycol (PEG) moiety with one to about 50 units of -OCH 2 CH 2 - is a type of heteroalkyl diyl group.
  • Heteroalkenyl diyl refers to a divalent form of a heteroalkenyl group.
  • Heteroalkynyldiyl refers to a divalent form of a heteroalkynyl group.
  • carrier refers to a saturated or partially unsaturated, monocyclic, fused bicyclic, or bridged polycyclic ring assembly containing from 3 to 12 ring atoms, or the number of atoms indicated.
  • Saturated monocyclic carbocyclic rings include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cyclooctyl.
  • Saturated bicyclic and polycyclic carbocyclic rings include, for example, norbomane, [2.2.2] bicyclooctane, decahydronaphthalene and adamantane.
  • Carbocyclic groups can also be partially unsaturated, having one or more double or triple bonds in the ring.
  • carbocyclic groups that are partially unsaturated include, but are not limited to, cyclobutene, cyclopentene, cyclohexene, cyclohexadiene (1,3- and 1 ,4-isomers), cycloheptene, cycloheptadiene, cyclooctene, cyclooctadiene (1,3-, 1,4- and 1,5-isomers), norbomene, and norbomadiene.
  • cycloalkyl diyl refers to a divalent cycloalkyl radical.
  • Aryl refers to a monovalent aromatic hydrocarbon radical of 6-20 carbon atoms (C 6 - C 20 ) derived by the removal of one hydrogen atom from a single carbon atom of a parent aromatic ring system.
  • Aryl groups can be monocyclic, fused to form bicyclic or tricyclic groups, or linked by a bond to form a biaryl group.
  • Representative aryl groups include phenyl, naphthyl and biphenyl.
  • Other aryl groups include benzyl, having a methylene linking group.
  • Some aryl groups have from 6 to 12 ring members, such as phenyl, naphthyl or biphenyl.
  • Other aryl groups have from 6 to 10 ring members, such as phenyl or naphthyl.
  • arylene or “aryldiyl” mean a divalent aromatic hydrocarbon radical of 6-20 carbon atoms (C 6 - C 20 ) derived by the removal of two hydrogen atom from a two carbon atoms of a parent aromatic ring system.
  • Some aryldiyl groups are represented in the exemplary structures as “Ar”.
  • Aryldiyl includes bicyclic radicals comprising an aromatic ring fused to a saturated, partially unsaturated ring, or aromatic carbocyclic ring.
  • Typical aryldiyl groups include, but are not limited to, radicals derived from benzene (phenyldiyl), substituted benzenes, naphthalene, anthracene, biphenylene, indenylene, indanylene, 1,2-dihydronaphthalene, 1, 2,3,4- tetrahydronaphthyl, and the like.
  • Aryldiyl groups are also referred to as “arylene”, and are optionally substituted with one or more substituents described herein.
  • heterocycle refers to a saturated or a partially unsaturated (i.e., having one or more double and/or triple bonds within the ring) carbocyclic radical of 3 to about 20 ring atoms in which at least one ring atom is a heteroatom selected from nitrogen, oxygen, phosphorus and sulfur, the remaining ring atoms being C, where one or more ring atoms is optionally substituted independently with one or more substituents described below.
  • a heterocycle may be a monocycle having 3 to 7 ring members (2 to 6 carbon atoms and 1 to 4 heteroatoms selected from N, O, P, and S) or a bicycle having 7 to 10 ring members (4 to 9 carbon atoms and 1 to 6 heteroatoms selected from N, O, P, and S), for example: a bicyclo [4,5], [5,5], [5,6], or [6,6] system.
  • Heterocycles are described in Paquette, Leo A.; “Principles of Modern Heterocyclic Chemistry” (W A Benjamin, New York, 1968), particularly Chapters 1, 3, 4, 6, 7, and 9; “The Chemistry of Heterocyclic Compounds, A series of Monographs” (John Wiley & Sons, New York, 1950 to present), in particular Volumes 13, 14, 16, 19, and 28; and J. Am. Chem. Soc. (1960) 82:5566. “Heterocyclyl” also includes radicals where heterocycle radicals are fused with a saturated, partially unsaturated ring, or aromatic carbocyclic or heterocyclic ring.
  • heterocyclic rings include, but are not limited to, morpholin-4-yl, piperidin-l-yl, piperazinyl, piperazin-4-yl-2-one, piperazin-4-yl-3-one, pyrrolidin-l-yl, thiomorpholin-4-yl, S- dioxothiomorpholin-4-yl, azocan-l-yl, azetidin-l-yl, octahydropyrido[l,2-a]pyrazin-2-yl, [l,4]diazepan-l-yl, pyrrolidinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, tetrahydropyranyl, dihydropyranyl, tetrahydrothiopyranyl, piperidino, morpholino, thiomorpholino, thioxanyl, piperazinyl, homopiperaz
  • heterocyclyl diyl refers to a divalent, saturated or a partially unsaturated (i.e., having one or more double and/or triple bonds within the ring) carbocyclic radical of 3 to about 20 ring atoms in which at least one ring atom is a heteroatom selected from nitrogen, oxygen, phosphorus and sulfur, the remaining ring atoms being C, where one or more ring atoms is optionally substituted independently with one or more substituents as described.
  • Examples of 5- membered and 6-membered heterocyclyldiyls include morpholinyldiyl, piperidinyldiyl, piperazinyldiyl, pyrrolidinyldiyl, dioxanyldiyl, thiomorpholinyldiyl, and S- dioxothiomorpholinyldiyl.
  • heteroaryl refers to a monovalent aromatic radical of 5-, 6-, or 7-membered rings, and includes fused ring systems (at least one of which is aromatic) of 5-20 atoms, containing one or more heteroatoms independently selected from nitrogen, oxygen, and sulfur.
  • heteroaryl groups are pyridinyl (including, for example, 2-hydroxypyridinyl), imidazolyl, imidazopyridinyl, pyrimidinyl (including, for example, 4-hydroxypyrimidinyl), pyrazolyl, triazolyl, pyrazinyl, tetrazolyl, furyl, thienyl, isoxazolyl, thiazolyl, oxadiazolyl, oxazolyl, isothiazolyl, pyrrolyl, quinolinyl, isoquinolinyl, tetrahydroisoquinolinyl, indolyl, benzimidazolyl, benzofuranyl, cinnolinyl, indazolyl, indolizinyl, phthalazinyl, pyridazinyl, triazinyl, isoindolyl, pteridinyl, purinyl, oxadiazol
  • heteroaryldiyl refers to a divalent aromatic radical of 5-, 6-, or 7-membered rings, and includes fused ring systems (at least one of which is aromatic) of 5-20 atoms, containing one or more heteroatoms independently selected from nitrogen, oxygen, and sulfur.
  • Examples of 5-membered and 6-membered heteroaryldiyls include pyridyldiyl, imidazolyl diyl, pyrimidinyl diyl, pyrazolyldiyl, triazolyldiyl, pyrazinyldiyl, tetrazolyldiyl, furyldiyl, thienyldiyl, isoxazolyl diyl diyl, thiazolyldiyl, oxadi azolyldiyl, oxazolyldiyl, isothiazolyldiyl, and pyrrolyldiyl.
  • the heterocycle or heteroaryl groups may be carbon (carbon-linked), or nitrogen (nitrogen-linked) bonded where such is possible.
  • carbon bonded heterocycles or heteroaryls are bonded at position 2, 3, 4, 5, or 6 of a pyridine, position 3, 4, 5, or 6 of a pyridazine, position 2, 4, 5, or 6 of a pyrimidine, position 2, 3, 5, or 6 of a pyrazine, position 2, 3, 4, or 5 of a furan, tetrahydrofuran, thiofuran, thiophene, pyrrole or tetrahydropyrrole, position 2, 4, or 5 of an oxazole, imidazole or thiazole, position 3, 4, or 5 of an isoxazole, pyrazole, or isothiazole, position 2 or 3 of an aziridine, position 2, 3, or 4 of an azetidine, position 2, 3, 4, 5, 6, 7, or 8 of a quinoline or position 1, 3, 4, 5, 6,
  • nitrogen bonded heterocycles or heteroaryls are bonded at position 1 of an aziridine, azetidine, pyrrole, pyrrolidine, 2-pyrroline, 3-pyrroline, imidazole, imidazolidine, 2-imidazoline, 3 -imidazoline, pyrazole, pyrazoline, 2-pyrazoline, 3- pyrazoline, piperidine, piperazine, indole, indoline, IH-indazole, position 2 of a isoindole, or isoindolinone, position 4 of a morpholine, and position 9 of a carbazole, or p-carboline.
  • halo and “halogen,” by themselves or as part of another substituent, refer to a fluorine, chlorine, bromine, or iodine atom.
  • quaternary ammonium salt refers to a tertiary amine that has been quaternized with an alkyl substituent (e g., a C 1 -C4 alkyl such as methyl, ethyl, propyl, or butyl).
  • an alkyl substituent e g., a C 1 -C4 alkyl such as methyl, ethyl, propyl, or butyl.
  • treat refers to any indicia of success in the treatment or amelioration of an injury, pathology, condition (e.g., cancer), or symptom (e.g., cognitive impairment), including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or making the symptom, injury, pathology, or condition more tolerable to the patient; reduction in the rate of symptom progression; decreasing the frequency or duration of the symptom or condition; or, in some situations, preventing the onset of the symptom.
  • the treatment or amelioration of symptoms can be based on any objective or subjective parameter, including, for example, the result of a physical examination.
  • cancer refers to cells which exhibit autonomous, unregulated growth, such that the cells exhibit an aberrant growth phenotype characterized by a significant loss of control over cell proliferation.
  • C 6 lls of interest for detection, analysis, and/or treatment in the context of the invention include cancer cells (e.g., cancer cells from an individual with cancer), malignant cancer cells, pre-metastatic cancer cells, metastatic cancer cells, and non-metastatic cancer cells. Cancers of virtually every tissue are known.
  • cancer burden refers to the quantum of cancer cells or cancer volume in a subject. Reducing cancer burden accordingly refers to reducing the number of cancer cells or the cancer cell volume in a subject.
  • cancer cell refers to any cell that is a cancer cell (e.g., from any of the cancers for which an individual can be treated, e.g., isolated from an individual having cancer) or is derived from a cancer cell, e.g., clone of a cancer cell.
  • a cancer cell can be from an established cancer cell line, can be a primary cell isolated from an individual with cancer, can be a progeny cell from a primary cell isolated from an individual with cancer, and the like.
  • the term can also refer to a portion of a cancer cell, such as a sub-cellular portion, a cell membrane portion, or a cell lysate of a cancer cell.
  • cancers are known to those of skill in the art, including solid tumors such as carcinomas, sarcomas, glioblastomas, melanomas, lymphomas, and myelomas, and circulating cancers such as leukemias.
  • solid tumors such as carcinomas, sarcomas, glioblastomas, melanomas, lymphomas, and myelomas
  • circulating cancers such as leukemias.
  • cancer includes any form of cancer, including but not limited to, solid tumor cancers (e.g., skin, lung, prostate, breast, gastric, bladder, colon, ovarian, pancreas, kidney, liver, glioblastoma, medulloblastoma, leiomyosarcoma, head & neck squamous cell carcinomas, melanomas, and neuroendocrine) and liquid cancers (e.g., hematological cancers); carcinomas; soft tissue tumors; sarcomas; teratomas; melanomas; leukemias; lymphomas; and brain cancers, including minimal residual disease, and including both primary and metastatic tumors.
  • solid tumor cancers e.g., skin, lung, prostate, breast, gastric, bladder, colon, ovarian
  • pancreas kidney, liver, glioblastoma, medulloblastoma, leiomyosarcoma, head & neck squamous cell carcinomas, melan
  • phrases “effective amount” and “therapeutically effective amount” refer to a dose or amount of a substance such as the antibody conjugate of the invention that produces therapeutic effects for which it is administered.
  • the exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, e.g., Lieberman, Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd, The Art, Science and Technology of Pharmaceutical Compounding (1999); Pickar, Dosage Calculations (1999); Goodman & Gilman ’s The Pharmacological Basis of Therapeutics, 11 th Edition (McGraw-Hill, 2006); and Remington: The Science and Practice of Pharmacy, 22 nd Edition, (Pharmaceutical Press, London, 2012)).
  • the therapeutically effective amount of the antibody conjugate may reduce the number of cancer cells; reduce the tumor size; inhibit (i.e., slow to some extent and preferably stop) cancer cell infiltration into peripheral organs; inhibit (i e , slow to some extent and preferably stop) tumor metastasis; inhibit, to some extent, tumor growth; and/or relieve to some extent one or more of the symptoms associated with the cancer.
  • the antibody conjugate may prevent growth and/or kill existing cancer cells, it may be cytostatic and/or cytotoxic.
  • efficacy can, for example, be measured by assessing the time to disease progression (TTP) and/or determining the response rate (RR)
  • “Recipient,” “individual,” “subject,” “host,” and “patient” are used interchangeably and refer to any mammalian subject for whom diagnosis, treatment, or therapy is desired (e.g., humans).
  • “Mammal” for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, sheep, goats, pigs, camels, etc. In certain embodiments, the mammal is human.
  • administering refers to parenteral, intravenous, intraperitoneal, intramuscular, intratumoral, intralesional, intranasal, or subcutaneous administration, oral administration, administration as a suppository, topical contact, intrathecal administration, or the implantation of a slow-release device, e.g., a mini-osmotic pump, to the subject.
  • a slow-release device e.g., a mini-osmotic pump
  • “about X” or “around X” indicates a value of from 0 9X to 1.1X, e g., from 0.95X to 1.05X or from 0.99X to 1.01X.
  • a reference to “about X” or “around X” specifically indicates at least the values X, 0.95X, 0.96X, 0.97X, 0.98X, 0.99X, 1.01X, 1.02X, 1.03X, 1.04X, and 1.05X. Accordingly, “about X” and “around X” are intended to teach and provide written description support for a claim limitation of, e.g., “0.98X.”
  • the antibody conjugate compositions of the invention comprise an antibody. Included in the scope of the embodiments of the invention are functional variants of the antibody constructs or antigen binding domain described herein.
  • the term “functional variant” as used herein refers to an antibody construct having an antigen binding domain with substantial or significant sequence identity or similarity to a parent antibody construct or antigen binding domain, which functional variant retains the biological activity of the antibody construct or antigen binding domain of which it is a variant.
  • Functional variants encompass, for example, those variants of the antibody constructs or antigen binding domain described herein (the parent antibody construct or antigen binding domain) that retain the ability to recognize target cells expressing a tumor-associated antigen or cell surface receptor to a similar extent, the same extent, or to a higher extent, as the parent antibody construct or antigen binding domain.
  • the functional variant can, for instance, be at least about 30%, about 50%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99% or more identical in amino acid sequence to the antibody construct or antigen binding domain.
  • a functional variant can, for example, comprise the amino acid sequence of the parent antibody construct or antigen binding domain with at least one conservative amino acid substitution.
  • the functional variants can comprise the amino acid sequence of the parent antibody construct or antigen binding domain with at least one nonconservative amino acid substitution.
  • the non-conservative amino acid substitution may enhance the biological activity of the functional variant, such that the biological activity of the functional variant is increased as compared to the parent antibody construct or antigen binding domain.
  • a functional variant can, for example, comprise the amino acid sequence of the parent antibody construct or antigen binding with at least one non-canonical amino acid (ncAA) substitution (L Wang, et al, (2001) Science , 292(5516):498-500, CC Liu, PG Schultz, (2010) Annu Rev Biochem. 79:413-44).
  • ncAA non-canonical amino acid
  • the antibodies comprising the antibody conjugate compositions of the invention include Fc engineered variants.
  • the mutations in the Fc region that result in modulated binding to one or more Fc receptors can include one or more of the following mutations: YTE (M252Y/S254T/T256E), LALAPA (L234A/L235A/P329A), SD (S239D), SDIE (S239D/I332E), SE (S267E), SELF (S267E/L328F), SDIE (S239D/I332E), SDIEAL (S239D/I332E/A330L), GA (G236A), ALIE (A330L/I332E), GASDALIE (G236A/S239D/A330L/I332E), V9 (G237D/P238D/P271G/A330R), and VI 1 (G237D/P238D/H 2 68D/P271G, and
  • the antibodies comprising the antibody conjugate compositions of the invention include glycan variants, such as afucosylation
  • the Fc region of the binding agents are modified to have an altered glycosylation pattern of the Fc region compared to the native non-modified Fc region.
  • the antibodies in the antibody conjugate compositions contain a modified Fc region, wherein the modification modulates the binding of the Fc region to one or more Fc receptors.
  • the antibodies in the antibody conjugate contain one or more modifications (e.g., amino acid insertion, deletion, and/or substitution) in the Fc region that results in modulated binding (e.g., increased binding or decreased binding) to one or more Fc receptors (e.g., FcyRI (CD64), FcyRIIA (CD32A), FcyRIIB (CD32B), FcyRIIIA (CD 16a), and/or FcyRIIIB (CD 16b)) as compared to the native antibody lacking the mutation in the Fc region.
  • FcyRI CD64
  • FcyRIIA CD32A
  • FcyRIIB CD32B
  • FcyRIIIA CD 16a
  • FcyRIIIB CD 16b
  • the antibodies in the antibody conjugate compositions contain one or more modifications (e.g., amino acid insertion, deletion, and/or substitution) in the Fc region that reduce the binding of the Fc region of the antibody to FcyRIIB. In some embodiments, the antibodies in the antibody conjugate compositions contain one or more modifications (e.g., amino acid insertion, deletion, and/or substitution) in the Fc region of the antibody that reduce the binding of the antibody to FcyRIIB while maintaining the same binding or having increased binding to FcyRI (CD64), FcyRIIA (CD32A), and/or FcRylllA (CD 16a) as compared to the native antibody lacking the mutation in the Fc region. In some embodiments, the antibodies in the antibody conjugate compositions contain one of more modifications in the Fc region that increase the binding of the Fc region of the antibody to FcyRIIB
  • the modulated binding is provided by mutations in the Fc region of the antibody relative to the native Fc region of the antibody.
  • the mutations can be in a CH 2 domain, a CH 3 domain, or a combination thereof.
  • a “native Fc region” is synonymous with a “wild-type Fc region” and comprises an amino acid sequence that is identical to the amino acid sequence of an Fc region found in nature or identical to the amino acid sequence of the Fc region found in the native antibody (e g , cetuximab)
  • Native sequence human Fc regions include a native sequence human IgGl Fc region, native sequence human IgG2 Fc region, native sequence human IgG3 Fc region, and native sequence human IgG4 Fc region, as well as naturally occurring variants thereof.
  • Native sequence Fc includes the various allotypes of Fes (Jefferis et al., (2009) mAbs, l(4):332-338).
  • the Fc region of the antibodies of the antibody conjugate compositions are modified to have an altered glycosylation pattern of the Fc region compared to the native non-modified Fc region.
  • Human immunoglobulin is glycosylated at the Asn297 residue in the Cy2 domain of each heavy chain
  • This N-linked oligosaccharide is composed of a core heptasaccharide, N-acetylglucosamine4Mannose3 (GlcNAc4Man3) Removal of the heptasaccharide with endoglycosidase or PNGase F is known to lead to conformational changes in the antibody Fc region, which can significantly reduce antibody-binding affinity to activating FcyR and lead to decreased effector function
  • the core heptasaccharide is often decorated with galactose, bisecting GlcNAc, fucose, or sialic acid, which differentially impacts Fc binding to activating and inhibitory FcyR.
  • the modification to alter the glycosylation pattern is a mutation.
  • Asn297 is mutated to glutamine (N297Q).
  • the antibodies of the antibody conjugate compositions are modified to contain an engineered Fab region with a non-naturally occurring glycosylation pattern.
  • hybridomas can be genetically engineered to secrete afucosylated mAb, desialylated mAb or deglycosylated Fc with specific mutations that enable increased FcRyllla binding and effector function.
  • the antibodies of the antibody conjugate compositions are engineered to be afucosylated or glycosylated.
  • the antibodies in the antibody conjugate compositions are a cysteine-engineered antibody which provides for site-specific conjugation of an adjuvant, label, or drug moiety to the antibody through cysteine substitutions at sites where the engineered cysteines are available for conjugation but do not perturb immunoglobulin folding and assembly or alter antigen binding and effector functions (Junutula, et al., (2008) Nature Biotech , 26(8):925-932; Dornan et al (2009) 5/00 ⁇ 114(13):2721-2729, US 7521541; US 7723485; US 2012/0121615; WO 2009/052249).
  • Cysteine engineered antibody or “cysteine engineered antibody variant” is an antibody in which one or more residues of an antibody are substituted with cysteine residues.
  • Cysteine-engineered antibodies can be conjugated to the isoindolinone- glutarimide (IG) moiety with uniform stoichiometry (e g., up to two IG moieties per antibody in an antibody that has a single engineered cysteine site).
  • IG isoindolinone- glutarimide
  • cysteine-engineered antibodies are used to prepare antibody conjugate compositions with a reactive cysteine thiol residue introduced at a site on the light chain, such as the 149-lysine site (LC K149C), or on the heavy chain such as the 122-serine site (HC S122C), as numbered by Kabat numbering
  • the cysteine-engineered antibodies have a cysteine residue introduced at the 375-serine site (EU numbering) of the heavy chain (HC S375C).
  • the cysteine-engineered antibodies have a cysteine residue introduced at the 118-alanine site (EU numbering) of the heavy chain (HC Al 18C).
  • cysteine-engineered antibodies have a cysteine residue introduced in: (i) the light chain at G64C, R142C, K188C, L201C, T129C, S114C, or E105C according to Kabat numbering; (ii) the heavy chain at DIOIC, V184C, T205C, or S122C according to Kabat numbering; or (iii) other cysteine-mutant antibodies, and as described in Bhakta, S.
  • the antibody is a full-length antibody. In certain embodiments, the antibody is an antigen binding fragment. In some embodiments, the antibody is a humanized antibody
  • the antibody is an anti-CD40 antibody, an antibody selected from an anti-LRRC 1 5 antibody, an anti-CTSK antibody, an anti-ADAM12 antibody, an anti-ITGAl l antibody, an anti-FAP antibody, an anti-NOX4 antibody, an anti-SGCD antibody, an anti- SYNDIG1 antibody, an anti-CDH11 antibody, an anti-PLPP4 antibody, an anti-SLC24A2 antibody, an anti-PDGFRB antibody, an anti-THYl antibody, an anti-ANTXRl antibody, an anti-GASl antibody, an anti-CALHM5 antibody, an anti-SDCl antibody, an anti-HER2 antibody, an anti-TR0P2 antibody, an anti-MSLN antibody, an anti-Nectin4 antibody, an anti- ASGR1 antibody, and an anti-MUC 1 6 antibody.
  • the antibody or Fc fusion protein is selected from: abagovomab, abatacept (also known as ORENCIA®), abciximab (also known as REOPRO®), c7E3 Fab), adalimumab (also known as HUMIRA®), adecatumumab, alemtuzumab (also known as CAMPATH®), MabCampath or Campath- 1H), altumomab, afelimomab, panitumumab, mafenatox, anrukizumab, apolizumab, arcitumomab, aselizumab, atlizumab, atorolimumab, bapineuzumab, basiliximab (also known as SIMULECT®), bavituximab, bectumomab (also known as LYMPHOSCAN®), belimumab (also known as LYMPHO-STAT
  • the antibody conjugate composition of the invention comprises an antibody constmct that comprises an antigen binding domain that specifically recognizes and binds HER2.
  • the antibody conjugate composition comprises an anti-HER2 antibody.
  • an anti-HER2 antibody of an antibody conjugate composition of the invention comprises a humanized anti-HER2 antibody, e.g., huMAb4D5-l, huMAb4D5-2, huMAb4D5-3, huMAb4D5-4, huMAb4D5-5, huMAb4D5-6, huMAb4D5-7 and huMAb4D5-8, as described in Table 3 of US 5821337, which is specifically incorporated by reference herein.
  • Those antibodies contain human framework regions with the complementarity-determining regions of a murine antibody (4D5) that binds to HER2.
  • the humanized antibody huMAb4D5-8 is also referred to as trastuzumab, commercially available under the tradename HERCEPTINTM (Genentech, Inc.).
  • the antibody construct or antigen binding domain comprises the CDR regions of trastuzumab.
  • the anti-HER2 antibody further comprises the framework regions of the trastuzumab.
  • the anti-HER2 antibody further comprises one or both variable regions of trastuzumab.
  • an anti-HER2 antibody of an antibody conjugate composition of the invention comprises a humanized anti-HER2 antibody, e.g., humanized 2C4, as described in US 7862817.
  • a humanized 2C4 antibody is pertuzumab (CAS Reg. No. 380610-27-5), PERJETATM (Genentech, Inc.).
  • Pertuzumab is a HER dimerization inhibitor (HDI) and functions to inhibit the ability of HER2 to form active heterodimers or homodimers with other HER receptors (such as EGFR/HER1, HER2, HER3 and HER4).
  • HDI HER dimerization inhibitor
  • the antibody construct or antigen binding domain comprises the CDR regions of pertuzumab
  • the anti-HER2 antibody further comprises the framework regions of the pertuzumab.
  • the anti-HER2 antibody further comprises one or both variable regions of pertuzumab.
  • the antibody conjugate composition of the invention comprises an antibody construct that comprises an antigen binding domain that specifically recognizes and binds the B-cell receptor CD22.
  • the antibody conjugate composition comprises an anti-CD22 antibody
  • the anti- CD22 antibody of an antibody conjugate composition is pinatuzumab (CAS Reg. No. 1639820- 81 -7), with complementarity determining regions (CDRs), heavy chain (HC), and light chain (LC) as described in US 8226945 and WO 2007/140371 which are incorporated by reference herein.
  • the antibody of an antibody conjugate composition is capable of binding one or more antigen targets selected from (e.g., specifically binds to a target selected from) 5T4, ABL, ABCF1, ACVR1, ACVR1B, ACVR2, ACVR2B, ACVRL1, AD0RA2A, Aggrecan, AGR2, AICDA, AIF1, AIGI, AKAP1, AKAP2, AMH, AMHR2, ANGPT1, ANGPT2, ANGPTL3, ANGPTL4, ANPEP, APC, APOCI, AR, aromatase, ATX, AX1, Axl, AZGP1 (zinc-a-glycoprotein), B7.1, B7.2, B7-H1, B7-H3, B7-H4, BAD, BAFF, BAG1, BAH, BCR, BCL2, BCL6, BDNF, BLNK, BLR1 (MDRI5), BlyS, BMP1, BMP2, BMP3B (GDFIO), BMP4, BMP6, BM
  • TNFSF6 FasL
  • TNFSF7 CD27 ligand
  • TNFSF8 CD30 ligand
  • TNFSF9 4-1BB ligand
  • TOLLLP Toll-like receptors
  • TOP2A topoisomerase lia
  • TP53 TPM1, TPM2, TRADD, TRAF1, TRAF2, TRAF3, TRAF4, TRAF5, TRAF6, TRKA, TREM1, TREM2, TROP2, TRPC6, TSLP, TWEAK, Tyrosinase, uPAR, VEGF, VEGFB, VEGFC, versican, VHL C5, VLA-4, Wnt-1, XCL1 (tymphotactin), XCL2 (SCM-Ib), XCRI (GPR5/CCXCR1), YYI, ZFPM2, CLEC4C (BDCA-2, DLEC, CD303, CLECSF7), CLEC4D (MCL, CLECSF8), CLEC4E (Mincle), CLEC6
  • CLEC5A MDL-1, CLECSF5), CLEC 1 B (CLEC-2), CLEC9A (DNGR-1), CLEC7A (Dectin-1), PDGFRa, SLAMF7, GP6 (GPVI), LILRA1 (CD85I), LILRA2 (CD85H, ILT1), LILRA4 (CD85G, ILT7), LILRA5 (CD85F, ILT11), LILRA6 (CD85b, ILT8), NCR1 (CD335, LY94, NKp46), NCR3 (CD335, LY94, NKp46), NCR3 (CD337, NKp30), OSCAR, TARM1, CD300C, CD300E, CD300LB (CD300B), CD300LD (CD300D), KIR2DL4 (CD158D), KIR2DS, KLRC2 (CD159C, NKG2C), KLRK1 (CD314, NKG2D), NCR2 (CD336, NKp44), PILRB,
  • the antibody binds to an antigen selected from CDH1, CD19, CD20, CD29, CD30, CD38, CD40, CD47, EpCAM, MUC 1 , MUC 1 6, EGFR, HER2, SLAMF7, and gp75.
  • the antibody of an antibody conjugate composition of the invention is capable of binding to one or more tumor-associated antigens (TAA), cell-surface receptors, and immune-specific antigens to confer specificity to the targeting of the conjugate and enable safe and systemic delivery of an active drug moiety.
  • TAA tumor-associated antigens
  • C 6 rtain tumor-associated antigens are known in the art, and can be prepared for use in generating antibodies using methods and information which are well known in the art.
  • researchers In attempts to discover effective cellular targets for cancer diagnosis and therapy, researchers have sought to identify transmembrane or otherwise tumor-associated polypeptides that are specifically expressed on the surface of one or more particular type(s) of cancer cell as compared to on one or more normal non-cancerous cell(s).
  • tumor-associated polypeptides are more abundantly expressed on the surface of the cancer cells as compared to on the surface of the non-cancerous cells.
  • identification of such tumor-associated cell surface antigen polypeptides allows more specificity in targeting cancer cells for destruction via antibody -based therapies.
  • TAAs include, but are not limited to, those listed below including (l)-(54).
  • information relating to these antigens is listed below and includes names, alternative names, Genbank accession numbers and primary reference(s), following nucleic acid and protein sequence identification conventions of the National C 6 nter for Biotechnology Information (NCBI).
  • Nucleic acid and protein sequences corresponding to TAAs listed below including (l)-(54) are available in public databases such as GenBank.
  • TAAs targeted by antibodies include all amino acid sequence variants and isoforms possessing at least about 70%, 80%, 85%, 90%, or 95% sequence identity relative to the sequences identified in the cited references, and/or which exhibit substantially the same biological properties or characteristics as a TAA having a sequence found in the cited references.
  • a TAA having a variant sequence generally is able to bind specifically to an antibody that binds specifically to the TAA with the corresponding sequence listed.
  • BMPR1B bone morphogenetic protein receptor-type IB, Genbank accession no. NM_001203
  • BMPR1B bone morphogenetic protein receptor-type IB, Genbank accession no. NM_001203
  • W02004063362 Claim 2
  • W02003042661 Claim 12
  • US2003134790-Al Page 38-39
  • W02002102235 Claim 13, Page 296
  • W02003055443 Page 91-92
  • WO200299122 Example 2; Page 528-530
  • W02003029421 (Claim 6); W02003024392 (Claim 2; Fig 112)
  • WO200298358 (Claim 1; Page 183); W0200254940 (Page 100-101); WO200259377(Page 349-350), W0200230268 (Claim 27; Page 376); W0200148204 (Example;
  • MPF MPF
  • MSLN MSLN
  • SMR megakaryocyte potentiating factor
  • mesothelin Genbank accession no. NM_005823
  • Yamaguchi N., et al. Biol. Chem. 269 (2), 805-808 (1994), Proc. Natl. Acad. Sci. U.S.A. 96 (20): 11531-11536 (1999), Proc. Natl. Acad. Sei. U.S.A. 93 (1): 136- 140 (1996), J. Biol. Chem.
  • Napi3b (NAPI-3B, NPTIIb, SLC34A2, solute carrier family 34 (sodium phosphate), member 2, type II sodium-dependent phosphate transporter 3b, Genbank accession no. NM_006424) J. Biol. Chem. 277 (22): 19665-19672 (2002), Genomics 62 (2)281-284 (1999), Field, J A , et al (1999) Biochem. Biophys. Res.
  • Serna 5b (FLJ10372, KIAA1445, Mm.42015, SEMA5B, SEMAG, Semaphorin 5b Hlog, sema domain, seven thrombospondin repeats (type 1 and type 1 -like), transmembrane domain (TM) and short cytoplasmic domain, (30emaphoring) 5B, Genbank accession no AB040878) Nagase T., et al. (2000) DNA Res.
  • PSCA hlg (2700050C 1 2Rik, C530008016Rik, RIKEN cDNA 2700050C 1 2, RIKEN cDNA 2700050C 1 2 gene, Genbank accession no. AY358628); Ross et al. (2002) Cancer Res.
  • ETBR Endothelin type B receptor, Genbank accession no. AY275463
  • Nakamuta M. et al. Biochem. Biophys. Res. Commun. 177, 34-39, 1991
  • Ogawa Y. et al. Biochem. Biophys. Res. Commun. 178, 248-255, 1991
  • Arai H. et al. Jpn. Circ. J. 56, 1303-1307, 1992
  • Arai H. et al. J. Biol. Chem. 268, 3463-3470, 1993
  • Sakamoto A. Yanagisawa M., et al. Biochem. Biophys. Res. Commun.
  • W02004040000 (Claim 151); W02003087768 (Claim 1); W02003016475 (Claim 1); W02003016475 (Claim 1); W0200261087 (Fig 1); W02003016494 (Fig 6); W02003025138 (Claim 12; Page 144), W0200198351 (Claim 1; Page 124-125); EP522868 (Claim 8; Fig 2); W0200177172 (Claim 1; Page 297-299); US2003109676; US6518404 (Fig 3); US5773223 (Claim la; Col 31-34); W02004001004.
  • MSG783 (RNF124, hypothetical protein FLJ20315, Genbank accession no. NM_017763); W02003104275 (Claim 1); W02004046342 (Example 2); W02003042661 (Claim 12); W02003083074 (Claim 14; Page 61); WG2003018621 (Claim 1); W02003024392 (Claim 2; Fig 93); WO200166689 (Example 6); Cross-references: LocusID:54894; NP_060233.2; NM_017763_l.
  • STEAP2 (HGNC_8639, IPCA-1, PCANAP1, STAMP1, STEAP2, STMP, prostate cancer associated gene 1, prostate cancer associated protein 1, six transmembrane epithelial antigen of prostate 2, six transmembrane prostate protein, Genbank accession no. AF455138) Lab. Invest.
  • TrpM4 (BR22450, FLJ20041, TRPM4, TRPM4B, transient receptor potential cation channel, subfamily M, member 4, Genbank accession no. NM_017636) Xu, X.Z., et al Proc. Natl. Acad. Set. U.S.A. 98 (19): 10692-10697 (2001), Cell 109 (3):397-407 (2002), J. Biol. Chem.
  • CRIPTO (CR, CR1, CRGF, CRIPTO, TDGF1, teratocarcinoma-derived growth factor, Genbank accession no. NP_003203 or NM_003212) Ciccodicola, A., et al. EMBO J. 8 (7): 1987-1991 (1989), Am. J. Hum. Genet.
  • CD21 (CR2 (Complement receptor 2) or C3DR (C3d/Epstein Barr virus receptor) or Hs.73792 Genbank accession no. M26004) Fujisaku et al. (1989) J. Biol. Chem. 264 (4):2118- 2125); Weis J. J., et al. J. Exp. Med. 167, 1047-1066, 1988; Moore M , et al. Proc. Natl. Acad. Sci. U.S.A. 84, 9194-9198, 1987; Barel M., et al. Mol. Immunol. 35, 1025-1031, 1998; Weis J.J., et al. Proc. Natl. Acad. Sci.
  • CD79b (CD79B, CD790, Igb (immunoglobulin-associated beta), B29, Genbank accession no. NM_000626 or 11038674) Proc. Natl. Acad. Sci. U.S.A. (2003) 100 (7):4126- 4131, Blood (2002) 100 (9):3068-3076, Muller et al. (1992) Eur. J. Immunol.
  • FcRH 2 (IFGP4, IRTA4, SPAP1A (SH 2 domain containing phosphatase anchor protein la), SPAP1B, SPAP1C, Genbank accession no. NM_030764, AY358130) Genome Res. 13 (10):2265-2270 (2003), Immunogenetics 54 (2):87-95 (2002), Blood 99 (8):2662-2669 (2002), Proc. Natl. Acad. Sci. USA. 98 (17):9772-9777 (2001), Xu, M.J., et al. (2001) Biochem. Biophys. Res. Commun.
  • HER2 ErbB2, Genbank accession no. Ml 1730
  • Coussens L. et al. Science (1985) 230(4730):l 132-1139
  • Yamamoto T. et al. Nature 319, 230-234, 1986
  • Semba K. et al. Proc. Natl. Acad. Sci. U.S.A. 82, 6497-6501, 1985
  • Swiercz J.M. et al. J. Cell Biol. 165, 869-880, 2004
  • Kuhns J.J. et al. J. Biol. Chem. 274, 36422-36427, 1999
  • Cho H.-S. et al.
  • NCA NCA (CEACAM6, Genbank accession no. Ml 8728); Barnet T ., et al. Genomics 3, 59-66, 1988; Tawaragi Y., et al. Biochem. Biophys. Res. Commun. 150, 89-96, 1988; Strausberg R.L., et al. Proc. Natl. Acad. Sci. U.S.A.
  • MDP DPEP1, Genbank accession no. BC017023
  • W02003016475 (Claim 1); WO200264798 (Claim 33; Page 85-87); JP05003790 (Fig 6-8); WO9946284 (Fig 9); Cross-references: MIM:179780; AAH17023.1; BC017023 1.
  • IL20Roc (IL20Ra, ZCYTOR7, Genbank accession no AF184971); Clark H F , et al. Genome Res. 13, 2265-2270, 2003; Mungall A.J., et al. Nature 425, 805-811, 2003; Blumberg H., et al. Cell 104, 9-19, 2001; Dumoutier L., et al. J. Immunol. 167, 3545-3549, 2001; Parrish- Novak J., et al. J. Biol. Chem. 277 , 47517-47523, 2002; Pletnev S., et al. (2003) Biochemistry 42: 12617-12624; Sheikh F., et al.
  • EphB2R (DRT, ERK, Hek5, EPHT3, Tyro5, Genbank accession no. NM_004442) Chan, J. and Wat, V.M., Oncogene 6 (6), 1057-1061 (1991) Oncogene 10 (5):897-905 (1995), Annu. Rev. Neurosci. 21:309-345 (1998), Int. Rev. Cytol.
  • W0200206317 (Example 2; Page 320-321, Claim 34; Page 321-322); WO200271928 (Page 468-469); W0200202587 (Example 1; Fig 1); W0200140269 (Example 3; Pages 190-192); W0200036107 (Example 2; Page 205-207); W02004053079 (Claim 12); W02003004989 (Claim 1); WO200271928 (Page 233-234, 452-453); WO 0116318.
  • PSCA Prostate stem cell antigen precursor, Genbank accession no. AJ297436
  • Reiter R.E. et al. Proc. Natl. Acad. Sci. U.S.A. 95, 1735-1740, 1998; Gu Z ., et al. Oncogene 19, 1288-1296, 2000; Biochem. Biophys. Res. Commun.
  • BAFF-R B cell -activating factor receptor, BlyS receptor 3, BR3, Genbank accession No. AF116456
  • BAFF receptor /pi d NP_443177.1 - Homo sapiens Thompson, J.S., et al. Science 293 (5537), 2108-2111 (2001); W02004058309; W02004011611;
  • W02003045422 (Example; Page 32-33); W02003014294 (Claim 35; Fig 6B); W02003035846 (Claim 70; Page 615-616); WO200294852 (Col 136-137); WO200238766 (Claim 3; Page 133); W0200224909 (Example 3; Fig 3); Cross-references: MIM:606269; NP_443177.1;
  • CD22 B-cell receptor CD22-B isoform, BL-CAM, Lyb-8, Lyb8, SIGLEC-2, FLJ22814, Genbank accession No. AK026467
  • CD79a (CD79A, CD79oc, immunoglobulin-associated alpha, a B cell-specific protein that covalently interacts with Ig beta (CD79B) and forms a complex on the surface with Ig M molecules, transduces a signal involved in B-cell differentiation), pl: 4.84, MW: 25028 TM: 2 [P] Gene Chromosome: 19ql3.2, Genbank accession No NP 001774.10) W02003088808, US20030228319; W02003062401 (claim 9); US2002150573 (claim 4, pages 13-14), WO9958658 (claim 13, Fig 16); WO9207574 (Fig 1); US5644033; Ha et al. (1992) J. Immunol.
  • CXCR5 (Burkitt’s lymphoma receptor 1, a G protein-coupled receptor that is activated by the CXCL13 chemokine, functions in lymphocyte migration and humoral defense, plays a role in HIV-2 infection and perhaps development of AIDS, lymphoma, myeloma, and leukemia); 372 aa, pl: 8.54 MW: 41959 TM: 7 [P] Gene Chromosome: 1 lq23.3, Genbank accession No.
  • NP_001707.1 WO 2004040000; W02004/015426; US2003105292 (Example 2); US6555339 (Example 2); WO 2002/61087 (Fig 1); W0200157188 (Claim 20, page 269); W0200172830 (pages 12-13); WO 2000/22129 (Example 1, pages 152-153, Example 2, pages 254-256); WO 199928468 (claim 1, page 38); US 5440021 (Example 2, col 49-52); WO9428931 (pages 56-58); WO 1992/17497 (claim 7, Fig 5); Dobner et al. (1992) Eur. J. Immunol. 22-.2795-2I99,- Barella et al. ( ⁇ 995) Biochem. J. 3Q9CT3-I79.
  • HLA-DOB Beta subunit of MHC class II molecule (la antigen) that binds peptides and presents them to CD4+ T lymphocytes); 273 aa, pl: 6.56 MW: 30820 TM: 1 [P] Gene Chromosome: 6p21.3, Genbank accession No. NP_002111.1) Tonnelle et al. (1985) EMBO J. 4(11):2839-2847; Jonsson et al. (1989) Immunogenetics 29(6):411-413; Beck et al. (1992) J. Mol. Biol. 228:433-441; Strausberg et al. (2002) Proc. Natl. Acad.
  • P2X5 Purinergic receptor P2X ligand-gated ion channel 5, an ion channel gated by extracellular ATP, may be involved in synaptic transmission and neurogenesis, deficiency may contribute to the pathophysiology of idiopathic detrusor instability
  • 422 aa pl: 7.63, MW: 47206 TM: 1
  • Gene Chromosome 17p 13.3, Genbank accession No. NP_002552.2) Le et al. (1991) FEBS Lett. 418(1-2): 195-199, W02004047749, W02003072035 (claim 10); Touchman et al. (2000) Genome Res. 10: 165-173; W0200222660 (claim 20); W02003093444 (claim 1); W02003087768 (claim 1); W02003029277 (page 82).
  • CD72 B-cell differentiation antigen CD72, Lyb-2
  • pl 8.66
  • MW 40225 TM: 1
  • Gene Chromosome 9pl3.3, Genbank accession No. NP 001773.1) W02004042346 (claim 65); WO 2003/026493 (pages 51-52, 57-58); WO 2000/75655 (pages 105-106); Von Hoegen et al. (1990) J. Immunol. 144(12):4870-4877; Strausberg et al. (2002) Proc. Natl. Acad. Sci USA 99: 16899-16903.
  • LY64 Lymphocyte antigen 64 (RP105), type I membrane protein of the leucine rich repeat (LRR) family, regulates B-cell activation and apoptosis, loss of function is associated with increased disease activity in patients with systemic lupus erythematosus); 661 aa, pl: 6.20, MW: 74147 TM: 1 [P] Gene Chromosome: 5ql2, Genbank accession No. NP_005573.1) US2002193567; WO9707198 (claim 11, pages 39-42); Miura et al. (1996) Genomics 38(3):299- 304; Miura et al. (1998) Blood 92:2815-2822; W02003083047; WO9744452 (claim 8, pages 57-61); W0200012130 (pages 24-26).
  • RP105 type I membrane protein of the leucine rich repeat
  • FcRHl Fc receptor-like protein 1, a putative receptor for the immunoglobulin Fc domain that contains C2 type Ig-like and ITAM domains, may have a role in B-lymphocyte differentiation); 429 aa, pl: 5.28, MW: 46925 TM: 1 [P] Gene Chromosome: Iq21-lq22, Genbank accession No NP_443170 1) W02003077836; W0200138490 (claim 6, Fig 18E-1- 18-E-2); Davis et al. (2001) Proc. Natl. Acad. Sci USA 98(17):9772-9777; W02003089624 (claim 8); EP1347046 (claim 1); W02003089624 (claim 7).
  • IRTA2 Immunoglobulin superfamily receptor translocation associated 2, a putative immunoreceptor with possible roles in B cell development and lymphomagenesis; deregulation of the gene by translocation occurs in some B cell malignancies
  • TENB2 (TMEFF2, tomoregulin, TPEF, HPP1, TR, putative transmembrane proteoglycan, related to the EGF/heregulin family of growth factors and follistatin); 374 aa, NCBI Accession: AAD55776, AAF91397, AAG49451, NCBI RefSeq: NP_057276; NCBI Gene: 23671; OMIM: 605734; SwissProt Q9UIK5; Genbank accession No.
  • PMEL17 (silver homolog; SILV; D12S53E; PMEL17; SI; SIL); ME20; gplOO) BC001414; BT007202; M32295; M77348; NM_006928; McGlinchey, R.P. et al. (2009) Proc. Natl. Acad. Sci. U.S.A. 106 (33), 13731-13736; Kummer, M.P. et al. (2009) J Biol. Chem. 284 (4), 2296-2306.
  • TMEFF1 transmembrane protein with EGF-Iike and two follistatin-like domains 1; Tomoregulin-1); H7365; C9orf2; C9ORF2; U19878; X83961; NM 080655; NM_003692; Harms, P.W. (2003) Genes Dev. 17 (21), 2624-2629; Gery, S. et al. (2003) Oncogene 22 (18):2723-2727.
  • GDNF-Ral GDNF family receptor alpha 1; GFRA1; GDNFR; GDNFRA, RETL1; TRNR1; RET1L; GDNFR-alphal; GFR-ALPHA-1
  • Ly6E lymphocyte antigen 6 complex, locus E; Ly67,RIG-E,SCA-2,TSA-l
  • NP_002337.1 NP_002346.2
  • de Nooij-van Dalen A.G. et al. (2003) Int. J. Cancer 103 (6), 768-774
  • Zammit D J. et al (2002) Mol. Cell. Biol. 22 (3):946-952
  • TMEM46 shisa homolog 2 (Xenopus laevis); SHISA2
  • NP_001007539.1 NM_001007538.1
  • Furushima K. et al. (2007) Bev. Biol. 306 (2), 480-492; Clark, H.F. et al. (2003) Genome Res. 13 (10):2265-2270.
  • Ly6G6D lymphocyte antigen 6 complex, locus G6D; Ly6-D, MEGT1;
  • LGR5 leucine-rich repeat-containing G protein-coupled receptor 5; GPR49, GPR67
  • NP_003658.1 NM_003667.2
  • Salanti G. et al. (2009) Am. J. Epidemiol. 170 (5):537- 545; Yamamoto, Y. et al. (2003) Hepatology 37 (3):528-533.
  • RET ret proto-oncogene; MEN2A; HSCR1; MEN2B; MTC 1 ; PTC; CDHF12; Hs.168114; RET51; RET-ELE1); NP 066124.1; NM_020975.4; Tsukamoto, H. et al. (2009) Cancer Sci. 100 (10): 1895-1901; Narita, N. et al. (2009) Oncogene 28 (34):3058-3068.
  • LY6K lymphocyte antigen 6 complex, locus K; LY6K; HSJ001348; FLJ35226; NP 059997.3; NM 017527.3; Ishikawa, N. et al. (2007) Cancer Res. 67 (24): 11601-11611; de Nooij -van Dalen, A.G. et al (2003) Int. J. Cancer 103 (6):768-774.
  • GPR19 G protein-coupled receptor 19; Mm.4787
  • NP 006134.1 NM_006143.2
  • GPR54 (KISSI receptor; KISS1R; GPR54; HOT7T175; AX0R12); NP_115940.2; NM_032551.4; Navenot, J M. et al. (2009) Mol. Pharmacol. 75 (6): 1300-1306; Hata, K. et al. (2009) Anticancer Res 29 (2):617-623.
  • ASPHD1 aspartate beta-hydroxylase domain containing 1; LOC253982; NP_859069.2; NM_181718.3; Gerhard, D.S. et al. (2004) Genome Res. 14 (10B):2121-2127.
  • Tyrosinase (TYR; OCAIA; OCA1A; tyrosinase; SHEP3); NP 000363 1; NM_000372.4; Bishop, D.T. et al. (2009) Nat. Genet. 41 (8):920-925; Nan, H. et al. (2009) Int. J. Cancer 125 (4): 909-917
  • TMEM118 ring finger protein, transmembrane 2, RNFT2; FLJ14627
  • GPR172A G protein-coupled receptor 172A; GPCR41; FLJ11856; D15Ertd747e); NP 078807.1; NM_024531.3; Ericsson, T.A. et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100
  • CD33 a member of the sialic acid binding, immunoglobulin-like lectin family, is a 67-kDa glycosylated transmembrane protein. CD33is expressed on most myeloid and monocytic leukemia cells in addition to committed myelomonocytic and erythroid progenitor cells. It is not seen on the earliest pluripotent stem cells, mature granulocytes, lymphoid cells, or nonhematopoietic cells (Sabbath et al., (1985) J. Clin. Invest. 75:756-56; Andrews et al., (1986) Blood 68: 1030-5). CD33 contains two tyrosine residues on its cytoplasmic tail, each of which is followed by hydrophobic residues similar to the immunoreceptor tyrosine-based inhibitory motif (ITIM) seen in many inhibitory receptors.
  • ITIM immunoreceptor tyrosine-based inhibitory motif
  • CLL-1 (CLEC 1 2A, MICE, and DCAL2)
  • CTL/CTLD C-type lectin/C- type lectin-like domain
  • CLL-1 has been shown to be a type II transmembrane receptor comprising a single C-type lectin-like domain (which is not predicted to bind either calcium or sugar), a stalk region, a transmembrane domain and a short cytoplasmic tail containing an ITIM motif.
  • TROP2 tumor-associated calcium signal transducer 2
  • TACSTD2 transmembrane glycoprotein encoded by the TACSTD2 gene
  • TROP2 is an intracellular calcium signal transducer that is differentially expressed in many cancers It signals cells for seif-renewal, proliferation, invasion, and survival. It has stem cell -like qualities. TROP2 is expressed in many normal tissues, though in contrast, it is overexpressed in many cancers (Ohmachi T, et al., (2006) Clin.
  • TROP2 Overexpression of TROP2 is of prognostic significance. Several ligands have been proposed that interact with TROP2. TROP2 signals the cells via different pathways and it is transcriptionally regulated by a complex network of several transcription factors.
  • Human TROP2 (TACSTD2: tumor-associated calcium signal transducer 2, GA733-1, EGP-1, Ml SI; hereinafter, referred to as hTROP2) is a single-pass transmembrane type 1 cell membrane protein consisting of 323 amino acid residues. While the presence of a cell membrane protein involved in immune resistance, which is common to human trophoblasts and cancer cells (Faulk W P, et al. (1978), Proc. Natl. Acad. Sci.
  • TROP2 an antigen molecule recognized by a monoclonal antibody against a cell membrane protein in a human choriocarcinoma cell line was identified and designated as TROP2 as one of the molecules expressed In human trophoblasts (Lipinski M, et al. (1981), Proc. Natl. Acad. Sci. 78(8), 5147-5150). This molecule was also designated as tumor antigen GA733-1 recognized by a mouse monoclonal antibody GA733 (Linnenbach A J, et al., (1989) Proc. Natl. Acad. Sci.
  • the antibody conjugate composition of the invention comprises an isoindolinone- glutarimide moiety (IG).
  • IG isoindolinone- glutarimide moiety
  • the antibody conjugate composition of the present disclosure may be prepared from an isoindolinone-glutarimide (IG) compound selected from Formula III: or a pharmaceutically acceptable salt, stereoisomer, mixture of stereoisomers, tautomer, or isotopic analog thereof, wherein: m is 0, 1 or 2;
  • X 2 is independently selected from the group consisting of F, Cl, Br, I, -CN, C 1 -C 12 alkyl, C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, C 1 -C 12 heteroalkyl, -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl), ( C 1 -C 6 alkyldiyl)-(C 6 -C 20 aryl), -(C 1 -C 6 alkyldiyl)-NR a R b , -( C 1 -C 6 alkyldiyl)-OR a , (C 1 -C 6 alkyldiyl)-(Ca-C 20 carbocyclyl), (
  • R a is independently selected from H, C 1 -C 6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C 1 -C 12 alkyl, C 2 -C 12 alkenyl, and C 2 -C 12 alkynyl;
  • R b is independently selected from H, OH, C 1 -C 6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C 1 -C 12 alkyl, C 2 -C 12 alkenyl, and C 2 -C 12 alkynyl; n is 0, 1, 2, 3, or 4; and
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein m is 0.
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein m is 1.
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein m is 2.
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X 1 is CH 2 .
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X 2 is selected from the group consisting of C 1 -C 12 heteroalkyl, -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl), and -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl).
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X 2 is — (C 1 — C 12 heteroalkyldiyl)-(C 6 -C 20 aryl).
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X 2 is: where ** indicates the point of attachment.
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X 4 is H.
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X 4 is selected from the group consisting of C 1 -C 12 heteroalkyl, -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl), and -(C 1 -C 12 heteroalkyldiyl )-(C 6 -C 20 aryldiyl)-0-(C 2 -C 20 heterocyclyl).
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X 4 is -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-0-(C 2 -C 20 heterocyclyl), and C 2 -C 20 heterocyclyl is a glucuronide.
  • An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X 4 of formula la is selected from the formulae: wherein R is selected from H, C 1 -C 6 alkyl, and O-(C 1 -C 6 alkyl); and * indicates the point of attachment.
  • exemplary isoindolinone-glutarimide (IG) compounds of Table la, lb and 1c were prepared and characterized according to the Examples herein. C 6 rtain exemplary IG compounds of Table la were tested for their effects in inhibiting cellular proliferation, including CAL51,; WSU-DLCL2, NCI-N87 and SKBR3.
  • CAL51 is a human breast adenocarcinoma cell line with triple-negative status for expression of estrogen, progesterone and HER2 receptors.
  • WSU- DLCL2 is a human B-C 6 ll non-Hodgkin lymphoma cell line that expresses high levels of CD22.
  • NCI-N87 is a human epithelial cell line established from a gastric carcinoma;
  • SKBR3 is a human epithelial cell line established from a breast adenocarcinoma; both NCI-N87 and SKBR3 cell lines express high levels of HER2 receptor Table la Isoindolinone-glutarimide (IG) compounds
  • the present disclosure provides branched phenyl maleimide compounds (e.g., compounds of Structure (I)) enable the formation of a covalent bond between an isoindolinone-glutarimide linker compound (IG-L) and an antibody (Ab).
  • branched phenyl maleimide compounds e.g., compounds of Structure (I)
  • IG-L isoindolinone-glutarimide linker compound
  • Ab antibody
  • some embodiments provide a compound having the following Structure (I): wherein: one of Y 1 , Y 2 , Y 3 , Y 4 and Y 5 is C-L'-R 1 , another one of Y 1 , Y 2 , Y 3 , Y 4 and Y 5 is C-L 2 - R 2 , and the remaining three of Y 1 , Y 2 , Y 3 , Y 4 and Y 5 are each independently N, C-R 3 , or C-L 3 - R 3a ;
  • R 1 , R 2 , and R 3a each independently comprise one or more moieties selected from an amino acid element, a charged element, a heteroalkylene element, a hydrophilic element, a trigger element, an immolative unit, a polar cap, an isoindolinone-glutarimide moiety, and combinations thereof; provided that at least one of R 1 and R 2 comprises a isoindolinone-glutarimide moiety; each occurrence of R 3 is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, aminyl, amidyl, aldehyde, hydroxyl, cyano, nitro, thiol, carboxy, carboxyalkyl, alkyl-S(O) 3 H, alkyl-O-P(O)sH, alkyl- P(O) 3 H, -O-carboxyalkyl, -O-alkyl
  • R 4a and R 4b are each independently hydrogen, deuterium, halo, or -S-R 4c wherein R 4c is substituted or unsubstituted C 6 -C 10 aryl or substituted or unsubstituted 5-12 membered heteroaryl; and
  • L 1 , L 2 , and L 3 are each independently a linker comprising an optionally substituted alkylene, an optionally substituted alkenylene, an optionally substituted alkynylene, an optionally substituted heteroalkylene, an optionally substituted heteroalkenylene, an optionally substituted heteroalkynylene, a heteroatomic linker, an optionally substituted cycloalkylene, an optionally substituted arylene, an optionally substituted heterocyclylene, an optionally substituted heteroarylene, or combinations thereof; as a stereoisomer, enantiomer or tautomer thereof or a mixture thereof; or a pharmaceutically acceptable salt, solvate or prodrug thereof.
  • C 6 rtain embodiments provide a compound having the following Structure (la): wherein: one of Y 1 , Y 2 , Y 3 , Y 4 and Y 5 is C-L'-R 1 , another one of Y 1 , Y 2 , Y 3 , Y 4 and Y 5 is C-L 2 - R 2 , and the remaining three of Y 1 , Y 2 , Y 3 , Y 4 and Y 5 are each independently N, C-R 3 , or C-L 3 - R 3a ;
  • R 1 , R 2 , and R 3a each independently comprise one or more moieties selected from an amino acid element, a charged element, a heteroalkylene element, a hydrophilic element, a trigger element, an immolative element, a polar cap, a payload, and combinations thereof; provided that at least one of R 1 and R 2 comprises a payload; each occurrence of R 3 is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, aminyl, amidyl, aldehyde, hydroxyl, cyano, nitro, thiol, carboxy, carboxyalkyl, alkyl-S(O) 3 H, alkyl-O-P(O) 3 H, alkyl- P(O) 3 H, -O-carboxyalkyl, -O-alkyl-S(O) 3 H, -O-alkyl-O-P(O
  • R 4a and R 4b are each independently hydrogen, deuterium, halo, or -S-R 4c wherein R 4c is substituted or unsubstituted C 6 -C 10 aryl or substituted or unsubstituted 5-12 membered heteroaryl; and
  • L 1 , L 2 , and L 3 are each independently direct bond or a linker comprising an optionally substituted alkylene, an optionally substituted alkenylene, an optionally substituted alkynylene, an optionally substituted heteroalkylene, an optionally substituted heteroalkenylene, an optionally substituted heteroalkynylene, a heteroatomic linker, an optionally substituted cycloalkylene, an optionally substituted arylene, an optionally substituted heterocyclylene, an optionally substituted heteroarylene, or combinations thereof; as a stereoisomer, enantiomer or tautomer thereof or a mixture thereof; or a pharmaceutically acceptable salt, solvate or prodrug thereof.
  • R 4a and R 4b are both hydrogen. In some embodiments, R 4a is halo or R 4b is halo. In some embodiments, R 4a , R 4b , or both have one of the following structures:
  • R 1 R 2 , and/or R 3a comprises elements selected from an amino acid element, a charged element, a heteroalkylene element, a hydrophilic element, a trigger element, an immolative element, a polar cap, a payload, and combinations thereof. It is understood that these elements can be connected in any order and be connected in a linear manner or via a branched connection.
  • R 1 R 2 , and/or R 3a comprises multiple occurrences of an element (e.g, two or more heteroalkylene elements, two or more hydrophilic elements, two or more polar caps, etc.).
  • R 1 , R 2 , or R 3a comprises a branch point as part of an amino acid element (e.g., lysine) wherein additional elements are attached via an epsilon amine of the lysine and other additional elements are linked to the amino acid element via one or more peptide bonds to the alpha carbon of a lysine.
  • an amino acid element comprises one of the following structures:
  • a compound of Structure (I) comprises one of the following structures:
  • R 1 has the following structure: wherein:
  • L la is an amino acid element
  • L lb is a charged element
  • L lc is a heteroalkylene element
  • L ld is a hydrophilic element
  • L le is a trigger element
  • R la is a isoindolinone-glutarimide moiety that is covalently bound to one occurrence of
  • L la , L lb , L lc , L ld , L le , or L lf and the isoindolinone-glutarimide moiety is optionally substituted with a polar cap.
  • n7 is 1, 2, or 3. In some embodiments, n7 is 1 or 2. In some embodiments, n7 is 1 .
  • R 1 has the following structure: wherein:
  • L la is an amino acid element
  • L lb is a charged element
  • L lc is a heteroalkylene element
  • L ld is a hydrophilic element
  • L le is a trigger element
  • R la is a isoindolinone-glutarimide moiety optionally substituted with a polar cap.
  • R 2 has the following structure: wherein:
  • L 2a is an amino acid element
  • L 2b is a charged element
  • L 2C is a heteroalkylene element
  • L 2d is a hydrophilic element
  • R 2a is hydrogen, alkyl, a isoindolinone-glutarimide moiety, or a polar cap
  • m6 is 1, 2, or 3. In some embodiments, m6 is 1 or 2. In some embodiments, m6 is 1.
  • R 3a has the following structure: wherein:
  • L 3a is an amino acid element
  • b is a charged element
  • L 3C is a heteroalkylene element
  • L 3d is a hydrophilic element
  • R 3b is hydrogen, alkyl, or a polar cap.
  • p6 is 1, 2, or 3. In some embodiments, p6 is 1 or 2. In some embodiments, p6 is 1 .
  • n7 is 1 and each of nl through n6 are 1. In some embodiments, n7 is 1 and each of nl through n4 are 0, n5 is 1, and nb is 1. In certain embodiments, n7 is 1 and nl is 0, n2 is 0, n3 is 1, n4 is 0, n5 is 1, and n6 is 1. In certain embodiments, n7 is 1 and nl is 1, n2 is 0, n3 is 1, n4 is 0, n5 is 1, and n6 is 1. In certain embodiments, n7 is 1 and nl is 1, n2 is 1, n3 is 1, n4 is 0, n5 is 1, and n6 is 1. In certain embodiments, n7 is 1 and nl is 1, n2 is 1, n3 is 1, n4 is 0, n5 is 1, and n6 is 1.
  • n7 is 1 and nl is 1, n2 is 1, n3 is 1, n4 is 1, n5 is 1, and n6 is I In certain embodiments, n7 is 1 and nl is 1, n2 is 0, n3 is 1, n4 is 0, n5 is 1, and n6 is 1 In certain embodiments, n7 is 2 In certain embodiments, n7 is 3
  • m6 is 1 and each of ml through m5 are 1. In some embodiments, m6 is 1, ml is 1, m2 is 0, m3 is 0, m4 is 1, and m5 is 0. In some embodiments, m6 is 1, ml is 1, m2 is 1, m3 is 0, m4 is 1, and m5 is 0. In some embodiments, m6 is 1, ml is 1, m2 is 0, m3 is 1, m4 is 1, and m5 is 0. In some embodiments, mb is 1, ml is 1, m2 is 0, m3 is 0, m4 is 1, and m5 is 1. In some embodiments, m6 is 2. In certain embodiments, m6 is 3.
  • p6 is 1 and each of pl through p5 is 1. In certain embodiments, p6 is 1, pl is 1, p2 is 0, p3 is 0, p4 is 1, and p5 is 0. In some embodiments, p6 is 1, pl is 1, p2 is 1, p3 is 0, p4 is 1, and p5 is 0.
  • p6 is 1, pl is 1, p2 is 0, p3 is 1, p4 is 1, and p5 is 0 In some embodiments, p6 is 1, pl is 1, p2 is 0, p3 is 0, p4 is 1, and p5 is 1 In some embodiments, p6 is 2 and at least one occurrence of pl is 1, p2 is 1, p3 is 0, p4 is 1, and p5 is 0. In some embodiments, pb is 2. In certain embodiments, pb is 3.
  • an amino acid element comprises one or more amino acids selected from the group consisting of glycine, alanine, serine, threonine, cysteine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tyrosine, tryptophan, aspartic acid, glutamic acid, asparagine, glutamine, histidine, lysine, arginine, sarcosine, and beta-alanine.
  • an amino acid element is selected from the group consisting of glycine, sarcosine, beta-alanine, and glutamic acid.
  • an amino acid element comprises a dipeptide, a tripeptide, a tetrapeptide, or a pentapeptide.
  • an amino acid element has one of the following structures: wherein: each occurrence of R 5a is independently hydrogen, alkyl, hydroxyalkyl, or alkoxyalkyl.
  • a charged element comprises moieties with a negative charge at about pH 7.4 (i.e., a range from 6.3 to 8 5).
  • a charged element comprises moieties with a positive charge at about pH 7.4 (i.e., a range from 6.3 to 8 5).
  • a charged element comprises one or more charged amino acid, one or more carboxylic acid, one or more sulfonic acid, one or more sulfonamide, one or more sulfate, one or more phosphate, one or more quaternary amine, one or more sulfamide, one or more sulfinimide, or combinations thereof.
  • a charged amino acid is aspartic acid, glutamic acid, histidine, lysine, or arginine.
  • R 1 , R 2 , or R 3a comprises a non-cleavable linker (e.g, a linker, or segment thereof, that does not include a trigger element or immolative unit).
  • a non-cleavable linker e.g, a linker, or segment thereof, that does not include a trigger element or immolative unit.
  • R 1 , R 2 , or R 3a comprises one of the following structures:
  • each occurrence of R 5b , R 5c R 5d , and R 5e is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, hydroxyl, cyano, nitro, thiol, carboxyalkyl, alkyl-S(O) 3 H, alkyl-O-P(O) 3 H, alkyl-P(O) 3 H, -O-carboxyalkyl, -O-alkyl-S(O) 3 H, -O-alkyl-O-P(O) 3 H, -O-alkyl-P(O) 3 H, -S(O) 3 H, -OP(O) 3 H, -P(O) 3 H, alkyl-O- P(O) 3 -alkyl, alkyl-P(O) 3 -alkyl, -O-alkyl-S(O) 3 H,
  • a hydrophilic element comprises polyethylene glycol, poly sarcosine, cyclodextrin, c-glycosides, or combinations thereof. In some embodiments, a hydrophilic element comprises one of the following structures:
  • a hydrophilic element comprises one of the following structures: In some embodiments, a hydrophilic element comprises one of the following structures:
  • a hydrophilic element has one of the following structures:
  • a hydrophilic element has the following structure:
  • a hydrophilic element has one of the following structures:
  • a hydrophilic element comprises a polysarcosine. In some embodiments, a hydrophilic element is a polysarcosine comprising the following structure:
  • a hydrophilic element is a polysarcosine with one of the following structures:
  • a hydrophilic element has a molecular weight greater than 150 g/mole, greater than 200 g/mole, greater than 300 g/mole, greater than 400 g/mole, greater than 500 g/mole, greater than 600 g/mole, greater than 700 g/mole, greater than 800 g/mole, greater than 900 g/mole, or greater than 1000 g/mole
  • a hydrophilic element has a molecular weight less than 150 g/mole, less than 200 g/mole, less than 300 g/mole, less than 400 g/mole, less than 500 g/mole, less than 600 g/mole, less than 700 g/mole, less than 800 g/mole, less than 900 g/mole, or less than 1000 g/mole.
  • L 1 is alkylene. In some embodiments, L 1 is C 1 -C 6 alkylene. In certain embodiments, L 2 is alkylene. In some embodiments, L 2 is C 1 -C 6 alkylene. In certain embodiments, I? is alkylene. In some embodiments, L 3 is C 1 -Cg alkylene.
  • L 1 is heteroalkylene. In some embodiments, L 1 is C 1 -C 6 heteroalkylene (i.e., contains from 1-6 carbon atoms and one or more heteroatoms). In certain embodiments, L 2 is heteroalkylene In some embodiments, L 2 is C 1 -Cg heteroalkylene In certain embodiments, I? is heteroalkylene. In some embodiments, L 3 is C 1 -Cg heteroalkylene.
  • L 1 , L 2 , or L 3 are C 1 -Cg heteroalkylene and contain heteroatoms selected form O and N.
  • I? is a direct bond.
  • L 1 , L 2 , or L 3 have one of the following structures:
  • a trigger element comprises a dipeptide, a tripeptide, a tetrapeptide, a pentapeptide, a glucuronide, a disulfide, a phosphate, a diphosphate, a triphosphate, a hydrazone, or combinations thereof.
  • a trigger element comprises beta-glucuronic acid.
  • a trigger element comprises a dipeptide, a tripeptide, a tetrapeptide, or a pentapeptide
  • a trigger element comprises two or more amino acids selected from the group consisting of valine, citrulline, alanine, glycine, phenylalanine, lysine, or combinations thereof.
  • a trigger element comprises a sequence of amino acids selected from the group consisting of valine-citrulline, valine-alanine, glycine-glycine-phenylalanine-glycine, and combinations thereof.
  • a trigger element comprises one of the following structures, including combinations thereof
  • a trigger element has a molecular weight greater than 150 g/mole, greater than 200 g/mole, greater than 300 g/mole, greater than 400 g/mole, greater than 500 g/mole, greater than 600 g/mole, greater than 700 g/mole, greater than 800 g/mole, greater than 900 g/mole, or greater than 1000 g/mole.
  • a trigger element has a molecular weight less than 150 g/mole, less than 200 g/mole, less than 300 g/mole, less than 400 g/mole, less than 500 g/mole, less than 600 g/mole, less than 700 g/mole, less than 800 g/mole, less than 900 g/mole, or less than 1000 g/mole.
  • a trigger element has the following structure:
  • a trigger element is specifically cleaved by an enzyme.
  • a trigger element can be cleaved by a lysosomal enzyme.
  • a trigger element can be peptide-based or can include peptidic regions that can act as substrates for enzymes.
  • Peptide based trigger elements can be more stable in plasma and extracellular milieu than chemically labile linkers.
  • Exemplary disulfide-containing trigger elements can include the following structures: wherein D is a isoindolinone-glutarimide moiety and R is independently selected at each occurrence from, for example, hydrogen or C 1 -C 6 alkyl. Increasing steric hindrance adjacent to the disulfide bond can increase the stability of the linker.
  • the above structures can result in increased in vivo stability when one or more R groups is selected from a lower alkyl, such as methyl.
  • Peptide bonds can have good serum stability, as lysosomal proteolytic enzymes can have very low activity in blood due to endogenous inhibitors and the unfavorably high pH value of blood compared to lysosomes.
  • Release of a isoindolinone-glutarimide moiety from conjugate of Structure (II) can occur due to the action of lysosomal proteases, e.g., cathepsin and plasmin. These proteases can be present at elevated levels in certain tumor tissues.
  • a trigger element can be cleavable by a lysosomal enzyme.
  • the lysosomal enzyme can be, for example, cathepsin B, P-glucuronidase, or P-galactosidase.
  • a cleavable peptide of a trigger element can be selected from tetrapeptides such as Gly- Phe-Leu-Gly, Ala-Leu-Ala-Leu, tripeptides such as Glu-Val-Cit, or dipeptides such as Val-Cit, Vai-Ala, Ala-Ala, and Phe-Lys. Dipeptides can have lower hydrophobicity compared to longer peptides
  • a trigger element may be a single amino acid residue.
  • the trigger element comprises asparagine, Asn as a legumain cleavable element (Miller, J.T. et al (2021) Bioconjugate Chem. 32(4):842-858
  • Enzymatically cleavable trigger elements be combined with an immolative unit and provide additional spatial separation between a isoindolinone-glutarimide moiety and the site of enzymatic cleavage.
  • the direct attachment of isoindolinone-glutarimide moiety to a peptidic trigger element can result in proteolytic release of a isoindolinone-glutarimide moiety or of an amino acid adduct of a isoindolinone-glutarimide moiety thereby impairing its activity.
  • the use of an immolative unit can allow for the release of the fully active, chemically unmodified isoindolinone-glutarimide moiety upon amide bond hydrolysis.
  • a trigger element can contain a chemically labile group such as hydrazone and/or disulfide groups.
  • a trigger element comprising chemically labile group or groups can exploit differential properties between the plasma and some cytoplasmic compartments.
  • the intracellular conditions that can facilitate release of a isoindolinone-glutarimide moiety for hydrazone containing trigger elements can be the acidic environment of endosomes and lysosomes, while the disulfide containing trigger elements can be reduced in the cytosol, which can contain high thiol concentrations, e.g., glutathione.
  • the plasma stability of a trigger element containing a chemically labile group can be increased by introducing steric hindrance using substituents near the chemically labile group
  • Acid-labile groups such as hydrazone
  • This pH dependent release mechanism can be associated with non-specific release of a isoindolinone- glutarimide moiety.
  • a trigger element can be varied by chemical modification, e.g., substitution, allowing tuning to achieve more efficient release in the lysosome with a minimized loss in circulation.
  • a trigger element comprises a hydrazone moiety having one of the following structures: wherein R is selected from C 1 -C 6 alkyl, aryl, and -O-C 1 -C 6 alkyl
  • Hydrazone-containing trigger elements can contain additional cleavage sites, such as additional acid-labile cleavage sites and/or enzymatically labile cleavage sites (e.g., a disulfide).
  • Conjugates and compounds including exemplary hydrazone-containing trigger elements can include, for example, the following structure: wherein R is selected from C 1 -C 6 alkyl, aryl, and -O-C 1 -C 6 alkyl
  • acid-labile groups that can be included in trigger elements include c/.v-aconityl- containing linkers.
  • rv.s-Aconityl chemistry can use a carboxylic acid juxtaposed to an amide bond to accelerate amide hydrolysis under acidic conditions.
  • Trigger elements can also include a disulfide group.
  • Disulfides can be thermodynamically stable at physiological pH and release a isoindolinone-glutarimide moiety upon internalization of the conjugate of Structure (II) into cells, wherein the cytosol can provide a significantly more reducing environment compared to the extracellular environment. Scission of disulfide bonds can require the presence of a cytoplasmic thiol cofactor, such as (reduced) glutathione (GSH), such that disulfide-containing trigger element can be reasonably stable in circulation, selectively releasing a isoindolinone-glutarimide moiety in the cytosol.
  • GSH cytoplasmic thiol cofactor
  • the intracellular enzyme protein disulfide isomerase can also contribute to the preferential cleavage of disulfide bonds inside cells.
  • GSH can be present in cells in the concentration range of 0.5-10 mM compared with a significantly lower concentration of GSH or cysteine, the most abundant low-molecular weight thiol, in circulation at approximately 5 pM.
  • Tumor cells where irregular blood flow can lead to a hypoxic state, can result in enhanced activity of reductive enzymes and therefore even higher glutathione concentrations.
  • the in vivo stability of a disulfide-containing trigger element can be enhanced by chemical modification of a trigger element, e.g., use of steric hindrance adjacent to the disulfide bond.
  • a trigger element can also be a B-glucuronic acid-based linker. Facile release of a isoindolinone-glutarimide moiety, can be realized through cleavage of the B-glucuronide glycosidic bond by the lysosomal enzyme B-glucuronidase. This enzyme can be abundantly present within lysosomes and can be overexpressed in some tumor types, while the enzyme activity outside cells can be low. B-Glucuronic acid-based linkers can be used to circumvent the tendency of a conjugate to undergo aggregation due to the hydrophilic nature of B-glucuronides.
  • a trigger element comprises a B-glucuronic acid
  • cleavable 0 -glucuronic acid-based linkers useful for linking drugs such as auristatins, camptothecin analogues, doxorubicin analogues, CBI minor-groove binders, and psymberin to antibodies have been described. Accordingly, these P-glucuronic acid-based trigger elements are used in the conjugates of Structure (II).
  • a trigger element comprises a P-galactoside-based linker. 0-Galactoside is present abundantly within lysosomes, while the enzyme activity outside cells is low.
  • a trigger element may include one or more peptides.
  • a peptide can be selected to contain natural amino acids, unnatural amino acids, or any combination thereof.
  • a peptide can be a tripeptide or a dipeptide.
  • a dipeptide comprises L-amino acids, such as Val-Cit; Cit-Val; Ala-Ala; Ala-Cit; Cit-Ala; Asn-Cit; Cit-Asn; Cit-Cit; Val-Glu; Glu-Val; Ser-Cit; Cit-Ser; Lys-Cit, Cit-Lys; Asp- Cit; Cit-Asp; Ala-Vai; Vai-Ala; Phe-Lys; Lys-Phe; Val-Lys; Lys-Val; Ala-Lys; Lys-Ala; Phe- Cit; Cit-Phe; Leu-Cit; Cit-Leu; Ile-Cit; Cit-Ile; Phe-Arg; Arg-Phe; Cit-Trp; and Trp-Cit, or salts thereof.
  • L-amino acids such as Val-Cit; Cit-Val; Ala-Ala; Ala-Cit; Cit-Ala; Asn-Cit; Cit
  • Trigger elements and immolative groups are known (WO 2022/076905) which is hereby incorporated by reference in their entirety.
  • One immolative unit can be a bifunctional para- aminobenzyl alcohol group, which can link to a trigger element through an amino group, forming an amide bond, while an amine containing isoindolinone-glutarimide moiety can be attached through carbamate functionalities to the benzylic hydroxyl group of the para- aminobenzyl alcohol (to give a //-amidobenzyl carbamate.
  • the resulting pro-compound can be activated upon protease-mediated cleavage, leading to a 1,6-elimination reaction releasing the unmodified isoindolinone-glutarimide moiety and remnants of the antibody-linker.
  • an immolative unit comprises paraaminobenzyloxycarbonyl, an aminal, a hydrazine, a disulfide, an amide, an ester, a hydrazine, a phosphotriester, a diester, a P-glucuronide, a double bond, a triple bond, an ether bond, a ketone, a diol, a cyano, a nitro, a quaternary amine, or combinations thereof
  • an immolative unit comprises a paramethoxybenzyl, a dialkyldialkoxysilane, a diaryldialkoxysilane, an orthoester, an acetal, an optionally substituted p-thiopropionate, a ketal, a phosphorami date, a hydrazone, a vinyl ether, an imine, an aconityl, a trityl, a polyketal, a bis
  • an immolative unit comprises one of the following structures:
  • an immolative unit comprises the following structure: wherein:
  • R 6a , R 6b , R 6C , and R 6d are independently hydrogen, an optionally substituted alkyl, an optionally substituted aryl, or optionally substituted heteroaryl, or
  • R 6a and R 6c together with the nitrogen and carbon atoms to which they are attached form azetidinyl, pyrrolodinyl, piperidinyl, or homopiperidinyl and R 6d is hydrogen;
  • Y 1 is -O-, -S-, or -NR 6b -;
  • an immolative unit comprises the following structure: wherein:
  • R 6e , R 6f , R 6g , and R 511 are independently hydrogen, an optionally substituted alkyl, an optionally substituted aryl, or optionally substituted heteroaryl, or
  • R 6a and R 6c together with the nitrogen and carbon atoms to which they are attached form azetidinyl, pyrrolodinyl, piperidinyl, or homopiperidinyl and R 6d is hydrogen;
  • Y 2 is -O-, -S-, or -NR 6f -;
  • an immolative unit comprises the following structure: wherein: each occurrence of R 10 is independently alkyl, alkoxy, or halo;
  • R 11 is hydrogen, alkyl, or -(CH 2 CH 2 O) Z 3-CH 3 ;
  • R 12 is hydrogen or alkyl
  • R 13 is hydrogen or alkyl; zl is 0 or 1; z2 is 0, 1, 2, 3, or 4; and z3 is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; or
  • an immolative unit comprises one of the following structures: wherein:
  • R 14a , R 14b , R 14C , R 14d , R 14e , and R 14f are each independently hydrogen, alkyl, hydroxyalkyl, or alkoxyalkyl; z4, z5, z6, and z7 are each independently 1, 2, 3, 4, 5, or 6;
  • an immolative unit comprises one of the following structures: wherein: z8 and z9 are each independently 1, 2, 3, 4, 5, or 6; or
  • an immolative unit comprises one of the following structures:
  • each occurrence of R 15 is independently H, methyl, ethyl, isopropyl, tert-butyl, or phenyl;
  • Y 3 is O or CH 2 ; and q5 is an integer ranging from 1-5.
  • an immolative unit has a molecular weight greater than 150 g/mole, greater than 200 g/mole, greater than 300 g/mole, greater than 400 g/mole, greater than 500 g/mole, greater than 600 g/mole, greater than 700 g/mole, greater than 800 g/mole, greater than 900 g/mole, or greater than 1000 g/mole.
  • an immolative unit has a molecular weight less than 150 g/mole, less than 200 g/mole, less than 300 g/mole, less than 400 g/mole, less than 500 g/mole, less than 600 g/mole, less than 700 g/mole, less than 800 g/mole, less than 900 g/mole, or less than 1000 g/mole.
  • an immolative unit and a trigger element together have the following structure: wherein a trigger element is denoted with “peptide” and comprises from one to ten amino acids, and * represents the point of attachment to a isoindolinone-glutarimide moiety.
  • the peptide comprises Val-Cit or Val-Ala.
  • Heterocyclic variants e.g., pyridinyl, pyrimidinyl, etc.
  • an immolative unit contains a phenol group that is covalently bound to the remainder of the molecule through the phenolic oxygen.
  • One such immolative unit relies on a methodology in which a diamino-ethane “Space Link” is used in conjunction with traditional “PABO”-based immolative unit to deliver phenols.
  • a trigger element can include non-cleavable portions or segments.
  • Polyethylene glycol (PEG) and related polymers can be included with cleavable groups such as a disulfide, a hydrazone or a dipeptide to form an immolative group and/or trigger element.
  • esters can be formed by the reaction of PEG carboxylic acids or activated PEG carboxylic acids with alcohol groups on a isoindolinone-glutarimide moiety such ester groups can hydrolyze under physiological conditions to release a isoindolinone-glutarimide moiety
  • Other hydrolytically degradable linkages can include carbonate linkages, imine linkages resulting from reaction of an amine and an aldehyde; phosphate ester linkages formed by reacting an alcohol with a phosphate group; acetal linkages that are the reaction product of an aldehyde and an alcohol; orthoester linkages that are the reaction product of a formate and an alcohol; and oligonucleotide linkages formed by a phosphoramidite group, including at the end of a polymer, and a 5’ hydroxyl group of an oligonucleotide.
  • a trigger element, immolative unit (IM), and isoindolinone- glutarimide moiety (IG) together have the following structure:
  • a trigger element is Asn-Cit, Arg-Cit, Val-Glu, Ser-Cit, Lys- Cit, Asp-Cit, Phe-Lys, Glu-Val-Cit, Glu-Val-Cit, Glu-Glu-Val-Cit, or Glu-Glu-Glu-Val-Cit, and an immolative unit is PABC.
  • the phenyl portion of the PABC is substituted with one or more substituents.
  • the substituents have one of the following structures:
  • an immolative group comprises one of the following structures:
  • a trigger element, an immolative unit (IM), and isoindolinone- glutarimide moiety (IG) together have one of the following structures:
  • an immolative unit has a structure selected from the following:
  • a substitution pattern may be 1, 2, 4 (i.e., 1 being a linkage to an IG, 2 being a linkage to the remainder of the molecule and 4 being a linkage to the carbohydrate) or 1, 3, 5 (i.e., 1 being a linkage to an IG, 3 being a linkage to the remainder of the molecule and 4 being a linkage to the carbohydrate).
  • cleavable linkers e.g., linkers with trigger elements or immolative unit
  • linkers need not be cleavable.
  • an IG release may not depend on the differential properties between the plasma and some cytoplasmic compartments.
  • the release of an IG can occur after internalization of the conjugate of Structure (II) via antigen-mediated endocytosis and delivery to lysosomal compartment, where the targeting moiety (or binding fragment thereof) can be degraded to the level of amino acids through intracellular proteolytic degradation. This process can release a isoindolinone- glutarimide moiety or isoindolinone-glutarimide moiety derivative.
  • a isoindolinone-glutarimide moiety or isoindolinone-glutarimide moiety derivative can be more hydrophilic and less membrane permeable, which can lead to less bystander effects and less non-specific toxicities compared to conjugates with a cleavable linker.
  • Conjugates with non-cleavable linkers can have greater stability in circulation than conjugates with cleavable linkers
  • Non-cleavable linkers can include alkylene chains, or can be polymeric, such as, for example, based upon polyalkylene glycol polymers, amide polymers, or can include segments of alkylene chains, poly alkylene glycols and/or amide polymers.
  • the linker can contain a polyethylene glycol segment having from 1 to 6 ethylene glycol units.
  • -L 1 -R. 1 or L 2 -R 2 comprises a linker that is non-cleavable in vivo.
  • a trigger element and an immolative unit (IM) together comprise one of the following structures:
  • a heteroalkylene element comprises polyethylene glycol or polypropylene glycol.
  • a heteroalkylene element comprises one of the following structures: wherein: each occurrence of R 5b , R 5c R 5d , and R 5e is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, hydroxyl, cyano, nitro, thiol, carboxyalkyl, alkyl-S(O) 3 H, alkyl-O-P(O) 3 H, alkyl-P(O) 3 H, -O-carboxyalkyl, -O-alkyl-S(O) 3 H, -O-alkyl-O-P(O) 3 H, -O-alkyl-P(O) 3 H, -S-alkyl-P(O) 3
  • a polar cap comprises one or more charged amino acid, one or more polyol, or combinations thereof.
  • a polar cap comprises a diol, a triol, a tetraol, or combinations thereof.
  • a polar cap comprises glycerol, trimethylolpropane, pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
  • a polar cap comprises one or more natural amino acids.
  • a polar cap comprises one or more non-natural amino acids.
  • a polar cap comprises one or more non-natural amino acids and one or more natural amino acids.
  • a polar cap comprises serine, threonine, cysteine, proline, asparagine, glutamine, lysine, arginine, histidine, aspartate, glutamate, 4- hydroxyproline, 5-hydroxylysine, homoserine, homocysteine, ornithine, beta-alanine, statine, or gamma aminobutyric acid
  • a polar cap comprises aspartic acid, serine, glutamic acid, serine-beta-glucose, or combinations thereof.
  • a polar cap comprises one of the following structures:
  • a polar cap has one of the following structures, including combinations thereof:
  • L 1 , L 2 , or L 3 comprise a linker selected from the group alkylene, alkylene-!/-, alkenylene, alkenylene-I?-, alkynylene, alkynylene-L a -, -L a -, -L a -alkylene-L a -, -L a - alkenylene-L a -, -L a -alkynylene-L a -, and combinations thereof, wherein each alkylene, alkenylene, and alkynylene is optionally substituted and each occurrence of L a is independently selected from -O-, -S-, -N(R 7 )-, -C(O)-, -C(S)-, -C(O)O-, -OC(O)-, -OC(O)O-, -C(O)N(R 7 )-, -N(R 7 )C
  • R 7 is independently selected at each occurrence from hydrogen, -NH 2 , -C(O)OCH 2 C6Hs; and Cnio alkyl, C2 10 alkenyl, C 2-10 alkynyl, C 3-12 cycloalkyl, and 3- to 12-membered heterocycle, each of which
  • each L 1 , L 2 , or L 3 is optionally substituted with one or more substituents selected from alkyl, alkenyl, alkynyl, halo, hydroxyl, cyano, -OR 8 , -SR 8 , amino, aminyl, amido, cycloalkyl, aryl, heterocyclyl, heteroaryl, cycloclkylalkyl, arylalkyl, heterocyclylalkyl, heteroarylalkyl, -C(O)R 8 , -C(O)N(R 8 ) 2 , -N(R 8 )C(O)R 8 , -C(O)OR 8 , -OC(O)R 8 , -S(O)R 8 , -S(O)2R 8 , -P(O)(OR 8 ) 2 , -OP(O)(OR 8 )2, nitro, oxo, thioxo,
  • L 1 , L 2 , or L 3 are independently selected from the following structures: wherein:
  • R a is hydrogen or alkyl; each occurrence of L b is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or a combination thereof; and each occurrence of L c is independently an optionally substituted alkylene linker and provided that at least one of L 1 , L 2 , or L 3 has the following structure:
  • L 1 and L 2 are independently selected from the following structures: wherein:
  • R a is hydrogen or alkyl; each occurrence of L b is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or a combination thereof; each occurrence of L c is independently an optionally substituted alkylene linker; provided that at least one of L 1 or L 2 has the following structure: In more embodiments, L 2 has the following structure:
  • L c is unsubstituted. In some embodiments, L c is a C 1 -Cg alkylene.
  • L c is a C2-C4 alkylene. In some embodiments, L c is a straight C 1 -C 6 alkylene. In more embodiments, L c is a straight, unsubstituted C 1 -C6 alkylene. In more embodiments, L c is a straight, unsubstituted C2-C4 alkylene.
  • the isoindolinone-glutarimide linker compound has one of the following structures (la- 1), (la-2), (la-3), (la-4), (Ia-5),or (la-6): each occurrence of L b is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or combinations thereof; and q6 is 0, 1, or 2. In some embodiments, q6 is 1 and L b is gly-gly.
  • the isoindolinone-glutarimide linker compound has one of the following Structures (Ic-1), (Ic-2), (Ic-3), or (Ic-4):
  • each occurrence of L b is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or combinations thereof; and q7 is 1, 2, or 3.
  • q7 is 2.
  • the isoindolinone-glutarimide linker compound has the following Structure (Id), (le), (If), or (Ig):
  • each occurrence of L b is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or combinations thereof; q8 is 0, 1, or 2; and q9 is 0, 1, or 2.
  • q9 is 0 and q8 is 1.
  • the isoindolinone-glutarimide linker compound has one of the following Structures (Ih) or (li): wherein: each occurrence of L b is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or combinations thereof.
  • L b is a direct bond, an optionally substituted alkylene linker or an optionally substituted heteroalkylene linker.
  • L b is a direct bond or has one of the following structures: wherein: each occurrence of R b is independently hydrogen, alkyl, hydroxyalkyl, or alkoxyalkyl.
  • each occurrence of R b is -CH 3 .
  • L 1 or L 2 has the following structure: wherein:
  • X 2 is C-L ⁇ R 1 and X 3 is C-L 2 -R 2 . In some embodiments, X 3 is C-L'-R 1 and X 2 is C-L 2 -R 2 . In some embodiments, X 1 , X 4 , and X 5 are all CR 3 . In some embodiments, X 1 , X 4 , and X 3 are all CH.
  • the conjugates of the invention are prepared by conjugation of an antibody with an isoindolinone-glutarimide linker compound, IG-L.
  • An isoindolinone-glutarimide linker compound is selected from Formulae Ila and Hb : wherein: m is 1 or 2;
  • X 2 is independently selected from the group consisting of F, Cl, Br, I, -CN, C 1 -C 12 alkyl, C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, C 1 -C 12 heteroalkyl, -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl), -(C 1 -C 12 heteroalkyldiyl)-(C6-Czo aryl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl), (C 1 -C 6 alkyl diyl)-(C 6 -C 20 aryl), -(
  • R a is independently selected from H, C 1 -C 6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C 1 -C 12 alkyl, C 2 -C 12 alkenyl, and C 2 -C 12 alkynyl;
  • R b is independently selected from H, OH, C 1 -C 6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C 1 -C 12 alkyl, C 2 -C 12 alkenyl, and C 2 -C 12 alkynyl; n is 0, 1, 2, 3, or 4,
  • X 3 is selected from the group consisting of a bond, O, C 1 -C 12 alkyldiyl, C 2 -C 12 alkenyldiyl, C 2 -C 12 alkynyldiyl, C 1 -C 12 heteroalkyldiyl, -(C 1 -C 6 alkyldiyl)-(C 6 -C 20 aryldiyl)-, -(C 1 -C 6 alkyl diyl)NR a -, -(C 1 -C 6 alkyldiyl)O-, -(C 1 -C 6 alkyldiyl)-(C 3 -C 20 carbocyclyldiyl)-, -(C 1 -C 6 alkyl diyl)-(C2-C 20 heterocyclyldiyl)-, -(C 1 -C 6 alkyldiyl)-(C 1 -C 20 heteroaryldiyl
  • X 4 is selected from the group consisting of H, C 1 -C 12 heteroalkyl, -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl);
  • X 5 is selected from the group consisting of C 1 -C 12 alkyldiyl, C 2 -C 12 alkenyldiyl, C 2 -C 12 alkynyldiyl, C 1 -C 12 heteroalkyldiyl, -(C 1 -C 6 alkyldiyl)-(C 6 -C 20 aryldiyl), -(C 1 -C 6 alkyldiyl)-(C 6 -C 20 atyldiyl)-O-(C 2 -C 20 heterocyclyl), -(C 1 -C 6 alkyldiyl)NR a -, -(C 1 -C 6 alkyldiyl)O-, -(C 1 -C 6 alkyldiyl)-(C 3 -C 20 carb ocyclyl diyl), -C 1 -C 6 alkyl diyl)-(C 2 -C 20 heterocycly
  • L is the antibody linker
  • Str 1 is a stretcher unit covalently attached to Z
  • PEP is a protease-cleavable, peptide unit covalently attached to Str 1 and IM;
  • IM is an immolative unit covalently attached the isoindolinone-glutarimide moiety; n is 0 or 1; and m is 0 or 1
  • An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein PEP-IM is selected from the structures: wherein ** indicates the point of attachment to the isoindolinone-glutarimide moiety.
  • An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein Z-Str 1 has the structure: wherein:
  • An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein R 1 is selected from -(CH 2 )s-, and -CH 2 CH 2 -.
  • An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein R 1 is selected from Cg-C 20 aryldiyl, (C 6 -C 20 aryldiyl)-(C 1 -C 12 alkyldiyl), and (C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl diyl).
  • An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein Z-Str 1 has the structure: wherein:
  • L 1 is selected from a bond, C 1 -C 12 alkyldiyl, and C 1 -C 40 heteroalkyl diyl;
  • L la is selected from an amino acid, amino, hydroxyl, halide, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof; o is 0, 1, or 2;
  • L 2 is selected from a bond, C 1 -C 12 alkyldiyl, and C 1 -C 40 heteroalkyl diyl;
  • An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein L 1 or L 2 comprise a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C 1 -C 40 heteroalkyl, and a glycoside, or combinations thereof.
  • L 1 or L 2 comprise a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C 1 -C 40 heteroalkyl, and a glycoside, or combinations thereof.
  • the invention includes all reasonable combinations, and permutations of the features, of the Formula II embodiments.
  • the linker units comprise functional groups and subunits which affect stability, permeability, solubility, and other pharmacokinetic, safety, and efficacy properties of the antibody conjugates.
  • the linker unit includes a reactive functional group which reacts, i e. conjugates, with a reactive functional group of the antibody.
  • a nucleophilic group such as a lysine side chain amino of the antibody reacts with an electrophilic reactive functional group of the isoindolinone-glutarimide-linker, IG-L compound to form the antibody conjugate.
  • a cysteine thiol of the antibody reacts with a maleimide or bromoacetamide group of the IG-L compound to form the antibody conjugate.
  • Considerations for the design of the antibody conjugates of the invention include: (1) preventing the premature release of the isoindolinone-glutarimide (IG) moiety during in vivo circulation and (2) ensuring that a biologically active form of the IG moiety is released at the desired site of action at an adequate rate.
  • IG isoindolinone-glutarimide
  • the complex structure of the antibody conjugate together with its functional properties requires careful design and selection of every component of the molecule including antibody, conjugation site, linker structure, and the IG moiety.
  • the linker determines the mechanism and rate of isoindolinone-glutarimide moiety release.
  • the linker unit (L) may be cleavable or non-cleavable.
  • Cleavable linker units may include a peptide sequence which is a substrate for certain proteases such as Cathepsins which recognize and cleave the peptide linker unit, separating the isoindolinone-glutarimide moiety from the antibody (Caculitan NG, et al (2017) Cancer Res. 77(24):7027-7037).
  • Cleavable linker units may include labile functionality such as an acid-sensitive disulfide group (Kellogg, BA et al (2011) Bioconjugate Chem. 22, 717-727; Gört, A. D. et al (2011) Clin. Cancer Res. 17, 6417-6427; Pillow, T., et al (2017) Chem. Sci. 8, 366-370, Zhang D, et al (2016) ACS Med Chem Lett. 7(1 l):988-993).
  • labile functionality such as an acid-sensitive disulfide group
  • the linker is non-cleavable under physiological conditions .
  • physiological conditions refers to a temperature range of 20-40 degrees C 6 lsius , atmospheric pressure (i.e. , 1 atm) , a pH of about 6 to about 8 , and the one or more physiological enzymes, proteases, acids , and bases.
  • the linker comprises a trivalent, branch point as part of an amino acid unit (e.g., lysine) wherein additional linker units are attached via the side chain amine of lysine or linked to other sites of an amino acid unit (US 11, 173,214).
  • an amino acid unit e.g., lysine
  • additional linker units are attached via the side chain amine of lysine or linked to other sites of an amino acid unit (US 11, 173,214).
  • a similar motif could be utilized with a glutamic acid of an amino acid unit.
  • An exemplary additional linker unit is a monovalent solubilizing unit such as one or more units of polyglycine, poly sarcosine, polyethyleneoxy (PEG), C 1 -C 40 heteroalkyl, and a glycoside, or combinations thereof.
  • the solubilizing unit may bear a group at the terminus such as an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
  • a group at the terminus such as an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
  • a solubilizing unit is a polysarcosine with one of the following structures:
  • an amino acid unit or peptide unit comprises one or more amino acids selected from the group consisting of glycine, alanine, serine, threonine, cysteine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tyrosine, tryptophan, aspartic acid, glutamic acid, asparagine, glutamine, histidine, lysine, arginine, sarcosine, and beta-alanine.
  • the invention includes an amino acid unit or a peptide linking unit, i.e. L or linker, between the antibody and the IG moiety, comprising a peptide comprising a linear sequence of specific amino acid residues which can be selectively cleaved by a protease such as a cathepsin, caspase, a tumor-associated elastase enzyme or an enzyme with proteaselike or elastase-like activity.
  • the peptide radical may be two to about twelve amino acids. Enzymatic cleavage of a bond within the peptide linker releases an active form of the IG moiety.
  • lysosomal proteases such as cathepsin and plasmin which may be present at elevated levels in certain tumor tissues.
  • the lysosomal enzyme can be, for example, cathepsin B, P-glucuronidase, or P-galactosidase.
  • a cleavable peptide of a peptide linker unit can be selected from tetrapeptides such as Gly-Phe-Leu-Gly, Ala-Leu-Ala-Leu, and Gly-Gly-Phe-Gly; tripeptides such as Glu-Val-Cit, and Ala- Ala-Ala; and dipeptides such as Val-Cit, Vai-Ala, Ala-Ala, and Phe-Lys.
  • the linker provides sufficient stability of the antibody conjugate in biological media, e.g. culture medium or serum and, at the same time, the desired intracellular action within tumor tissue as a result of its specific enzymatic or hydrolytic cleavability with release of the IG moiety, i.e. “isoindolinone-glutarimide moiety”.
  • the enzymatic activity of a protease, cathepsin, or elastase can catalyze cleavage of a covalent bond of the antibody conjugate under physiological conditions
  • the enzymatic activity being the expression product of cells associated with tumor tissue
  • the enzymatic activity on the cleavage site of the targeting peptide converts the antibody conjugate to an active IG drug free of targeting antibody and linking group.
  • the cleavage site may be specifically recognized by the enzyme Cathepsin or elastase may catalyze the cleavage of a specific peptidic bond between the C-terminal amino acid residue of the specific peptide and the IG moiety of the antibody conjugate.
  • the invention includes a linking unit, i.e. L or linker, between the antibody and the IG moiety, comprising a substrate for glucuronidase (Jeffrey SC, et al (2006) Bioconjug Chem. 17(3):831-40; US11,413,353; US11,173,214), or sulfatase (Bargh ID, et al (2020) Chem Sei. 1 1 (9):2375-2380) cleavage.
  • L includes a Glue unit and comprises a formula selected from:
  • Specific cleavage of the antibody conjugate takes advantage of the presence of tumor infiltrating cells of the immune system and leukocyte- secreted enzymes, to promote the activation of an anticancer drug at the tumor site.
  • Reactive electrophilic reactive functional groups (Q in Formula II) suitable for the isoindolinone-glutarimide linker compound (IG-L) include, but are not limited to, N- hydroxysuccinimidyl (NHS) esters and N-hydroxysulfosuccinimidyl (sulfo-NHS) esters (amine reactive); carbodiimides (amine and carboxyl reactive); hydroxymethyl phosphines (amine reactive); mal eimides (thiol reactive); halogenated acetamides such as A'-iodoacetamides (thiol reactive); aryl azides (primary amine reactive); fluorinated aryl azides (reactive via carbon- hydrogen (C-H) insertion); pentafluorophenyl (PFP) esters (amine reactive); tetrafluorophenyl (TFP) and sulfotetrafluorophenyl (STP) esters (amine reactive); imidoest
  • linkers such as those comprising peptide units and substrates for protease may be labile in the blood stream, thereby releasing unacceptable amounts of the drug prior to internalization in a target cell (Khot, A et al (2015) Bioanafysis 7(13): 1633-1648)
  • Other linkers may provide stability in the bloodstream, but intracellular release effectiveness may be negatively impacted.
  • Linkers that provide for desired intracellular release may have poor stability in the bloodstream.
  • the amount of adjuvant/drug moiety loaded on the antibody i.e. drug loading
  • Aggregate formation may be correlated to the number of equivalents of drug moieties conjugated to the antibody. Under high drug loading, formed aggregates must be removed for therapeutic applications. As a result, drug loading-mediated aggregate formation decreases antibody conjugate yield and can render process scale-up difficult
  • the invention includes all reasonable combinations, and permutations of the features, of the Formula Ila and Hb embodiments.
  • the isoindolinone-glutarimide linker compound has one of the following structures:
  • R lb is an isoindolinone-glutarimide moiety (IG);
  • R 2b has one of the following structures:
  • L lg has one of the following structures:
  • the isoindolinone-glutarimide linker compound has one of the following structures:
  • the isoindolinone-glutarimide linker compound has one of the following structures:
  • the isoindolinone-glutarimide linker compound has one of the following structures:
  • IG-L isoindolinone-glutarimide linker compounds
  • the isoindolinone-glutarimide antibody conjugates (IGAC) of the invention induce target-specific protein degradation. Tumor targeting brings specificity to minimize off-target effects
  • the isoindolinone-glutarimide antibody conjugates (IGAC) of the invention comprise an isoindolinone-glutarimide moiety covalently attached to an antibody by an antibody linker, wherein the antibody binds to a tumor-associated antigen or cell-surface receptor.
  • L is the antibody linker
  • IG is the isoindolinone-glutarimide moiety; and p is an integer from 1 to 12.
  • An exemplary embodiment of the IGAC of Formula I includes wherein a phenolic oxygen of the isoindolinone-glutarimide moiety is attached to the antibody linker.
  • An exemplary embodiment of the IGAC of Formula I includes wherein the nitrogen of the glutarimide group is attached to the antibody linker.
  • An exemplary embodiment of the IGAC of Formula I includes wherein a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C 1 -C 40 heteroalkyl, and a glycoside, or combinations thereof is attached to: (1) a phenolic oxygen, or (2) the nitrogen of the glutarimide group of the isoindolinone-glutarimide moiety.
  • a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C 1 -C 40 heteroalkyl, and a glycoside, or combinations thereof is attached to: (1) a phenolic oxygen, or (2) the nitrogen of the glutarimide group of the isoindolinone-glutarimide moiety.
  • An exemplary embodiment of the IGAC of Formula I includes wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
  • An exemplary embodiment of the IGAC is selected from Formulae la and lb: wherein: m is 0, 1 or 2;
  • X 2 is independently selected from the group consisting of F, Cl, Br, I, -CN, C 1 -C 12 alkyl, C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, C 1 -C 12 heteroalkyl, -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl), -(C 1 -C 12 heteroalkyldi
  • R b is independently selected from H, OH, C 1 -C 6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C 1 -C 12 alkyl, C 2 -C 12 alkenyl, and C 2 -C 12 alkynyl; n is 0, 1, 2, 3, or 4;
  • X 3 is selected from the group consisting of a bond, O, C 1 -C 12 alkyldiyl, C 2 -C 12 alkenyldiyl, C 2 -C 12 alkynyldiyl, C 1 -C 12 heteroalkyldiyl, -(C 1 -C 6 alkyldiyl)-(C 6 -C 20 aryldiyl)-, -(C 1 -C 6 alkyl diyl)NR a -, -(C 1 -C 6 alkyldiyl)O-, -(C 1 -C 6 alkyldiyl)-(C 3 -C 20 carbocyclyldiyl)-, -(C 1 -C 6 alkyl diyl)-(C2-C 20 heterocyclyldiyl)-, -(C 1 -C 6 alkyldiyl)-(C 1 -C 20 heteroaryldiyl
  • X 4 is selected from the group consisting of H, C 1 -C 12 heteroalkyl, -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl);
  • X 5 is selected from the group consisting of a bond, C 1 -C 12 alkyldiyl, C 2 -C 12 alkenyldiyl, C 2 -C 12 alkynyldiyl, C 1 -C 12 heteroalkyldiyl, -(C 1 -C 6 alkyldiyl)-(C 6 -C 20 aryldiyl), -(C 1 -C 6 alkyldiyl)-(C 6 -C 20 aryldiyl)-0-(C 2 -C 20 heterocyclyl), -(C 1 -C 6 alkyldiyl)NR a -, -(C 1 -C 6 alkyldiyl)O-, -(C 1 -C 6 alkyldiyl)-(C 3 -C 20 carbocyclyldiyl), -C 1 -C 6 alkyl diyl)-(C 2 -C
  • An exemplary embodiment of the IGAC of Formula I includes wherein the antibody linker is covalently attached to a cysteine amino acid of the antibody.
  • An exemplary embodiment of the IGAC of Formula I includes wherein the antibody is a cysteine-engineered antibody.
  • An exemplary embodiment of the IGAC of Formulae la and lb includes wherein m is 0.
  • An exemplary embodiment of the IGAC of Formulae la and lb includes wherein m is 1 .
  • An exemplary embodiment of the IGAC of Formulae la and lb includes wherein m is 2.
  • An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X 1 is CH 2 .
  • An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X 2 is selected from the group consisting of C 1 -C 12 heteroalkyl, -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl), and -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl).
  • An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X 2 is -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl).
  • An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X 2 is: wherein:
  • An exemplary embodiment of the IGAC of Formulae la includes wherein X 3 is O.
  • An exemplary embodiment of the IGAC of Formulae la includes wherein X 3 is -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyldiyl).
  • An exemplary embodiment of the IGAC of Formulae la includes wherein X 3 is selected from -(C 1 -C 12 heteroalkyl diyl)-(C 6 -C 20 aryldiyl)-O- -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-N(R a )-, and -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyldiyl).
  • An exemplary embodiment of the IGAC of Formulae la includes wherein X 3 is selected from the structures: and wherein:
  • R 6 is independently selected from F, Cl, Br, I, -CN, OH, -O-(C 1 -C 12 alkyl), C 1 -C 12 alkyl, C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, C 1 -C 12 heteroalkyl, C 6 -C 20 aryl, C 3 -C 20 carbocyclyl, C 2 -C 20 heterocyclyl, and C 1 -C 20 heteroaryl; nl is 1, 2, 3, or 4;
  • Y 1 is selected from CF2 and NH
  • Y 2 is selected from NH, O, and CH 2 .
  • An exemplary embodiment of the IGAC of Formulae la includes wherein X 3 is selected from: and wherein:
  • R 4 is selected from H and C 1 -C 12 alkyl
  • R 6 is independently selected from F, Cl, Br, I, -CN, OH, C 1 -C 12 alkyl, C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, and C 1 -C 12 heteroalkyl; and q is selected from 0, 1, 2, 3, and 4.
  • An exemplary embodiment of the IGAC of Formulae la includes wherein X 3 is -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl).
  • An exemplary embodiment of the IGAC of Formulae la includes wherein X 3 is selected from: wherein:
  • R 6 is independently selected from F, Cl, Br, I, -CN, OH, C 1 -C 12 alkyl, C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, and C 1 -C 12 heteroalkyl; and q is selected from 0, 1, 2, 3, and 4.
  • An exemplary embodiment of the IGAC of Formula la includes wherein X 2 is -OH and n is 1 .
  • An exemplary embodiment of the IGAC of Formula la includes wherein X 4 is H.
  • An exemplary embodiment of the IGAC of Formula la includes wherein X 4 is selected from the group consisting of C 1 -C 12 heteroalkyl, -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryl), -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl), and -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-0-(C 2 -C 20 heterocyclyl).
  • An exemplary embodiment of the IGAC of Formula la includes wherein X 4 is -(C 1 -C 12 heteroalkyldiyl)-(C 6 -C 20 aryldiyl)-0-(C 2 -C 20 heterocyclyl), and C 2 -C 20 heterocyclyl is a glucuronide.
  • An exemplary embodiment of the IGAC of Formula la includes wherein X 4 of formula la is selected from the formulae:
  • R is selected from H, C 1 -C 6 alkyl, and O-( C 1 -C 6 alkyl); and * indicates the point of attachment to IG.
  • An exemplary embodiment of the IGAC of Formula I includes Formula lb:
  • An exemplary embodiment of the IGAC of Formula lb includes wherein n is 2, 3 or 4 and one of X 2 is -OH.
  • An exemplary embodiment of the IGAC of Formula lb includes wherein X 5 is selected from -(C 1 -C 12 heteroalkyl diyl )-(C 6 -C 20 aryldiyl) and -(C 1 -C 6 alkyldiyl)-(C 6 -C 20 aryldiyl).
  • Exemplary embodiments of the IGAC of Formula I includes Formulae Ic-g: le;
  • R is independently selected from H, C 1 -C 6 alkyl, and O-( C 1 -C 6 alkyl); n a is an integer from 1 to 5; and Y is CH 2 or O.
  • An exemplary embodiment of the IGAC of Formulas Ic-g includes wherein R is -CH 3 and n a is 1.
  • An exemplary embodiment of the IGAC of Formulas Ic-g includes X 2 is -OH and n is 1.
  • Exemplary embodiments of the IGAC of Formula I include Formulae Ih and li: wherein R is selected from H, C 1 -C 6 alkyl, and O-(C 1 -C 6 alkyl); and X 5a is -(C 1 -C 6 alkyldiyl)-(C 6 -C 20 aryldiyl)-0-(C 2 -C 20 heterocyclyl).
  • An exemplary embodiment of the IGAC of Formulas Ih and li includes wherein C 2 -C 20 heterocyclyl of X 5a is a glucuronide.
  • An exemplary embodiment of the IGAC of Formulas Ih and li includes wherein X 5a is: wherein * indicates the point of attachment.
  • An exemplary embodiment of the IGAC of Formulas Ih and li includes wherein L has the structure: wherein:
  • L 1 is selected from a bond, C 1 -C 12 alkyldiyl, and C 1 -C 40 heteroalkyl diyl;
  • L la is selected from an amino acid, amino, hydroxyl, halide, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof; o is 0, 1, or 2;
  • L 2 is selected from a bond, C 1 -C 12 alkyldiyl, and C 1 -C 40 heteroalkyl diyl; * indicates the point of attachment to a cysteine thiol of Ab; and
  • t is selected from 0, 1, 2, 3, and 4.
  • An exemplary embodiment of the IGAC of Formulae Ij-m includes wherein L 1 is a bond and L la is F.
  • An exemplary embodiment of the IGAC of Formula I includes wherein the antibody linker comprises an immolating group.
  • An exemplary embodiment of the IGAC of Formula I includes wherein the antibody linker comprises a peptide unit.
  • Str is a stretcher unit covalently attached to the antibody
  • PEP is a protease-cleavable, peptide unit covalently attached to Str and IM or IG;
  • IM is an immolative unit covalently attached to IG; n is 0 or 1 ; and m is 0 or 1 .
  • An exemplary embodiment of the IGAC of Formula I includes wherein IG is attached to L by Str.
  • An exemplary embodiment of the IGAC of Formula I includes wherein IG is attached to L by PEP.
  • An exemplary embodiment of the IGAC of Formula I includes wherein IG is attached to L by IM.
  • An exemplary embodiment of the IGAC of Formula I includes wherein Str is a branched linker covalently attached to: (i) the antibody; and (ii) a solubilizing unit comprising a group selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C 1 -C 40 heteroalkyl, and a glycoside, or combinations thereof, wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
  • An exemplary embodiment of the IGAC of Formula I includes wherein the solubilizing unit and the terminus of the solubilizing unit covalently attached to Str are selected from the structures: wherein * indicates the point of attachment to Str
  • An exemplary embodiment of the IGAC of Formula I includes wherein L is a branched linker and PEP is covalently attached to: (i) Str and IM or IG; and (ii) a solubilizing unit comprises a group selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C 1 -C 40 heteroalkyl, and a glycoside, or combinations thereof, wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
  • An exemplary embodiment of the IGAC of Formula I includes wherein L is a branched linker and IM is covalently attached to: (i) IG; and (ii) a solubilizing unit comprises a group selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C 1 -C 40 heteroalkyl, and a glycoside, or combinations thereof, wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
  • An exemplary embodiment of the IGAC of Formula I includes wherein Str has the structure: wherein:
  • An exemplary embodiment of the IGAC of Formula I includes wherein R 1 is selected from -(CH 2 ) 5 -, and -CH 2 CH 2 -.
  • An exemplary embodiment of the IGAC of Formula I includes wherein R 1 is selected from C 6 -C 20 aryldiyl, (C 6 -C 20 aryldiyl)-(C 1 -C 12 alkyldiyl), and (C 6 -C 20 aryldiyl)-(C 1 -C 12 heteroalkyl diyl).
  • An exemplary embodiment of the IGAC of Formula I includes wherein Str is selected from the structure: wherein: one of Y 1 , Y 2 , Y 3 , Y 4 and Y 5 is C-L’-R 1 , another one of Y 1 , Y 2 , Y 3 , Y 4 and Y 5 is C-L 2 - R 2 , and the remaining three of Y 1 , Y 2 , Y 3 , Y 4 and Y 5 are each independently N, C-R 3 , or C-L 3 - R 3a ;
  • R 1 , R 2 , and R 3a each independently comprise one or more moieties selected from an amino acid element, a charged element, a heteroalkylene element, a hydrophilic element, a trigger element, an immolative unit, a polar cap, a isoindolinone-glutarimide moiety, and combinations thereof; provided that at least one of R 1 and R 2 comprises the isoindolinone-glutarimide moiety; each occurrence of R 3 is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, aminyl, amidyl, aldehyde, hydroxyl, cyano, nitro, thiol, carboxy, carboxyalkyl, alkyl-S(O) 3 H, alkyl-O-P(O) 3 H, alkyl- P(O) 3 H, -O-carboxyalkyl, -O-alkyl
  • R 4a and R 4b are each independently hydrogen, deuterium, halo, or -S-R 4c wherein R 4c is substituted or unsubstituted C 6 -C 10 aryl or substituted or unsubstituted 5-12 membered heteroaryl; and
  • L 1 , L 2 , and L 3 are each independently a linker comprising an optionally substituted alkylene, an optionally substituted alkenylene, an optionally substituted alkynylene, an optionally substituted heteroalkylene, an optionally substituted heteroalkenylene, an optionally substituted heteroalkynylene, a heteroatomic linker, an optionally substituted cycloalkylene, an optionally substituted arylene, an optionally substituted heterocyclylene, an optionally substituted heteroarylene, or combinations thereof; and
  • An exemplary embodiment of the IGAC of Formula I includes wherein Str is selected from the structure: wherein:
  • L 1 is selected from a bond, C 1 -C 12 alkyldiyl, and C 1 -C 40 heteroalkyl diyl;
  • L la is selected from an amino acid, amino, hydroxyl, halide, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof; o is 0, 1, or 2;
  • L 2 is selected from a bond, C 1 -C 12 alkyldiyl, and C 1 -C 40 heteroalkyl diyl;
  • An exemplary embodiment of the IGAC of Formula I includes wherein L 1 or L 2 comprise a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C 1 -C 40 heteroalkyl, and a glycoside, or combinations thereof.
  • L 1 or L 2 comprise a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C 1 -C 40 heteroalkyl, and a glycoside, or combinations thereof.
  • An exemplary embodiment of the IGAC of Formula I includes wherein L 1 or L 2 comprises glucuronic acid having the structure:
  • An exemplary embodiment of the IGAC of Formula I is selected from formulas: wherein * indicates the point of attachment to a cysteine thiol of Ab and ** indicates the point of attachment to IG.
  • An exemplary embodiment of the IGAC of Formula I includes wherein n is 1, m is 1, and PEP-IM has the formula: wherein * indicates the point of attachment to Str and ** indicates the point of attachment to IG;
  • AA is independently selected from a natural or unnatural amino acid side chain, or one or more of AA, and an adjacent nitrogen atom form a 5 -membered ring proline amino acid, and the wavy line indicates a point of attachment;
  • Cyc is selected from C 6 -C 20 aryldiyl and C 1 -C 20 heteroaryldiyl, optionally substituted with one or more groups selected from F, Cl, NO 2 , -OH, -OCH 3 , and glucuronic acid having the structure:
  • R 9 is independently selected from the group consisting of H, C 1 -C 12 alkyl, and - (CH 2 CH 2 O)n-(CH 2 ) m -OH, where m is an integer from 1 to 5, and n is an integer from 2 to 50, or two R 9 groups together form a 5- or 6-membered heterocyclyl ring; y is an integer from 2 to 12, and z is 0 or 1.
  • An exemplary embodiment of the IGAC of Formula I includes wherein AA is independently selected from the side chain of a naturally occurring amino acid.
  • An exemplary embodiment of the IGAC of Formula I includes wherein AA is independently selected from H, -CH 3 , -CH(CH 3 ) 2 , -CFhlGeHs), -CH 2 C(O)NH 2 , -CH 2 CH 2 CO2H, -CH 2 CO2H, -CH 2 CH 2 CH 2 CH 2 NH 2 , -CH 2 CH 2 CH 2 NHC(NH)NH 2 , -CH 2 CH(CH 3 ) 2 , -CH 2 SO 3 H, and -CH 2 CH 2 CH 2 NHC(O)NH 2 ; or two AA form a 5-membered ring proline amino acid.
  • An exemplary embodiment of the IGAC of Formula I includes wherein PEP-IM comprises at least one natural or unnatural amino acid side chain AA substituted with C 1 -C 40 heteroalkyl.
  • An exemplary embodiment of the IGAC of Formula I includes wherein C 1 -C 40 heteroalkyl comprises a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), and a glycoside, or combinations thereof
  • An exemplary embodiment of the IGAC of Formula I includes wherein y is 2, PEP is a dipeptide, and PEP-IM has the formula: wherein AA 1 and AA 2 are independently selected from a side chain of a naturally- occurring amino acid.
  • An exemplary embodiment of the IGAC of Formula I includes wherein the dipeptide is selected from ala-ala, val-cit, and phe-ala.
  • An exemplary embodiment of the IGAC of Formula I includes wherein AA 1 is - CH(CH 3 ) 2 , and AA 2 is -CH 2 CH 2 CH 2 NHC(O)NH 2 .
  • An exemplary embodiment of the IGAC of Formula I includes wherein AA 1 and AA 2 are each -CH 3 .
  • An exemplary embodiment of the IGAC of Formula I includes wherein y is 3, PEP is a tripeptide, and PEP-IM has the formula:
  • An exemplary embodiment of the IGAC of Formula I includes wherein y is 4, PEP is a tetrapeptide PEP-IM, and has the formula:
  • An exemplary embodiment of the IGAC of Formula I includes where z is 1 and IM has the formula:
  • ** indicates the point of attachment to IG.
  • An exemplary embodiment of the IGAC of Formula I includes where R 7 has the formula: wherein:
  • R 8 is selected from H and C 1 -C 6 alkyl
  • ** indicates the point of attachment to IG.
  • An exemplary embodiment of the IGAC of Formula I includes where R 8 is H.
  • An exemplary embodiment of the IGAC of Formula I includes where R 8 is -CH 3 .
  • IGAC of Formula I includes wherein IM is selected from the formulae:
  • the isoindolinone-glutarimide antibody conjugates (IGAC) of the invention include those with anti-cancer activity.
  • the IGAC selectively deliver an effective dose of an isoindolinone-glutarimide drug to tumor tissue or hematopoietic cell, whereby greater selectivity (z.e., a lower efficacious dose) may be achieved while increasing the therapeutic index (“therapeutic window”) relative to unconjugated isoindolinone-glutarimide drug.
  • Drug loading in Table 3 is represented as DAR, the number of isoindolinone-glutarimide (IG) moi eties per antibody in an IGAC of Formula I.
  • Drug (IG) loading may range from 1 to about 8 drug moieties (D) per antibody.
  • IGAC of Formula I include mixtures or collections of antibodies conjugated with a range of IG drug moieties, from 1 to about 8.
  • the number of IG drug moieties that can be conjugated to an antibody is limited by the number of reactive or available amino acid side chain residues such as lysine and cysteine.
  • free cysteine residues are introduced into the antibody amino acid sequence by the methods described herein.
  • p may be 1, 2, 3, 4, 5, 6, 7, or 8, and ranges thereof, such as from 1 to 8 or from 2 to 5.
  • Exemplary IGAC of Formula I include, but are not limited to, antibodies that have 1, 2, 3, or 4 engineered cysteine amino acids (Lyon, R. et al. (2012) Methods in Enzym. 502:123-138).
  • one or more free cysteine residues are already present in an antibody forming intra-chain and inter-chain disulfide bonds (native disulfide groups), without the use of engineering, in which case the existing free, reduced cysteine residues may be used to conjugate the antibody to a drug
  • an antibody is exposed to reducing conditions prior to conjugation of the antibody in order to generate one or more free cysteine residues.
  • p may be limited by the number of attachment sites on the antibody
  • an antibody may have only one or a limited number of cysteine thiol groups, or may have only one or a limited number of sufficiently reactive thiol groups, to which the drug may be attached.
  • one or more lysine amino groups in the antibody may be available and reactive for conjugation with a IG-lmker compound of Formula II.
  • higher drug loading e.g. p >5
  • the average drug loading for an antibody conjugate ranges from 1 to about 8; from about 2 to about 6; or from about 3 to about 5
  • an antibody is subjected to denaturing conditions to reveal reactive nucleophilic groups such as lysine or cysteine.
  • the loading (drug/antibody ratio) of an antibody conjugate may be controlled in different ways, and for example, by: (i) limiting the molar excess of the IG-linker intermediate compound relative to antibody, (ii) limiting the conjugation reaction time or temperature, and (iii) partial or limiting reductive denaturing conditions for optimized antibody reactivity.
  • the resulting product is a mixture of antibody conjugate compounds with a distribution of one or more IG drug moieties attached to an antibody.
  • the average number of drugs per antibody may be calculated from the mixture by a dual ELISA antibody assay, which is specific for antibody and specific for the drug.
  • Individual IGAC molecules may be identified in the mixture by mass spectroscopy and separated by HPLC, for example hydrophobic interaction chromatography, HIC (McDonagh et al. (2006) Prot. Engr. Design & Selection 19(7):299-307; Hamblett et al. (2004) Clin. Cancer Res.
  • a homogeneous antibody conjugate with a single loading value may be isolated from the conjugation mixture by electrophoresis or chromatography.
  • Exemplary embodiments of the isoindolinone-glutarimide antibody conjugates (IGAC) of Formula I are compiled in Table 3. Assessment of IGAC biological activity and other properties may be conducted according to the methods of Example 102.
  • the C 6 ll proliferation dose response IC50 value is an average of repetitive assays C 6 rtain exemplary IGAC were tested for their effects in inhibiting cellular proliferation, including CAL51 ; WSU-DLCL2, NCI-N87 and SKBR3 cell lines.
  • CAL51 is a human breast adenocarcinoma cell line with triple-negative status for expression of estrogen, progesterone and HER2 receptors.
  • WSU-DLCL2 is a human B-C 6 ll non-Hodgkin lymphoma cell line that expresses high levels of CD22.
  • NCI-N87 is a human epithelial cell line established from a gastric carcinoma;
  • SKBR3 is a human epithelial cell line established from a breast adenocarcinoma; both NCI-N87 and SKBR3 cell lines express high levels of HER2 receptor.
  • the invention provides a composition, e g., a pharmaceutically or pharmacologically acceptable composition or formulation, comprising an isoindolinone-glutarimide antibody conjugate (IGAC) composition of the invention as described herein and a pharmaceutically acceptable diluent, vehicle, carrier or excipient.
  • IGAC isoindolinone-glutarimide antibody conjugate
  • the isoindolinone-glutarimide antibody conjugate (IGAC) composition can be the same or different in the pharmaceutical composition, i.e., the composition can comprise IGAC that have the same number of isoindolinone-glutarimide (IG) moieties linked to the same positions on the antibody and/or IGAC that have the same number of (IG) moieties linked to different positions on the antibody, that have different numbers of (IG) moieties linked to the same positions on the antibody, or that have different numbers of (IG) moieties linked to different positions on the antibody.
  • a pharmaceutical composition comprises a mixture of the IGAC, wherein the average drug (IG) loading per antibody in the mixture of antibody conjugate compounds is about 2 to about 8.
  • An IGAC of the invention can have an average IG to antibody ratio (DAR) of about 0.4 to about 10.
  • DAR average IG to antibody ratio
  • the average number of IG moieties per antibody (DAR) in preparations of IGAC from conjugation reactions may be characterized by conventional means such as mass spectrometry, ELISA assay, and HPLC.
  • IGAC immunoglobulin-like IGAC
  • separation, purification, and characterization of homogeneous IGAC where p is a certain value from antibody drug conjugates (ADC) with other drug loadings may be achieved by purification means such as reverse phase HPLC or electrophoresis.
  • An isoindolinone-glutarimide antibody conjugate (IGAC) composition can be formulated for parenteral administration, such as intradermal, subcutaneous, intramuscular (IM), or intravenous (IV) injections, infusion, or administration into a body cavity or lumen of an organ.
  • the IGAC as a pharmaceutical composition can be injected into otherwise placed into a specific site of the body, such as a tumor.
  • Compositions for injection will commonly comprise a solution of the IGAC dissolved in a pharmaceutically acceptable carrier Among the acceptable vehicles and solvents that can be employed are water and an isotonic solution of one or more salts such as sodium chloride, e.g., Ringer's solution.
  • sterile fixed oils can conventionally be employed as a solvent or suspending medium.
  • any bland fixed oil can be employed, including synthetic monoglycerides or diglycerides.
  • fatty acids such as oleic acid can likewise be used in the preparation of inj ectables.
  • These pharmaceutical compositions desirably are sterile and generally free of undesirable matter.
  • These pharmaceutical compositions can be made sterilized by conventional, well known sterilization techniques.
  • the pharmaceutical compositions can contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents, e g., sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like.
  • the pharmaceutical composition may contain any suitable concentration of the IGAC .
  • concentration of the IGAC in the pharmaceutical composition can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight, and the like, in accordance with the particular mode of administration selected and the patient's needs.
  • concentration of IGAC in a solution formulation for injection will range from about 0.1% (w/w) to about 10% (w/w).
  • the isoindolinone-glutarimide antibody conjugate (IGAC) compositions of the invention may be useful in the treatment of diseases and disorders such as cancer.
  • the IGAC direct a tumor-associated antigen-binding antibody to a cell that expresses the antigen and deliver a cereblon-degrading moiety to the target cell.
  • a target protein such as GSPT1 is ubiquitinated and subsequently degraded
  • the invention provides a method for treating cancer with a pharmaceutical composition of the IGAC.
  • the method includes administering a therapeutically effective amount of an antibody conjugate composition as described herein to a subject in need thereof, such as a patient that has cancer and is in need of treatment for the cancer.
  • the method includes administering a therapeutically effective amount of an IGAC selected from Table 3.
  • the IGAC include those with anticancer activity ( Figures 1-4).
  • the IGAC selectively delivers an effective dose of an active form of the isoindolinone- glutarimide protein target degrader moiety to tumor tissue, whereby greater selectivity (i.e., a lower efficacious dose) may be achieved while increasing the therapeutic index (“therapeutic window”) relative to an unconjugated protein target degrader compound
  • the IGAC may be used to treat various hyperproliferative diseases or disorders, e.g. characterized by the overexpression of a tumor antigen.
  • hyperproliferative disorders include benign or malignant solid tumors and hematological disorders such as leukemia and lymphoid malignancies.
  • cancers to be treated herein include, but are not limited to, carcinoma, lymphoma, blastoma, sarcoma, leukemia or lymphoid malignancies including acute myeloid leukemia, squamous cell cancer, epithelial squamous cell cancer, lung cancer including smallcell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung and squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, rectal cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, and head and neck cancer.
  • carcinoma lymphoma, blastoma, sarcoma,
  • the IGAC may be useful in therapy to treat solid tumors such as lung cancer; non-small cell lung cancer, squamous cell lung cancer, small cell lung cancer, breast cancer, and neuroendocrine cancers such as neuroendocrine prostate cancer, castration-resistant neuroendocrine prostate cancer (NEPC) and lung neuroendocrine tumors.
  • the IGAC may be useful in therapy to treat blood-borne hematological cancers such as leukemias; acute myelogenous leukemia (AML) and myelomas; multiple myeloma (MM).
  • an IGAC for use as a medicament is provided.
  • the invention provides an IGAC for use in a method of treating an individual comprising administering to the individual an effective amount of the antibody conjugate composition in a pharmaceutical composition.
  • the method further comprises administering to the individual an effective amount of at least one additional therapeutic agent, e.g., as described herein
  • the invention provides for the use of an IGAC in the manufacture or preparation of a medicament.
  • the medicament is for treatment of cancer, the method comprising administering to an individual having cancer an effective amount of the medicament.
  • the method further comprises administering to the individual an effective amount of at least one additional therapeutic agent, e.g., as described herein.
  • Dosing can be by any suitable route, e.g. by injections, such as intravenous or subcutaneous injections, depending in part on whether the administration is brief or chronic.
  • Various dosing schedules including but not limited to single or multiple administrations over various time-points, bolus administration, and pulse infusion are contemplated herein.
  • the IGAC dose can range from about 5 mg/kg (body weight) to about 50 mg/kg, from about 10 pg/kg to about 5 mg/kg, or from about 100 pg/kg to about 1 mg/kg.
  • the IGAC dose can be about 100, 200, 300, 400, or 500 pg/kg.
  • the IGAC dose can be about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mg/kg.
  • the IGAC dose can also be outside of these ranges, depending on the particular conjugate as well as the type and severity of the cancer or disorder being treated. Frequency of administration can range from a single dose to multiple doses per week, or more frequently. In some embodiments, the IGAC is administered from about once per month to about five times per week. In some embodiments, the IGAC is administered once per week.
  • the IGAC can be used either alone or in combination with other therapeutic agents in a therapy regimen.
  • IGAC may be administered concurrently in a regimen with one or more other drugs during the same treatment cycle, on the same day of treatment as the one or more other drugs, and, optionally, at the same time as the one or more other drugs.
  • the concurrently administered drugs are each administered on day-1 of a 3-week cycle.
  • an IGAC may be co-administered with at least one additional therapeutic agent, such as a chemotherapeutic agent.
  • Such combination therapies encompass combined administration (where two or more therapeutic agents are included in the same or separate formulations), and separate administration, in which case, administration of the IGAC can occur prior to, simultaneously, and/or following, administration of the additional therapeutic agent.
  • IGAC can also be used in combination with radiation therapy.
  • the reaction mixture was poured into water (50.0 mL) and stirred for 10 min, then filtered to give a filter cake, the filter cake was concentrated to give a residue.
  • the residue was purified by Prep- HPLC (column: Waters Xbridge 150*25mm* 5um;mobile phase: [water(FA)-ACN];B%: 11%- 41%,10min) to afford l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl)urea (119.12 mg, 267 umol, 29% yield, 99% purity) as a yellow solid.
  • Step B Preparation of Int Is Int 1r
  • Int Ir (1.80 g, 4.86 mmol, 1.00 eq) in tetrahydrofuran (100 mL) and methanol (10.0 mL) was added palladium carbon (180 mg, 10% purity) at nitrogen atmosphere.
  • the mixture was stirred under hydrogen atmosphere at 25 °C for 12 h.
  • the reaction was filtered to give a filter cake.
  • the reaction was diluted with water (50.0 mL) and extracted with ethyl acetate (3 x 50.0 mL). The combined organic layer was washed with brine (50.0 mL) and dried over anhydrous sodium sulfate, filtered and concentrated to give a residue.
  • the mixture was filtered to give a filtrate.
  • the filtrate was purified by reversed phase-HPLC (column: Shim-pack C 1 8 150*25*10um, mobile phase: [water(0.1% formic acid)- acetonitrile]) to afford 2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindoline-5-carbaldehyde, Int Iv, (120 mg, 441 umol, 28% yield) as a yellow solid.
  • Step D Preparation of Compound IG-16
  • 3-(6-(aminomethyl)-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int DD, (100 mg, 366 umol, 1.00 eq) in dimethyl formamide (3.00 mL) was added triethylamine (55.5 mg, 549 umol, 76.4 uL, 1.50 eq) and 2-chloro-4-isocyanato-l -methylbenzene (73.6 mg, 439 umol, 1.20 eq) .
  • the mixture was stirred at 25°C for 2 h.
  • the mixture was concentrated in vacuum to give a residue.
  • Step D Preparation of Int 2g and Int 2h
  • the filter cake was diluted with water (10.0 mL).
  • the residue was purified by reversed-phase HPLC(column: Phenom enex luna C 18 150*25mm* 10um;mobile phase: [water(FA)-ACN];B%: 7%- 37%,10min),and the fraction was lyophilized to afford a mixture of 5-amino-2-(2,6-dioxopiperidin- 3-yl)-6-hydroxyisoindoline-l, 3-dione, Int 2g, and 4-amino-2-(2,6-dioxopiperidin-3-yl)-5- hydroxyisoindoline- 1,3 -dione, Int 2h, (200 mg, 318.07 umol,) as a yellow solid.
  • 2-chloro-4-methoxypyrimidine (68.5 mg, 474 umol, 1.00 eq), dicyclohexyl-(2-(2,6-dimethoxyphenyl)phenyl)phosphane (S-Phos) (38.9 mg, 94 7 umol, 0.20 eq) and tris(dibenzylidenethyl acetoacetate)dipalladium(O) (43.38 mg, 47.37 umol, 0.1 eq) were added and the mixture was stirred at 60 °C for 3 h. The mixture was diluted with ethyl acetate (5 mL) and washed with brine (3 > ⁇ 2 mL).
  • the filter cake was purified by flash silica gel chromatography (ISCO®; 80 g SepaFlash® Silica Flash Column, Eluent of 0-30% ethyl acetate/petroleum ether gradient @ 100 mL/min) to give methyl 4-hydroxy-2-methyl-3- nitrobenzoate, Int 2o, (1 .50 g, 7. 10 mmol, 24% yield) as a yellow solid.
  • the reaction mixture was concentrated under reduced pressure to give a residue
  • the residue was purified by reversed-phase HPLC(column: Waters Xbridge 150 * 25 mm * 5 um; mobile phase: [water( NHiHCChl-ACN]; B%: 32% - 62%, 9 min).
  • the desired fraction was lyophilized to afford 3-(4-amino-6-methoxy-l- oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 2y, (100 mg, 200 umol, 8% yield) as a white solid.
  • Methyl 6-fluoro-2-methyl-3-nitro-benzoate (1.00 g, 4.69 mmol, 1.00 eq) was added into a solution of sodium methoxide (507 mg, 9.38 mmol, 2.00 eq) in methanol (10.0 mL). The mixture was stirred at 25 °C for 12 h. The mixture was concentrated to give a residue. The mixture was concentrated to afford methyl 6-methoxy-2-methyl-3-nitro-benzoate, Int 2z, (980 mg, 4.35 mmol, 93% yield) as a yellow oily substance.

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Abstract

The invention provides antibody conjugates of Formula I comprising an antibody linked by conjugation to one or more isoindolinone-glutarimide moieties. The invention also provides isoindolinone-glutarimide derivative intermediate compositions comprising a reactive functional group. Such intermediate compositions are suitable substrates for formation of the antibody conjugates through a linker or linking moiety. The invention further provides methods of treating diseases and disorders such as cancer with the antibody conjugates.

Description

ISOINDOLINONE-GLUTARIMIDE ANTIBODY CONJUGATES, AND USES THEREOF
CROSS REFERENCE TO RELATED APPLICATIONS
This non -provisional application claims the benefit of priority to U.S. Provisional Applications No. 63/467,543, filed 18 May 2023, and No. 63/557,080, filed on 23 February 2024, each of which are incorporated by reference in their entirety.
FIELD OF THE INVENTION
The disclosure relates generally to antibody conjugate compositions, intermediates for their manufacture, and methods of their use. The compositions are useful for facilitating intracellular degradation of target proteins.
BACKGROUND OF THE INVENTION
The ubiquitin proteasome system can be manipulated to conduct targeted degradation of specific proteins. Promoting the targeted degradation of pathogenic proteins using small molecule degraders is a new modality in the treatment of diseases, including redirecting the activity of E3 ligases such as cereblon. Proteolysis targeting chimera compounds called PROTAC (Sakamoto, K. M , et al. (2001) Proc. Natl. Acad. Sci. USA 98:8554-8559; Sun, X. et al. (2019) Signal Transduct. Target. Ther. 4:64; Schapira, M., et al (2019) Nat. Rev. Drug Discov. 18:949-963) and “molecular glue” compounds (Yang, Z., et al (2021) Cell Research 31 : 1315-1318; Tan, X. et al. (2007) Nature 446:640-645; Han, T. et al. (2017) Science 356, eaal3755) are two modes of TPD. PROTAC comprise three parts, including a ligand for binding a target protein, another ligand for recruiting an E3 ligase, and a linker to help anchor the target protein to the E3 ubiquitin ligase to promote its ubiquitination and subsequent proteasomal degradation. Similar to PROTAC, molecular glues can also cause ubiquitination and degradation of a target protein. In contrast to PROTAC, molecular glues are small molecular weight compounds that trigger a compact protein-protein interaction between a target protein and an E3 ubiquitin ligase. Molecular glues are typically smaller than PROTAC and may have better pharmacological properties, higher membrane permeability, better cellular uptake, and better penetration of the blood-brain barrier. Molecular glues promote the poly-ubiquitination and proteasomal degradation of various disease-associated protein targets (Chamberlain, P., et al (2019) Drug Disc. Today. Tech. 31:29-34; WO 2022/152821). The molecular glue molecules bind to both the E3 ligase and the target protein, thereby mediating an alteration of the ligase surface and enabling an interaction with the target protein. Examples include the IMiD (immunomodulatory imide drug) class including thalidomide, lenalidomide and pomalidomide, each approved for use in treating hematological cancers. More efficient targeting strategies are still required.
GSPT1 contains a well-defined degron, a peptidic motif that signals for degradation, allowing for the recruitment of the E3 ligase cereblon (CRBN) and subsequent proteasomal degradation in the presence of molecular glue degraders. GSPT1 (G1 to S phase transition 1) is a translation termination factor that recognizes the termination codon by binding eRFl, forcing the proteins to dissociate from the ribosome after translation Downregulation of GSPT1 can cause the abnormal expression of key proteins, inhibit proliferation or induce apoptosis in diverse tumor cells (Chauvin, C., et al. (2007) Mol. Cell. Biol. 27:5619-5629; Matyskiela, M. E., et al. (2016) Nature 535:252-257; Yang, I, et al. J. Med. Chem. (2019) 62:9471-9487).
Targeted therapeutic agents to treat hyperproliferative disorders like cancer, and other disease are of interest.
SUMMARY OF THE INVENTION
The invention is generally directed to an antibody conjugate composition comprising an isoindolinone-glutarimide moiety covalently attached to an antibody by an antibody linker, wherein the antibody binds to a tumor-associated antigen or cell-surface receptor. The antibody conjugate composition has Formula I:
Figure imgf000003_0001
or a pharmaceutically acceptable salt thereof, wherein:
Ab is the antibody;
L is the antibody linker;
IG is the isoindolinone-glutarimide moiety; and p is an integer from 1 to 12
Another aspect of the invention is an antibody conjugate composition selected from Formulae la and lb:
Figure imgf000004_0001
wherein the substituents are defined herein.
Another aspect of the invention is an isoindolinone-glutarimide linker compound selected from Formulae Ila and lib:
Figure imgf000004_0002
lib wherein the substituents are defined herein.
Another aspect of the invention is the antibody conjugate composition prepared by conjugation of a cysteine amino acid of an antibody with an isoindolinone-glutarimide linker compound.
Another aspect of the invention is a process for preparing the antibody conjugate comprising reacting a cysteine amino acid of an antibody with an isoindolinone-glutarimide linker compound. Another aspect of the invention is a pharmaceutical composition comprising a therapeutically effective amount of the antibody conjugate composition, and one or more pharmaceutically acceptable diluent, vehicle, carrier or excipient Another aspect of the invention is a method for treating cancer comprising administering a therapeutically effective amount of the pharmaceutical composition to a patient in need thereof,
Another aspect of the invention is a use of the antibody conjugate composition in the manufacture of a medicament for the treatment of cancer in a mammal.
Another aspect of the invention is the antibody conjugate composition for use in a method for treating cancer.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 shows a graph of in vivo tumor volume over time in the treatment of CD22+ WSU-DLCL2 syngeneic tumor bearing CB17 SCID mice with pinatuzumab, and anti-CD22 conjugates IGAC-59 and IGAC-62 (Table 3).
Figure 2 shows a graph of in vivo tumor volume over time in the treatment of CD22+ WSU-DLCL2 syngeneic tumor bearing CB17 SCID mice with pinatuzumab, and anti-CD22 conjugates IGAC-53, IGAC-60 and IGAC-62 (Table 3).
Figure 3 shows a graph of in vivo tumor volume over time in the treatment of HER2+ NCI-N87 gastric tumor xenograft bearing female BALB/c nude mice with anti-HER2 conjugates IGAC-58 and IGAC-61 (Table 3).
Figure 4 shows a graph of in vivo tumor volume over time in the treatment of HER2+ NCI-N87 gastric tumor xenograft bearing female BALB/c nude mice with anti-HER2 conjugates IGAC-54, IGAC-55, IGAC-56 and IGAC-57 (Table 3).
DETAILED DESCRIPTION OF THE INVENTION
Reference will now be made in detail to certain embodiments of the invention, examples of which are illustrated in the accompanying structures and formulas. While the invention will be described in conjunction with the enumerated embodiments, it will be understood that they are not intended to limit the invention to those embodiments. On the contrary, the invention is intended to cover all alternatives, modifications, and equivalents, which may be included within the scope of the invention as defined by the claims.
One skilled in the art will recognize many methods and materials similar or equivalent to those described herein, which could be used in the practice of the present invention. The invention is in no way limited to the methods and materials described.
DEFINITIONS
The terms “antibody” or “antibody construct” refer to a polypeptide comprising an antigen binding region (including the complementarity determining region (CDRs)) from an immunoglobulin gene or fragments thereof. The term “antibody” specifically encompasses monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e g., bispecific antibodies), and antibody fragments that exhibit the desired biological activity. An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one “heavy” chain (about 50-70 kDa) connected by disulfide bonds. Each chain is composed of structural domains, which are referred to as immunoglobulin domains. These domains are classified into different categories by size and function, e g., variable domains or regions on the light and heavy chains (VL and VH, respectively) and constant domains or regions on the light and heavy chains (CL and CH, respectively). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids, referred to as the paratope, primarily responsible for antigen recognition, i.e., the antigen binding domain. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively. IgG antibodies are large molecules of about 150 kDa composed of four peptide chains. IgG antibodies contain two identical class y heavy chains of about 50 kDa and two identical light chains of about 25 kDa, thus a tetrameric quaternary structure The two heavy chains are linked to each other and to a light chain each by disulfide bonds. The resulting tetramer has two identical halves, which together form the Y-like shape Each end of the fork contains an identical antigen binding domain. There are four IgG subclasses (IgGl, IgG2, IgG3, and IgG4) in humans, named in order of their abundance in serum (i.e., IgGl is the most abundant). Typically, the antigen binding domain of an antibody will be most critical in specificity and affinity of binding to cancer cells.
“Bispecific” antibodies (bsAbs) are antibodies that bind two distinct epitopes to cancer (Suurs F.V. et al
Figure imgf000006_0001
Pharmacology & Therapeutics 201: 103-119). Bispecific antibodies may engage immune cells to destroy tumor cells, deliver isoindolinone-glutarimide moi eties to tumors, and/or block tumor signaling pathways. An antibody that targets a particular antigen includes a bispecific or multispecific antibody with at least one antigen binding region that targets the particular antigen. In some embodiments, the targeted monoclonal antibody is a bispecific antibody with at least one antigen binding region that targets tumor cells. Such antigens include but are not limited to: mesothelin, prostate specific membrane antigen (PSMA), HER2, TROP2, CEA, CEACAM5, EGFR, 5T4, Nectin4, CCL-1, CCR7, CD19, CD20, CD22, CD30, CD33, CD70, CD79b, CD 123, CDH3, B7H3, B7H4 (also known as 08E), Integrin-beta6, protein tyrosine kinase 7 (PTK7), glypican-3, GPC-1, LIV-1, Folate receptor alpha, Claudinl8.2, RG1, fucosyl-GMl, tissue factor (CD142), cKit (CD117), Axl, , GC-C, CTLA-4, and CD44 (WO 2017/196598). Other antigen binding regions of bispecific antibodies include those in the following section: ANTIBODY TARGETS.
In some embodiments, the antibody construct is an antigen-binding antibody “fragment,” which comprises at least an antigen-binding region of an antibody, alone or with other components that together constitute the antibody construct. Many different types of antibody “fragments” are known in the art, including, for instance, (i) a Fab fragment, which is a monovalent fragment consisting of the VL, VH, CL, and CHi domains, (ii) a F(ab’)2 fragment, which is a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region, (iii) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (iv) a Fab’ fragment, which results from breaking the disulfide bridge of an F(ab’)2 fragment using mild reducing conditions, (v) a disulfide-stabilized Fv fragment (dsFv), and (vi) a single chain Fv (scFv), which is a monovalent molecule consisting of the two domains of the Fv fragment (i.e., VL and VH) joined by a synthetic linker which enables the two domains to be synthesized as a single polypeptide chain. In some embodiments, the antibody construct is an antibody or a fusion protein comprising (i) an antigen binding domain and (ii) an Fc domain.
The antibody or antibody fragment can be part of a larger construct, for example, a conjugate or fusion construct of the antibody fragment to additional regions. For instance, in some embodiments, the antibody fragment can be fused to an Fc region as described herein In other embodiments, the antibody fragment (e.g., a Fab or scFv) can be part of a chimeric antigen receptor or chimeric T-cell receptor, for instance, by fusing to a transmembrane domain (optionally with an intervening linker or “stalk” (e.g., hinge region)) and optional intercellular signaling domain. For instance, the antibody fragment can be fused to the gamma and/or delta chains of a t-cell receptor, so as to provide a T-cell receptor like construct that binds PD-L1 . In yet another embodiment, the antibody fragment is part of a bispecific T-cell engager (BiTEs) comprising a CD1 or CD3 binding domain and linker.
In some embodiments, the antibody construct comprises an Fc domain. In certain embodiments, the antibody construct is a fusion protein. The antigen binding domain can be a single-chain variable region fragment (scFv). A single-chain variable region fragment (scFv), which is a truncated Fab fragment including the variable (V) domain of an antibody heavy chain linked to a V domain of a light antibody chain via a synthetic peptide, can be generated using routine recombinant DNA technology techniques. Similarly, disulfide-stabilized variable region fragments (dsFv) can be prepared by recombinant DNA technology. The antibody construct or antigen binding domain may comprise one or more variable regions (e.g., two variable regions) of an antigen binding domain of an antibody, each variable region comprising a CDR1, a CDR2, and a CDR3. “Cysteine-mutant antibody” is an antibody in which one or more amino acid residues of an antibody are substituted with cysteine residues. A cysteine-mutant antibody may be prepared from the parent antibody by antibody engineering methods (Junutula, J et al., (2008b) Nature Biotech., 26(8):925-932; Doman et al. (2QQ9) Blood 114(13):2721-2729; US 7521541; US 7723485; US 2012/0121615; WO 2009/052249). Cysteine residues provide for site-specific conjugation of a drug moiety such as a isoindolinone-glutarimide compound to the antibody through the reactive cysteine thiol groups at the engineered cysteine sites but do not perturb immunoglobulin folding and assembly or alter antigen binding and effector functions. Cysteine- mutant antibodies can be conjugated to the isoindolinone-glutarimide linker compound with uniform stoichiometry of the antibody conjugate (e.g., up to two isoindolinone-glutarimide moieties per antibody in an antibody that has a single engineered, mutant cysteine site). The isoindolinone-glutarimide linker compound has a reactive electrophilic group to react specifically with the free cysteine thiol groups of the cysteine-mutant antibody.
“Epitope” means any antigenic determinant or epitopic determinant of an antigen to which an antigen binding domain binds (i.e., at the paratope of the antigen binding domain). Antigenic determinants usually consist of chemically active surface groupings of molecules, such as amino acids or sugar side chains, and usually have specific three dimensional structural characteristics, as well as specific charge characteristics
The terms “Fc receptor” or “FcR” refer to a receptor that binds to the Fc region of an antibody There are three main classes of Fc receptors: (1) FcyR which bind to IgG, (2) FcaR which binds to IgA, and (3) FceR which binds to IgE. The FcyR family includes several members, such as Fcyl (CD64), FcyRIIA (CD32A), FcyRIIB (CD32B), FcyRIIIA (CD16A), and FcyRIIIB (CD16B). The Fey receptors differ in their affinity for IgG and also have different affinities for the IgG subclasses (e.g., IgGl, IgG2, IgG3, and IgG4).
Nucleic acid or amino acid sequence “identity,” as referenced herein, can be determined by comparing a nucleic acid or amino acid sequence of interest to a reference nucleic acid or amino acid sequence. The percent identity is the number of nucleotides or amino acid residues that are the same (i.e., that are identical) as between the optimally aligned sequence of interest and the reference sequence divided by the length of the longest sequence (i.e., the length of either the sequence of interest or the reference sequence, whichever is longer). Alignment of sequences and calculation of percent identity can be performed using available software programs. Examples of such programs include CLUSTAL-W, T-Coffee, and ALIGN (for alignment of nucleic acid and amino acid sequences), BLAST programs (e g., BLAST 2.1, BL2SEQ, BLASTp, BLASTn, and the like) and FASTA programs (e.g., FASTA3x, FASTM, and S SEARCH) (for sequence alignment and sequence similarity searches). Sequence alignment algorithms also are disclosed in, for example, Altschul et al., J. Molecular Biol., 215(3): 403-410 (1990), Beigert et al., Proc. Natl. Acad. Sci. USA, 106(\Q\. 3770-3775 (2009), Durbin et al., eds., Biological Sequence Analysis: Probalistic Models of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, UK (2009), Soding, Bioinformatics, 21(7): 951- 960 (2005), Altschul et al , Nucleic Acids Res., 25(17): 3389-3402 (1997), and Gusfield, Algorithms on Strings, Trees and Sequences, Cambridge University Press, Cambridge UK (1997)). Percent (%) identity of sequences can be also calculated, for example, as 100 x [(identical positions)/min(TGA, TGB)], where TGA and TGB are the sum of the number of residues and internal gap positions in peptide sequences A and B in the alignment that minimizes TGA and TGB. See, e.g., Russell et al., J. Mol Biol., 244: 332-350 (1994).
The “antibody construct” or “binding agent” comprises Ig heavy and light chain variable region polypeptides that together form the antigen binding site. Each of the heavy and light chain variable regions are polypeptides comprising three complementarity determining regions (CDR1, CDR2, and CDR3) connected by framework regions. The antibody construct can be any of a variety of types of binding agents known in the art that comprise Ig heavy and light chains. For instance, the binding agent can be an antibody, an antigen-binding antibody “fragment,” or a T-cell receptor.
“Amino acid” refers to any monomeric unit that can be incorporated into a peptide, polypeptide, or protein. Amino acids include naturally-occurring a-amino acids and their stereoisomers, as well as unnatural (non-naturally occurring) amino acids and their stereoisomers. “Stereoisomers” of a given amino acid refer to isomers having the same molecular formula and intramolecular bonds but different three-dimensional arrangements of bonds and atoms (e.g., an L-amino acid and the corresponding D-amino acid). The amino acids can be glycosylated (e.g., //-linked glycans, O-linked glycans, phosphoglycans, C-linked glycans, or glypication) or deglycosylated. Amino acids may be referred to herein by either the commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission.
Naturally-occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, y-carboxyglutamate, and O-phosphoserine. Naturally-occurring a-amino acids include, without limitation, alanine (Ala), cysteine (Cys), aspartic acid (Asp), glutamic acid (Glu), phenylalanine (Phe), glycine (Gly), histidine (His), isoleucine (He), arginine (Arg), lysine (Lys), leucine (Leu), methionine (Met), asparagine (Asn), proline (Pro), glutamine (Gin), serine (Ser), threonine (Thr), valine (Vai), tryptophan (Trp), tyrosine (Tyr), and combinations thereof. Stereoisomers of naturally- occurring a-amino acids include, without limitation, D-alanine (D-Ala), D-cysteine (D-Cys), D-aspartic acid (D-Asp), D-glutamic acid (D-Glu), D-phenylalanine (D-Phe), D-histidine (D-His), D-isoleucine (D-Ile), D-arginine (D-Arg), D-lysine (D-Lys), D-leucine (D-Leu), D-methionine (D-Met), D-asparagine (D-Asn), D-proline (D-Pro), D-glutamine (D-Gln), D-serine (D-Ser), D-threonine (D-Thr), D-valine (D-Val), D-tryptophan (D-Trp), D-tyrosine (D-Tyr), and combinations thereof.
Naturally-occurring amino acids include those formed in proteins by post-translational modification, such as citrulline (Cit).
Unnatural (non-naturally occurring) amino acids include, without limitation, amino acid analogs, amino acid mimetics, synthetic amino acids, A-substituted glycines, and A-methyl amino acids in either the L- or D-configuration that function in a manner similar to the naturally- occurring amino acids. For example, “amino acid analogs” can be unnatural amino acids that have the same basic chemical structure as naturally-occurring amino acids (i.e., a carbon that is bonded to a hydrogen, a carboxyl group, an amino group) but have modified side-chain groups or modified peptide backbones, e.g., homoserine, norleucine, methionine sulfoxide, and methionine methyl sulfonium. “Amino acid mimetics” refer to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally -occurring amino acid.
“Linker” refers to a functional group that covalently bonds two or more moieties in an antibody conjugate compound. For example, the linking moiety can serve to covalently bond a drug isoindolinone-glutarimide moiety to an antibody in an antibody conjugate composition. Useful bonds for connecting linking moieties to proteins and other materials include, but are not limited to, amides, amines, esters, carbamates, ureas, thioethers, thiocarbamates, thiocarbonates, and thioureas.
“Divalent” refers to a chemical moiety that contains two points of attachment for linking two functional groups; polyvalent linking moieties can have additional points of attachment for linking further functional groups. Divalent radicals may be denoted by the suffix “diyl”. For example, divalent linking moieties include divalent polymer moieties such as divalent poly(ethylene glycol), divalent cycloalkyl, divalent heterocycloalkyl, divalent aryl, and divalent heteroaryl group. A “divalent cycloalkyl, heterocycloalkyl, aryl, or heteroaryl group” refers to a cycloalkyl, heterocycloalkyl, aryl, or heteroaryl group having two points of attachment for covalently linking two moieties in a molecule or material. Cycloalkyl, heterocycloalkyl, aryl, or heteroaryl groups can be substituted or unsubstituted. Cycloalkyl, heterocycloalkyl, aryl, or heteroaryl groups can be substituted with one or more groups selected from halo, hydroxy, amino, alkylamino, amido, acyl, nitro, cyano, alkoxy, and others. A wavy line (“
Figure imgf000011_0001
”) and one or more asterisks (*) represents a point of attachment of the specified chemical moiety to another moiety. If the specified chemical moiety has two wavy lines (“ present, it will be understood that the chemical moiety can be used bilaterally, i.e., as read from left to right or from right to left. In some embodiments, a specified moiety having two wavy lines
Figure imgf000011_0002
present is considered to be used as read from left to right.
“Alkyl” refers to a straight (linear) or branched, saturated, aliphatic radical having the number of carbon atoms indicated. Alkyl can include any number of carbons, for example from one to six, one to eight, one to twelve, one to twenty, or one to forty. Examples of alkyl groups include, but are not limited to, methyl (Me, -CH3), ethyl (Et, -CH2CH3), 1 -propyl (n-Pr, n- propyl, -CH2CH2CH3), 2-propyl (i-Pr, i-propyl, -CH(CH3)2), 1 -butyl (n-Bu, n-butyl, - CH2CH2CH2CH3), 2-m ethyl- 1 -propyl (i-Bu, i-butyl, -CH2CH(CH3)2), 2 -butyl (s-Bu, s-butyl, - CH(CH3)CH2CH3), 2-methyl-2-propyl (t-Bu, t-butyl, -C(CH3)3), 1 -pentyl (n-pentyl, - CH2CH2CH2CH2CH3), 2-pentyl (-CH(CH3)CH2CH2CH3), 3 -pentyl (-CH(CH2CH3)2), 2-methyl- 2-butyl (-C(CH3)2CH2CH3), 3-methyl-2-butyl (-CH(CH3)CH(CH3)2), 3-methyl-l -butyl (- CH2CH2CH(CH3)2), 2-methyl-l -butyl (-CH2CH(CH3)CH2CH3), 1 -hexyl (- CH2CH2CH2CH2CH2CH3), 2-hexyl (-CH(CH3)CH2CH2CH2CH3), 3 -hexyl (- CH(CH2CH3)(CH2CH2CH3)), 2-methyl-2-pentyl (-C(CH3)2CH2CH2CH3), 3-methyl-2-pentyl (- CH(CH3)CH(CH3)CH2CH3), 4-methyl-2-pentyl (-CH(CH3)CH2CH(CH3)2), 3-methyl-3-pentyl (- C(CH3)(CH2CH3)2), 2-methyl-3-pentyl (-CH(CH2CH3)CH(CH3)2), 2,3-dimethyl-2-butyl (- C(CH3)2CH(CH3)2), 3,3-dimethyl-2-butyl (-CH(CH3)C(CH3)3, 1 -heptyl, 1-octyl, and the like. Alkyl groups can be substituted or unsubstituted. “Substituted alkyl” groups can be substituted with one or more groups selected from halo, hydroxy, amino, oxo (=0), alkylamino, amido, acyl, nitro, cyano, and alkoxy.
The term “alkyldiyl” refers to a divalent alkyl radical. Examples of alkyldiyl groups include, but are not limited to, methylene (-CH2-), ethylene (-CH2CH2-), propylene (- CH2CH2CH2-), and the like. An alkyldiyl group may also be referred to as an “alkylene” group.
“Alkenyl” refers to a straight (linear) or branched, unsaturated, aliphatic radical having the number of carbon atoms indicated and at least one carbon-carbon double bond, sp2. Alkenyl can include from two to about 12 or more carbons atoms Alkenyl groups are radicals having “cis” and “trans” orientations, or alternatively, “E” and “Z” orientations. Examples include, but are not limited to, ethylenyl or vinyl (-CH=CH2), allyl (-CH2CH=CH2). butenyl, pentenyl, and isomers thereof. Alkenyl groups can be substituted or unsubstituted. “Substituted alkenyl” groups can be substituted with one or more groups selected from halo, hydroxy, amino, oxo (=0), alkylamino, amido, acyl, nitro, cyano, and alkoxy. The terms “ alkenyl ene” or “alkenyldiyl” refer to a linear or branched-chain divalent hydrocarbon radical. Examples include, but are not limited to, ethylenylene or vinylene (- CH=CH-), allyl (-CH2CH=CH-), and the like.
“Alkynyl” refers to a straight (linear) or branched, unsaturated, aliphatic radical having the number of carbon atoms indicated and at least one carbon-carbon triple bond, sp. Alkynyl can include from two to about 12 or more carbons atoms. For example, C2-C6 alkynyl includes, but is not limited to ethynyl (-CACI I), propynyl (propargyl, -CI FCUCI I), butynyl, pentynyl, hexynyl, and isomers thereof Alkynyl groups can be substituted or unsubstituted. “Substituted alkynyl” groups can be substituted with one or more groups selected from halo, hydroxy, amino, oxo (=0), alkylamino, amido, acyl, nitro, cyano, and alkoxy.
The term “alkynylene” or “alkynyldiyl” refer to a divalent alkynyl radical.
"Heteroalkyl" or “heteroalkylene” refer to a monovalent, straight or branched chain alkyl group, as defined above, comprising at least one heteroatom including but not limited to Si, N, O, P or S within the alkyl chain or at a terminus of the alkyl chain. In some embodiments, a heteroatom is within the alkyl chain. In other embodiments, a heteroatom is at a terminus of the alkylene and thus serves to join the alkyl to the remainder of the molecule. In some embodiments, a heteroalkyl group may have 1 to 12 carbon atoms (C1-C12 heteroalkyl). In some embodiments, a heteroalkyl group may have 1 to 24 carbon atoms (C1-C24 heteroalkyl). In some embodiments, a heteroalkyl group may have 1 to 40 carbon atoms (C1-C40 heteroalkyl). Unless stated otherwise specifically in the specification, a heteroalkyl group is optionally substituted. For example, heteroalkyl groups can be substituted with 1 -6 fluoro (F) substituents, for example, on the carbon backbone (as -CHF- or -CF2-) or on terminal carbons of straight chain or branched heteroalkyls (such as -CHF2 or -CF3). Examples of heteroalkyl groups include, but are not limited to, -CH2CH2OCH3, -CH2CH2NHCH3, -CH2CH2N(CH3)2, - C(=O)NHCH2CH2NHCH3, -C(=O)N(CH3)CH2CH2N(CH3)2, - C(=O)NHCH2CH2NHC(=O)CH2CH3, -C(=O)N(CH3)CH2CH2N(CH3)C(=O)CH2CH3, - OCH2CH2CH2NH(CH3), -OCH2CH2CH2N(CH3)2, -OCH2CH2CH2NHC(=O)CH2CH3, - OCH2CH2CH2N(CH3)C(=O)CH2CH3, -CH2CH2CH2NH(CH3), -OCH2CH2CH2N(CH3)2, -CH2CH2CH2NHC(=O)CH2CH3, -CH2CH2CH2N(CH3)C(=O)CH2CH3, -CH2SCH2CH3, -CH2CH2S(O)CH3, -NHCH2CH2NHC(=O)CH2CH3, -CH2CH2S(O)2CH3, - CH2CH2OCF3, and -Si(CH3)3. Up to two heteroatoms may be consecutive, such as, for example, -CH2NHOCH3 and -CH2OSi(CH3)3. A terminal polyethylene glycol (PEG) moiety is a type of heteroalkyl group. Exemplary heteroalkyl groups also include ethylene oxide (e.g., polyethylene oxide), propylene oxide, amino acid chains (i.e., short to medium length peptides such as containing 1-15 amino acids), and alkyl chains connected via a variety of functional groups such as amides, disulfides, ketones, phosphonates, phosphates, sulfates, sulfones, sulfonamides, esters, ethers, -S-, carbamates, ureas, thioureas, anhydrides, or the like (including combinations thereof). In some embodiments, a heteroalkyl group includes a poly amino acid having 1-10 amino acids. In some embodiments, a heteroalkyl group includes a polyamino acid having 1-5 amino acids.
Heteroalkyl groups include a solubilizing unit comprising one or more groups of polyglycine, polysarcosine, polyethyleneoxy (PEG), and a glycoside, or combinations thereof.
"Heteroalkenyl" refers to a heteroalkyl group, as defined above, that contains at least one carbon-carbon double bond. "Heteroalkynyl" refers to a heteroalkyl group, as defined above, that contains at least one carbon-carbon triple bond.
“Heteroalkyldiyl” refers to a divalent form of a heteroalkyl group as defined above. In some embodiments, a heteroalkyldiyl group may have 1 to 12 carbon atoms (C1- C12 heteroalkyl diyl). In some embodiments, a heteroalkyldiyl group may have 1 to 24 carbon atoms (C1-C24 heteroalkyldiyl). In some embodiments, a heteroalkyldiyl group may have 1 to 40 carbon atoms (C1-C40 heteroalkyldiyl). Examples of heteroalkyl diyl groups include, but are not limited to, -CH2CH2OCH2-, -CH2CH2OCF2-, - CH2CH2NHCH2 , CH2OC(-O)NH - CH2OP(=O)(OH)OCH2 , C(=O)NHCH2CH2NHCH2-, -C(=O)N(CH3)CH2CH2N(CH3)CH2-, - C(=O)NHCH2CH2NHC(=O)CH2CH2-, -C(=O)N(CH3)CH2CH2N(CH3)C(=O)CH2CH2-, -OCH2CH2OCH2CH2-, -OCH2CH2OCH2C(=O)-, -OCH2CH2OCH2CH2C(=O)-, - OCH2CH2NHCH2-, -OCH2CH2N(CH3)CH2- -OCH2CH2CH2NHCH2-, - OCH2CH2CH2N(CH3)CH2-, -OCH2CH2CH2NHC(=O)CH2CH2-, - OCH2CH2CH2N(CH3)C(=O)CH2CH2-, -CH2CH2CH2NHCH2— , - CH2CH2CH2N(CH3)CH2- -CH2CH2CH2NHC(=O)CH2CH2-, - CH2CH2CH2N(CH3)C(=O)CH2CH2-, -CH2CH2NHC(=O)-, -CH2CH2N(CH3)CH2-, - CH2CH2N+(CH3)2-, -NHCH2CH2(NH2)CH2-, and -NHCH2CH2(NHCH3)CH2-. A divalent polyethylene glycol (PEG) moiety with one to about 50 units of -OCH2CH2- is a type of heteroalkyl diyl group. “Heteroalkenyl diyl” refers to a divalent form of a heteroalkenyl group. “Heteroalkynyldiyl” refers to a divalent form of a heteroalkynyl group.
The terms “carbocycle”, “carbocyclyl”, “carbocyclic ring” and “cycloalkyl” refer to a saturated or partially unsaturated, monocyclic, fused bicyclic, or bridged polycyclic ring assembly containing from 3 to 12 ring atoms, or the number of atoms indicated. Saturated monocyclic carbocyclic rings include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cyclooctyl. Saturated bicyclic and polycyclic carbocyclic rings include, for example, norbomane, [2.2.2] bicyclooctane, decahydronaphthalene and adamantane. Carbocyclic groups can also be partially unsaturated, having one or more double or triple bonds in the ring. Representative carbocyclic groups that are partially unsaturated include, but are not limited to, cyclobutene, cyclopentene, cyclohexene, cyclohexadiene (1,3- and 1 ,4-isomers), cycloheptene, cycloheptadiene, cyclooctene, cyclooctadiene (1,3-, 1,4- and 1,5-isomers), norbomene, and norbomadiene.
The term “cycloalkyl diyl” refers to a divalent cycloalkyl radical.
“Aryl” refers to a monovalent aromatic hydrocarbon radical of 6-20 carbon atoms (C6- C20) derived by the removal of one hydrogen atom from a single carbon atom of a parent aromatic ring system.. Aryl groups can be monocyclic, fused to form bicyclic or tricyclic groups, or linked by a bond to form a biaryl group. Representative aryl groups include phenyl, naphthyl and biphenyl. Other aryl groups include benzyl, having a methylene linking group. Some aryl groups have from 6 to 12 ring members, such as phenyl, naphthyl or biphenyl. Other aryl groups have from 6 to 10 ring members, such as phenyl or naphthyl.
The terms “arylene” or “aryldiyl” mean a divalent aromatic hydrocarbon radical of 6-20 carbon atoms (C6- C20) derived by the removal of two hydrogen atom from a two carbon atoms of a parent aromatic ring system. Some aryldiyl groups are represented in the exemplary structures as “Ar”. Aryldiyl includes bicyclic radicals comprising an aromatic ring fused to a saturated, partially unsaturated ring, or aromatic carbocyclic ring. Typical aryldiyl groups include, but are not limited to, radicals derived from benzene (phenyldiyl), substituted benzenes, naphthalene, anthracene, biphenylene, indenylene, indanylene, 1,2-dihydronaphthalene, 1, 2,3,4- tetrahydronaphthyl, and the like. Aryldiyl groups are also referred to as “arylene”, and are optionally substituted with one or more substituents described herein.
The terms “heterocycle,” “heterocyclyl” and “heterocyclic ring” are used interchangeably herein and refer to a saturated or a partially unsaturated (i.e., having one or more double and/or triple bonds within the ring) carbocyclic radical of 3 to about 20 ring atoms in which at least one ring atom is a heteroatom selected from nitrogen, oxygen, phosphorus and sulfur, the remaining ring atoms being C, where one or more ring atoms is optionally substituted independently with one or more substituents described below. A heterocycle may be a monocycle having 3 to 7 ring members (2 to 6 carbon atoms and 1 to 4 heteroatoms selected from N, O, P, and S) or a bicycle having 7 to 10 ring members (4 to 9 carbon atoms and 1 to 6 heteroatoms selected from N, O, P, and S), for example: a bicyclo [4,5], [5,5], [5,6], or [6,6] system. Heterocycles are described in Paquette, Leo A.; “Principles of Modern Heterocyclic Chemistry” (W A Benjamin, New York, 1968), particularly Chapters 1, 3, 4, 6, 7, and 9; “The Chemistry of Heterocyclic Compounds, A series of Monographs” (John Wiley & Sons, New York, 1950 to present), in particular Volumes 13, 14, 16, 19, and 28; and J. Am. Chem. Soc. (1960) 82:5566. “Heterocyclyl” also includes radicals where heterocycle radicals are fused with a saturated, partially unsaturated ring, or aromatic carbocyclic or heterocyclic ring. Examples of heterocyclic rings include, but are not limited to, morpholin-4-yl, piperidin-l-yl, piperazinyl, piperazin-4-yl-2-one, piperazin-4-yl-3-one, pyrrolidin-l-yl, thiomorpholin-4-yl, S- dioxothiomorpholin-4-yl, azocan-l-yl, azetidin-l-yl, octahydropyrido[l,2-a]pyrazin-2-yl, [l,4]diazepan-l-yl, pyrrolidinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, tetrahydropyranyl, dihydropyranyl, tetrahydrothiopyranyl, piperidino, morpholino, thiomorpholino, thioxanyl, piperazinyl, homopiperazinyl, azetidinyl, oxetanyl, thietanyl, homopiperidinyl, oxepanyl, thiepanyl, oxazepinyl, diazepinyl, thiazepinyl, 2-pyrrolinyl, 3- pyrrolinyl, indolinyl, 2H-pyranyl, 4H-pyranyl, dioxanyl, 1,3-dioxolanyl, pyrazolinyl, dithianyl, dithiolanyl, dihydropyranyl, dihydrothienyl, dihydrofuranyl, pyrazolidinylimidazolinyl, imidazolidinyl, 3-azabicyco[3. 1.0]hexanyl, 3-azabicyclo[4. 1 ,0]heptanyl, azabicyclo[2.2.2]hexanyl, 3H-indolyl quinolizinyl and N-pyridyl ureas. Spiro heterocyclyl moieties are also included within the scope of this definition. Examples of spiro heterocyclyl moieties include azaspiro[2.5]octanyl and azaspiro[2.4]heptanyl. Examples of a heterocyclic group wherein 2 ring atoms are substituted with oxo (=0) moieties are pyrimi dinonyl and 1,1- dioxo-thiomorpholinyl. The heterocycle groups herein are optionally substituted independently with one or more substituents described herein
The term “heterocyclyl diyl” refers to a divalent, saturated or a partially unsaturated (i.e., having one or more double and/or triple bonds within the ring) carbocyclic radical of 3 to about 20 ring atoms in which at least one ring atom is a heteroatom selected from nitrogen, oxygen, phosphorus and sulfur, the remaining ring atoms being C, where one or more ring atoms is optionally substituted independently with one or more substituents as described. Examples of 5- membered and 6-membered heterocyclyldiyls include morpholinyldiyl, piperidinyldiyl, piperazinyldiyl, pyrrolidinyldiyl, dioxanyldiyl, thiomorpholinyldiyl, and S- dioxothiomorpholinyldiyl.
The term “heteroaryl” refers to a monovalent aromatic radical of 5-, 6-, or 7-membered rings, and includes fused ring systems (at least one of which is aromatic) of 5-20 atoms, containing one or more heteroatoms independently selected from nitrogen, oxygen, and sulfur. Examples of heteroaryl groups are pyridinyl (including, for example, 2-hydroxypyridinyl), imidazolyl, imidazopyridinyl, pyrimidinyl (including, for example, 4-hydroxypyrimidinyl), pyrazolyl, triazolyl, pyrazinyl, tetrazolyl, furyl, thienyl, isoxazolyl, thiazolyl, oxadiazolyl, oxazolyl, isothiazolyl, pyrrolyl, quinolinyl, isoquinolinyl, tetrahydroisoquinolinyl, indolyl, benzimidazolyl, benzofuranyl, cinnolinyl, indazolyl, indolizinyl, phthalazinyl, pyridazinyl, triazinyl, isoindolyl, pteridinyl, purinyl, oxadiazolyl, thiadiazolyl, thiadiazolyl, furazanyl, benzofurazanyl, benzothiophenyl, benzothiazolyl, benzoxazolyl, quinazolinyl, quinoxalinyl, naphthyridinyl, and furopyridinyl. Heteroaryl groups are optionally substituted independently with one or more substituents described herein.
The term “heteroaryldiyl” refers to a divalent aromatic radical of 5-, 6-, or 7-membered rings, and includes fused ring systems (at least one of which is aromatic) of 5-20 atoms, containing one or more heteroatoms independently selected from nitrogen, oxygen, and sulfur. Examples of 5-membered and 6-membered heteroaryldiyls include pyridyldiyl, imidazolyl diyl, pyrimidinyl diyl, pyrazolyldiyl, triazolyldiyl, pyrazinyldiyl, tetrazolyldiyl, furyldiyl, thienyldiyl, isoxazolyl diyl diyl, thiazolyldiyl, oxadi azolyldiyl, oxazolyldiyl, isothiazolyldiyl, and pyrrolyldiyl.
The heterocycle or heteroaryl groups may be carbon (carbon-linked), or nitrogen (nitrogen-linked) bonded where such is possible. By way of example and not limitation, carbon bonded heterocycles or heteroaryls are bonded at position 2, 3, 4, 5, or 6 of a pyridine, position 3, 4, 5, or 6 of a pyridazine, position 2, 4, 5, or 6 of a pyrimidine, position 2, 3, 5, or 6 of a pyrazine, position 2, 3, 4, or 5 of a furan, tetrahydrofuran, thiofuran, thiophene, pyrrole or tetrahydropyrrole, position 2, 4, or 5 of an oxazole, imidazole or thiazole, position 3, 4, or 5 of an isoxazole, pyrazole, or isothiazole, position 2 or 3 of an aziridine, position 2, 3, or 4 of an azetidine, position 2, 3, 4, 5, 6, 7, or 8 of a quinoline or position 1, 3, 4, 5, 6, 7, or 8 of an isoquinoline.
By way of example and not limitation, nitrogen bonded heterocycles or heteroaryls are bonded at position 1 of an aziridine, azetidine, pyrrole, pyrrolidine, 2-pyrroline, 3-pyrroline, imidazole, imidazolidine, 2-imidazoline, 3 -imidazoline, pyrazole, pyrazoline, 2-pyrazoline, 3- pyrazoline, piperidine, piperazine, indole, indoline, IH-indazole, position 2 of a isoindole, or isoindolinone, position 4 of a morpholine, and position 9 of a carbazole, or p-carboline. The terms “halo” and “halogen,” by themselves or as part of another substituent, refer to a fluorine, chlorine, bromine, or iodine atom.
The term “carbonyl,” by itself or as part of another substituent, refers to C(=O) or - C(=O)-, i.e., a carbon atom double-bonded to oxygen and bound to two other groups in the moiety having the carbonyl.
As used herein, the phrase “quaternary ammonium salt” refers to a tertiary amine that has been quaternized with an alkyl substituent (e g., a C1-C4 alkyl such as methyl, ethyl, propyl, or butyl).
The terms “treat,” “treatment,” and “treating” refer to any indicia of success in the treatment or amelioration of an injury, pathology, condition (e.g., cancer), or symptom (e.g., cognitive impairment), including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or making the symptom, injury, pathology, or condition more tolerable to the patient; reduction in the rate of symptom progression; decreasing the frequency or duration of the symptom or condition; or, in some situations, preventing the onset of the symptom. The treatment or amelioration of symptoms can be based on any objective or subjective parameter, including, for example, the result of a physical examination.
The terms “cancer,” “neoplasm,” and “tumor” are used herein to refer to cells which exhibit autonomous, unregulated growth, such that the cells exhibit an aberrant growth phenotype characterized by a significant loss of control over cell proliferation. C6lls of interest for detection, analysis, and/or treatment in the context of the invention include cancer cells (e.g., cancer cells from an individual with cancer), malignant cancer cells, pre-metastatic cancer cells, metastatic cancer cells, and non-metastatic cancer cells. Cancers of virtually every tissue are known. The phrase “cancer burden” refers to the quantum of cancer cells or cancer volume in a subject. Reducing cancer burden accordingly refers to reducing the number of cancer cells or the cancer cell volume in a subject. The term “cancer cell” as used herein refers to any cell that is a cancer cell (e.g., from any of the cancers for which an individual can be treated, e.g., isolated from an individual having cancer) or is derived from a cancer cell, e.g., clone of a cancer cell. For example, a cancer cell can be from an established cancer cell line, can be a primary cell isolated from an individual with cancer, can be a progeny cell from a primary cell isolated from an individual with cancer, and the like. In some embodiments, the term can also refer to a portion of a cancer cell, such as a sub-cellular portion, a cell membrane portion, or a cell lysate of a cancer cell. Many types of cancers are known to those of skill in the art, including solid tumors such as carcinomas, sarcomas, glioblastomas, melanomas, lymphomas, and myelomas, and circulating cancers such as leukemias. As used herein, the term “cancer” includes any form of cancer, including but not limited to, solid tumor cancers (e.g., skin, lung, prostate, breast, gastric, bladder, colon, ovarian, pancreas, kidney, liver, glioblastoma, medulloblastoma, leiomyosarcoma, head & neck squamous cell carcinomas, melanomas, and neuroendocrine) and liquid cancers (e.g., hematological cancers); carcinomas; soft tissue tumors; sarcomas; teratomas; melanomas; leukemias; lymphomas; and brain cancers, including minimal residual disease, and including both primary and metastatic tumors.
The phrases “effective amount” and “therapeutically effective amount” refer to a dose or amount of a substance such as the antibody conjugate of the invention that produces therapeutic effects for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, e.g., Lieberman, Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd, The Art, Science and Technology of Pharmaceutical Compounding (1999); Pickar, Dosage Calculations (1999); Goodman & Gilman ’s The Pharmacological Basis of Therapeutics, 11th Edition (McGraw-Hill, 2006); and Remington: The Science and Practice of Pharmacy, 22nd Edition, (Pharmaceutical Press, London, 2012)). In the case of cancer, the therapeutically effective amount of the antibody conjugate may reduce the number of cancer cells; reduce the tumor size; inhibit (i.e., slow to some extent and preferably stop) cancer cell infiltration into peripheral organs; inhibit (i e , slow to some extent and preferably stop) tumor metastasis; inhibit, to some extent, tumor growth; and/or relieve to some extent one or more of the symptoms associated with the cancer. To the extent the antibody conjugate may prevent growth and/or kill existing cancer cells, it may be cytostatic and/or cytotoxic. For cancer therapy, efficacy can, for example, be measured by assessing the time to disease progression (TTP) and/or determining the response rate (RR)
“Recipient,” “individual,” “subject,” “host,” and “patient” are used interchangeably and refer to any mammalian subject for whom diagnosis, treatment, or therapy is desired (e.g., humans). “Mammal” for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, sheep, goats, pigs, camels, etc. In certain embodiments, the mammal is human.
As used herein, the term “administering” refers to parenteral, intravenous, intraperitoneal, intramuscular, intratumoral, intralesional, intranasal, or subcutaneous administration, oral administration, administration as a suppository, topical contact, intrathecal administration, or the implantation of a slow-release device, e.g., a mini-osmotic pump, to the subject. The terms “about” and “around,” as used herein to modify a numerical value, indicate a close range surrounding the numerical value. Thus, if “X” is the value, “about X” or “around X” indicates a value of from 0 9X to 1.1X, e g., from 0.95X to 1.05X or from 0.99X to 1.01X. A reference to “about X” or “around X” specifically indicates at least the values X, 0.95X, 0.96X, 0.97X, 0.98X, 0.99X, 1.01X, 1.02X, 1.03X, 1.04X, and 1.05X. Accordingly, “about X” and “around X” are intended to teach and provide written description support for a claim limitation of, e.g., “0.98X.”
ANTIBODIES
The antibody conjugate compositions of the invention comprise an antibody. Included in the scope of the embodiments of the invention are functional variants of the antibody constructs or antigen binding domain described herein. The term “functional variant” as used herein refers to an antibody construct having an antigen binding domain with substantial or significant sequence identity or similarity to a parent antibody construct or antigen binding domain, which functional variant retains the biological activity of the antibody construct or antigen binding domain of which it is a variant. Functional variants encompass, for example, those variants of the antibody constructs or antigen binding domain described herein (the parent antibody construct or antigen binding domain) that retain the ability to recognize target cells expressing a tumor-associated antigen or cell surface receptor to a similar extent, the same extent, or to a higher extent, as the parent antibody construct or antigen binding domain.
In reference to the antibody construct or antigen binding domain, the functional variant can, for instance, be at least about 30%, about 50%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99% or more identical in amino acid sequence to the antibody construct or antigen binding domain.
A functional variant can, for example, comprise the amino acid sequence of the parent antibody construct or antigen binding domain with at least one conservative amino acid substitution. Alternatively, or additionally, the functional variants can comprise the amino acid sequence of the parent antibody construct or antigen binding domain with at least one nonconservative amino acid substitution. In this case, it is preferable for the non-conservative amino acid substitution to not interfere with or inhibit the biological activity of the functional variant. The non-conservative amino acid substitution may enhance the biological activity of the functional variant, such that the biological activity of the functional variant is increased as compared to the parent antibody construct or antigen binding domain. A functional variant can, for example, comprise the amino acid sequence of the parent antibody construct or antigen binding with at least one non-canonical amino acid (ncAA) substitution (L Wang, et al, (2001) Science , 292(5516):498-500, CC Liu, PG Schultz, (2010) Annu Rev Biochem. 79:413-44).
The antibodies comprising the antibody conjugate compositions of the invention include Fc engineered variants. In some embodiments, the mutations in the Fc region that result in modulated binding to one or more Fc receptors can include one or more of the following mutations: YTE (M252Y/S254T/T256E), LALAPA (L234A/L235A/P329A), SD (S239D), SDIE (S239D/I332E), SE (S267E), SELF (S267E/L328F), SDIE (S239D/I332E), SDIEAL (S239D/I332E/A330L), GA (G236A), ALIE (A330L/I332E), GASDALIE (G236A/S239D/A330L/I332E), V9 (G237D/P238D/P271G/A330R), and VI 1 (G237D/P238D/H268D/P271G/A330R), and/or one or more mutations at the following amino acids: E345R, E345R/E430G, E345K, E233, G237, P238, H268, P271, L328 and A330. Additional Fc region modifications for modulating Fc receptor binding are described in, for example, US 2016/0145350, US 7416726 and US 5624821, which are hereby incorporated by reference in their entireties herein.
The antibodies comprising the antibody conjugate compositions of the invention include glycan variants, such as afucosylation In some embodiments, the Fc region of the binding agents are modified to have an altered glycosylation pattern of the Fc region compared to the native non-modified Fc region.
In some embodiments, the antibodies in the antibody conjugate compositions contain a modified Fc region, wherein the modification modulates the binding of the Fc region to one or more Fc receptors.
In some embodiments, the antibodies in the antibody conjugate contain one or more modifications (e.g., amino acid insertion, deletion, and/or substitution) in the Fc region that results in modulated binding (e.g., increased binding or decreased binding) to one or more Fc receptors (e.g., FcyRI (CD64), FcyRIIA (CD32A), FcyRIIB (CD32B), FcyRIIIA (CD 16a), and/or FcyRIIIB (CD 16b)) as compared to the native antibody lacking the mutation in the Fc region. In some embodiments, the antibodies in the antibody conjugate compositions contain one or more modifications (e.g., amino acid insertion, deletion, and/or substitution) in the Fc region that reduce the binding of the Fc region of the antibody to FcyRIIB. In some embodiments, the antibodies in the antibody conjugate compositions contain one or more modifications (e.g., amino acid insertion, deletion, and/or substitution) in the Fc region of the antibody that reduce the binding of the antibody to FcyRIIB while maintaining the same binding or having increased binding to FcyRI (CD64), FcyRIIA (CD32A), and/or FcRylllA (CD 16a) as compared to the native antibody lacking the mutation in the Fc region. In some embodiments, the antibodies in the antibody conjugate compositions contain one of more modifications in the Fc region that increase the binding of the Fc region of the antibody to FcyRIIB
In some embodiments, the modulated binding is provided by mutations in the Fc region of the antibody relative to the native Fc region of the antibody. The mutations can be in a CH2 domain, a CH3 domain, or a combination thereof. A “native Fc region” is synonymous with a “wild-type Fc region” and comprises an amino acid sequence that is identical to the amino acid sequence of an Fc region found in nature or identical to the amino acid sequence of the Fc region found in the native antibody (e g , cetuximab) Native sequence human Fc regions include a native sequence human IgGl Fc region, native sequence human IgG2 Fc region, native sequence human IgG3 Fc region, and native sequence human IgG4 Fc region, as well as naturally occurring variants thereof. Native sequence Fc includes the various allotypes of Fes (Jefferis et al., (2009) mAbs, l(4):332-338).
In some embodiments, the Fc region of the antibodies of the antibody conjugate compositions are modified to have an altered glycosylation pattern of the Fc region compared to the native non-modified Fc region. Human immunoglobulin is glycosylated at the Asn297 residue in the Cy2 domain of each heavy chain This N-linked oligosaccharide is composed of a core heptasaccharide, N-acetylglucosamine4Mannose3 (GlcNAc4Man3) Removal of the heptasaccharide with endoglycosidase or PNGase F is known to lead to conformational changes in the antibody Fc region, which can significantly reduce antibody-binding affinity to activating FcyR and lead to decreased effector function The core heptasaccharide is often decorated with galactose, bisecting GlcNAc, fucose, or sialic acid, which differentially impacts Fc binding to activating and inhibitory FcyR. Additionally, it has been demonstrated that a2,6-sialyation enhances anti-inflammatory activity in vivo, while afucosylation leads to improved FcyRIIIa binding and a 10-fold increase in antibody-dependent cellular cytotoxicity and antibodydependent phagocytosis. Specific glycosylation patterns, therefore, can be used to control inflammatory effector functions.
In some embodiments, the modification to alter the glycosylation pattern is a mutation. For example, a substitution at Asn297. In some embodiments, Asn297 is mutated to glutamine (N297Q). Methods for controlling immune response with antibodies that modulate FcyR- regulated signaling are described, for example, in US 7416726, US 2007/0014795 and US 2008/0286819, which are hereby incorporated by reference in their entireties.
In some embodiments, the antibodies of the antibody conjugate compositions are modified to contain an engineered Fab region with a non-naturally occurring glycosylation pattern. For example, hybridomas can be genetically engineered to secrete afucosylated mAb, desialylated mAb or deglycosylated Fc with specific mutations that enable increased FcRyllla binding and effector function. In some embodiments, the antibodies of the antibody conjugate compositions are engineered to be afucosylated or glycosylated.
In some embodiments, the antibodies in the antibody conjugate compositions are a cysteine-engineered antibody which provides for site-specific conjugation of an adjuvant, label, or drug moiety to the antibody through cysteine substitutions at sites where the engineered cysteines are available for conjugation but do not perturb immunoglobulin folding and assembly or alter antigen binding and effector functions (Junutula, et al., (2008) Nature Biotech , 26(8):925-932; Dornan et al (2009) 5/00^ 114(13):2721-2729, US 7521541; US 7723485; US 2012/0121615; WO 2009/052249). A “cysteine engineered antibody” or “cysteine engineered antibody variant” is an antibody in which one or more residues of an antibody are substituted with cysteine residues. Cysteine-engineered antibodies can be conjugated to the isoindolinone- glutarimide (IG) moiety with uniform stoichiometry (e g., up to two IG moieties per antibody in an antibody that has a single engineered cysteine site).
In some embodiments, cysteine-engineered antibodies are used to prepare antibody conjugate compositions with a reactive cysteine thiol residue introduced at a site on the light chain, such as the 149-lysine site (LC K149C), or on the heavy chain such as the 122-serine site (HC S122C), as numbered by Kabat numbering In other embodiments, the cysteine-engineered antibodies have a cysteine residue introduced at the 375-serine site (EU numbering) of the heavy chain (HC S375C). In other embodiments, the cysteine-engineered antibodies have a cysteine residue introduced at the 118-alanine site (EU numbering) of the heavy chain (HC Al 18C). This site is alternatively numbered 121 by Sequential numbering or 114 by Kabat numbering. In other embodiments, the cysteine-engineered antibodies have a cysteine residue introduced in: (i) the light chain at G64C, R142C, K188C, L201C, T129C, S114C, or E105C according to Kabat numbering; (ii) the heavy chain at DIOIC, V184C, T205C, or S122C according to Kabat numbering; or (iii) other cysteine-mutant antibodies, and as described in Bhakta, S. et al, (2013) “Engineering THIOMABs for Site-Specific Conjugation of Thiol -Reactive Linkers”, Laurent Ducry (ed.), Antibody-Drug Conjugates, Methods in Molecular Biology , vol. 1045, pages 189- 203; WO 2011/156328; US 9000130.
In some embodiments, the antibody is a full-length antibody. In certain embodiments, the antibody is an antigen binding fragment. In some embodiments, the antibody is a humanized antibody
In some embodiments, the antibody is an anti-CD40 antibody, an antibody selected from an anti-LRRC15 antibody, an anti-CTSK antibody, an anti-ADAM12 antibody, an anti-ITGAl l antibody, an anti-FAP antibody, an anti-NOX4 antibody, an anti-SGCD antibody, an anti- SYNDIG1 antibody, an anti-CDH11 antibody, an anti-PLPP4 antibody, an anti-SLC24A2 antibody, an anti-PDGFRB antibody, an anti-THYl antibody, an anti-ANTXRl antibody, an anti-GASl antibody, an anti-CALHM5 antibody, an anti-SDCl antibody, an anti-HER2 antibody, an anti-TR0P2 antibody, an anti-MSLN antibody, an anti-Nectin4 antibody, an anti- ASGR1 antibody, and an anti-MUC16 antibody.
In some embodiments, the antibody or Fc fusion protein is selected from: abagovomab, abatacept (also known as ORENCIA®), abciximab (also known as REOPRO®), c7E3 Fab), adalimumab (also known as HUMIRA®), adecatumumab, alemtuzumab (also known as CAMPATH®), MabCampath or Campath- 1H), altumomab, afelimomab, panitumumab, mafenatox, anrukizumab, apolizumab, arcitumomab, aselizumab, atlizumab, atorolimumab, bapineuzumab, basiliximab (also known as SIMULECT®), bavituximab, bectumomab (also known as LYMPHOSCAN®), belimumab (also known as LYMPHO-STAT-B®), bertilimumab, besilesomab, bevacizumab (also known as AVASTIN®), biciromab brail obarbital, bivatuzumab mertansine, campath, canakinumab (also known as ACZ885), cantuzumab mertansine, capromab (also known as PROSTASCINT®), catumaxomab (also known as REMOVAB®), cedelizumab (also known as CIMZIA®), certolizumab pegol, cetuximab (also known as ERBITUX®), clenoliximab, dacetuzumab, dacliximab, daclizumab (also known as ZENAPAX®), datopotamab, denosumab (also known as AMG 162), detumomab, dorlimomab aritox, dorlixizumab, duntumumab, durimulumab, durmulumab, ecromeximab, eculizumab (also known as SOLIRIS®), edobacomab, edrecolomab (also known as Mabl7-1A, PANOREX®), efalizumab (also known as RAPTIVA®), efungumab (also known as MYCOGRAB®), elsilimomab, enapotamab, enfortumab, enlimomab pegol, epitumomab cituxetan, efalizumab, epitumomab, epratuzumab, erlizumab, ertumaxomab (also known as REXOMUN®), etanercept (also known as ENBREL®), etaracizumab (also known as etaratuzumab, VITAXIN®, ABEGRIN®), exbivirumab, fanolesomab (also known as NEUTROSPEC®), faralimomab, felvizumab, fontolizumab (also known as HUZAF®), galiximab, gantenerumab, gavilimomab (also known as ABXCBL®), gemtuzumab ozogamicin (also known as MYLOTARG®), golimumab (also known as CNTO 148), gomiliximab, ibalizumab (also known as TNX-355), ibritumomab tiuxetan (also known as ZEVALIN®), igovomab, imciromab, indusatumab, infliximab (also known as REMICADE®), inolimomab, inotuzumab ozogamicin, ipilimumab (also known as MDX-010, MDX-101), iratumumab, keliximab, labetuzumab, ladiratuzumab, lemalesomab, lebrilizumab, lerdelimumab, lexatumumab (also known as, HGS-ETR2, ETR2-ST01), lexitumumab, libivirumab, lintuzumab, loncastuximab, losatuxizumab, lucatumumab, lumiliximab, mapatumumab (also known as HGSETR1, TRM-1), maslimomab, matuzumab (also known as EMD72000), mepolizumab (also known as BOSATRIA®), metelimumab, milatuzumab, miltuximab, minretumomab, mirvetuximab, mitumomab, morolimumab, motavizwnab (also known as NUMAX®), muromonab (also known as OKT3), nacolomab tafenatox, naptumomab estafenatox, natalizumab (also known as TYSABRI®, ANTEGREN®), nebacumab, nerelimomab, nimotuzumab (also known as THERACIM hR3®, THERA-CIM-hR3®, THERALOC®), nofetumomab merpentan (also known as VERLUMA®), ocrelizumab, odulimomab, ofatumumab, omalizumab (also known as XOLAIR®), oregovomab (also known as OVAREX®), otelixizumab, pagibaximab, palivizumab (also known as SYNAGIS®), panitumumab (also known as ABX-EGF, VECTIBIX®), pascolizumab, pemtumomab (also known as THERAGYN®), pertuzumab (also known as 2C4, OMNITARG®), pexelizumab, pinatuzumab, pintumomab, polatuzumab, priliximab, pritumumab, ranibizumab (also known as LUCENTIS®), raxibacumab, regavirumab, reslizumab, rituximab (also known as RITUXAN®, Mab THERA®), rovelizumab, ruplizumab, Sacituzumab, satumomab, sevirumab, sibrotuzumab, siplizumab (also known as MEDI-507), sontuzumab, stamulumab (also known as MYO-029), sulesomab (also known as LEUKOSCAN®), tacatuzumab tetraxetan, tadocizumab, talizumab, taplitumomab paptox, tefibazumab (also known as AUREXIS®), telimomab aritox, teneliximab, teplizumab, ticilimumab, tocilizumab (also known as ACTEMRA®), tisotumab, toralizumab, tositumomab, trastuzumab (also known as HERCEPTIN®), tremelimumab (also known as CP- 675,206), tucotuzumab celmoleukin, tuvirumab, urtoxazumab, ustekinumab (also known as CNTO 1275), vapaliximab, veltuzumab, vepalimomab, visilizumab (also known as NUVION®), volociximab (also known as M200), votumumab (also known as HUMASPECT®), zalutumumab, zanolimumab (also known as HuMAX-CD4), ziralimumab, zolimomab aritox, daratumumab, elotuxumab, obintunzumab, olaratumab, brentuximab vedotin, afibercept, abatacept, belatacept, afibercept, etanercept, romiplostim, SBT-040 (sequences listed in US 2017/0158772. In some embodiments, the antibody is rituximab.
In an exemplary embodiment, the antibody conjugate composition of the invention comprises an antibody constmct that comprises an antigen binding domain that specifically recognizes and binds HER2. In certain embodiments, the antibody conjugate composition comprises an anti-HER2 antibody. In one embodiment of the invention, an anti-HER2 antibody of an antibody conjugate composition of the invention comprises a humanized anti-HER2 antibody, e.g., huMAb4D5-l, huMAb4D5-2, huMAb4D5-3, huMAb4D5-4, huMAb4D5-5, huMAb4D5-6, huMAb4D5-7 and huMAb4D5-8, as described in Table 3 of US 5821337, which is specifically incorporated by reference herein. Those antibodies contain human framework regions with the complementarity-determining regions of a murine antibody (4D5) that binds to HER2. The humanized antibody huMAb4D5-8 is also referred to as trastuzumab, commercially available under the tradename HERCEPTIN™ (Genentech, Inc.). Trastuzumab (CAS 180288- 69-1, HERCEPTIN®, huMAb4D5-8, rhuMAb HER2, Genentech) is a recombinant DNA- derived, IgGl kappa, monoclonal antibody that is a humanized version of a murine anti-HER2 antibody (4D5) that selectively binds with high affinity in a cell-based assay (Kd = 5 nM) to the extracellular domain of HER2 (US 5677171; US 5821337; US 6054297; US 6165464; US 6339142; US 6407213; US 6639055; US 6719971; US 6800738; US 7074404; Coussens et al (1985) Science 230:1132-9; Slamon et al (1989) Science 244:707-12; Slamon et al (2001) New Engl. J. Med. 344:783-792).
In an embodiment of the invention, the antibody construct or antigen binding domain comprises the CDR regions of trastuzumab. In an embodiment of the invention, the anti-HER2 antibody further comprises the framework regions of the trastuzumab. In an embodiment of the invention, the anti-HER2 antibody further comprises one or both variable regions of trastuzumab.
In another embodiment of the invention, an anti-HER2 antibody of an antibody conjugate composition of the invention comprises a humanized anti-HER2 antibody, e.g., humanized 2C4, as described in US 7862817. An exemplary humanized 2C4 antibody is pertuzumab (CAS Reg. No. 380610-27-5), PERJETA™ (Genentech, Inc.). Pertuzumab is a HER dimerization inhibitor (HDI) and functions to inhibit the ability of HER2 to form active heterodimers or homodimers with other HER receptors (such as EGFR/HER1, HER2, HER3 and HER4). See, for example, Harari and Yarden, Oncogene 19:6102-14 (2000); Yarden and Sliwkowski. Nat Rev Mol Cell Biol 2: 127-37 (2001); Sliwkowski Nat Struct Biol 10:158-9 (2003); Cho et al. Nature 421 :756-60 (2003); and Malik et al. Pro Am Soc Cancer Res 44: 176-7 (2003) PERJETA™ is approved for the treatment of breast cancer
In an embodiment of the invention, the antibody construct or antigen binding domain comprises the CDR regions of pertuzumab In an embodiment of the invention, the anti-HER2 antibody further comprises the framework regions of the pertuzumab. In an embodiment of the invention, the anti-HER2 antibody further comprises one or both variable regions of pertuzumab.
In an exemplary embodiment, the antibody conjugate composition of the invention comprises an antibody construct that comprises an antigen binding domain that specifically recognizes and binds the B-cell receptor CD22. In certain embodiments, the antibody conjugate composition comprises an anti-CD22 antibody In one embodiment of the invention, the anti- CD22 antibody of an antibody conjugate composition is pinatuzumab (CAS Reg. No. 1639820- 81 -7), with complementarity determining regions (CDRs), heavy chain (HC), and light chain (LC) as described in US 8226945 and WO 2007/140371 which are incorporated by reference herein.
ANTIBODY TARGETS
In some embodiments, the antibody of an antibody conjugate composition is capable of binding one or more antigen targets selected from (e.g., specifically binds to a target selected from) 5T4, ABL, ABCF1, ACVR1, ACVR1B, ACVR2, ACVR2B, ACVRL1, AD0RA2A, Aggrecan, AGR2, AICDA, AIF1, AIGI, AKAP1, AKAP2, AMH, AMHR2, ANGPT1, ANGPT2, ANGPTL3, ANGPTL4, ANPEP, APC, APOCI, AR, aromatase, ATX, AX1, Axl, AZGP1 (zinc-a-glycoprotein), B7.1, B7.2, B7-H1, B7-H3, B7-H4, BAD, BAFF, BAG1, BAH, BCR, BCL2, BCL6, BDNF, BLNK, BLR1 (MDRI5), BlyS, BMP1, BMP2, BMP3B (GDFIO), BMP4, BMP6, BMPS, BMPRTA, BMPR1B, BMPR2, BPAG1 (plectin), BRCA1, C19orflO (IL27w), C3, C4A, C5, C5R1, CANT1, CAPRIN-1, CASP1, CASP4, CAV1, CCBP2 (D6/JAB61), CCLI (1-309), CCLI1 (eotaxin), CCL13 (MCP-4), CCL15 (MIP-Id), CCL16 (HCC-4), CCL17 (TARC), CCLI 8 (PARC), CCL19 (MIP-3b), CCL2 (MCP-1), MCAF, CCL20 (MIP-3a), CCL21 (MEP-2), SLC, exodus-2, CCL22(MDC/STC-1), CCL23 (MPIF-I), CCL24 (MPIF-2/eotaxin-2), CCL25 (TECK), CCL26 (eotaxin-3), CCL27 (CTACK/ILC), CCL28, CCL3 (MIP-Ia), CCL4 (MIPIb), CCL5 (RANTES), CCL7 (MCP-3), CCL8 (mcp-2), CCNA1, CCNA2, CCND1, CCNE1, CCNE2, CCR1 (CKR1/HM145), CCR2 (mcp-IRB/RA), CCR3 (CKR3/CMKBR3), CCR4, CCR5 (CMKBR5/ChemR13), CCR6 (CMKBR6/CKR- L3/STRL22/DRY6), CCR7 (CKR7/EBI1), CCR8 (CMKBR8/TERI/CKR-L1), CCR9 (GPR-9- 6), CCRL1 (VSHK1), CCRL2 (L-CCR), CD 164, CD 19, CDIC, CD2, CD20, CD21, CD200, CD22, CD24, CD27, CD28, CD3, CD30, CD33, CD35, CD37, CD38, CD3E, CD3G, CD3Z, CD4, CD38, CD40, CD40L, CD44, CD45RB, CD47, CD52, CD69, CD72, CD74, CD79A, CD79B, CD8, CD80, CD81, CD83, CD86, CD117 (cKit), CD123, CD137, CD152, CD274, CDH1 (Ecadherin), CDH3 (Pcadherin), CDH1O, CDH12, CDH13, CDH18, CDH19, CDH2O, CDH5, CDH7, CDH8, CDH9, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK9, CDKN1A (p21 Wap 1 /Cipl), CDKN1B (p27Kipl), CDKN1C, CDKN2A (pl6INK4a), CDKN2B, CDKN2C, CDKN3, CEACAM5, CEACAM6, CEBPB, CERI, CHGA, CHGB, Chitinase, CHST1O, CKLFSF2, CKLFSF3, CKLFSF4, CKLFSF5, CKLFSF6, CKLFSF7, CKLFSF8, CLDN3, CLDN7 (claudin-7), CLDN18.2 (claudin 18.2), CLL-1, CLN3, CLU (clusterin), cMet, CMKLR1, CMKOR1 (RDC1), CNR1, COL18A1, COLIAI, COL4A3, COL6A1, CR2, Cripto, CRP, CSF1 (M-CSF), CSF2 (GM-CSF), CSF3 (GCSF), CTL8, CTNNB1 (b-catenin), CTSB (cathepsin B), CX3CL1 (SCYD1), CX3CR1 (V28), CXCL1 (GRO1), CXCL1O (IP-IO), CXCLI1 (l-TAC/IP-9), CXCL12 (SDF1), CXCL13, CXCL14, CXCL16, CXCL2 (GRO2), CXCL3 (GR03), CXCL5 (ENA-78/LIX), CXCL6 (GCP-2), CXCL9 (MIG), CXCR3 (GPR9/CKR-L2), CXCR4, CXCR6 (TYMSTR/STRL33/Bonzo), CYB5, CYC1 , CYSLTR1, DAB2IP, DES, DKFZp451J0118, DNCL1, DPP4, E2F1, Engel, Edge, Fennel, EFNA3, EFNB2, EGF, EGFR, ELAC2, ENG, Enola, ENO2, ENO3, EPHA1, EPHA2, EPHA3, EPHA4, EPHA5, EPHA6, EPHA7, EPHA8, EPHA9, EPRA10, EPHB1, EPHB2, EPHB3, EPHB4, EPHB5, EPHB6, EPHRIN-A1, EPHRIN-A2, EPHRINA3, EPHRIN-A4, EPHRIN-A5, EPHRIN-A6, EPHRIN-B1, EPHRIN-B2, EPHRIN-B3, EPHB4, EPG, ERBB2 (Her-2), EREG, ERK8, Estrogen receptor, Earl, ESR2, F3 (TF), FADD, farnesyltransferase, FasL, FAP, FASNf, FCER1A, FCER2, FCGR3A, FGF, FGF1 (aFGF), FGF10, FGF11, FGF12, FGF12B, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2 (bFGF). FGF20, FGF21, FGF22, FGF23, FGF3 (int-2), FGF4 (HST), FGF5, FGF6 (HST-2), FGF7 (KGF), FGF8, FGF9, FGFR3, FIGF (VEGFD), FILI (EPSILON), FBL1 (ZETA), FLJ12584, FLJ25530, FLRT1 (fibronectin), FLT1, FLT-3, FOLR1 (folate receptor alpha), FOS, FOSL1 (FRA-1), FY (DARC), GABRP (GABAa), GAGEB1, GAGECI, GALNAC4S-6ST, GATA3, GD2, GDF5, GFI1, GGT1, GM-CSF, GNAS1, GNRH1, GPC-1, GPR2 (CCR10), GPR31, GPR44, GPR81 (FKSG80), GRCC1 O (CIO), GRP, GSN (Gelsolin), GSTP1, HAVCR2, HDAC, HDAC4, HDAC5, HDAC7A, HDAC9, Hedgehog, HGF, HIF1A, FHP1, histamine and histamine receptors, HLA-A, HLA- DRA, HLA-E, HM74, HMOXI, HSP90, HUMCYT2A, ICEBERG, ICOSL, ID2, IFN-a, IFNA1, IFNA2, IFNA4, IFNA5, EFNA6, BFNA7, IFNB1, IFNgamma, IFNW1, IGBP1, IGF1, IGFIR, IGF2, IGFBP2, IGFBP3, IGFBP6, DL-1, ILIO, ILIORA, ILIORB, IL-1, IL1R1 (CD121a), IL1R2 (CD121b), IL-IRA, IL-2, IL2RA (CD25), IL2RB (CD122), IL2RG (CD132), IL-4, IL-4R (CD123), IL-5, IL5RA (CD125), IL3RB (CD131), IL-6, IL6RA, (CD126), IR6RB (CD130), IL- 7, IL7RA (CD127), IL-8, CXCR1 (IL8RA), CXCR2, (IL8RB/CD128), IL-9, IL9R (CD129), ILIO, ILIORA (CD210), ILIORB (CDW210B), IL-11, IL 1 IRA, IL- 12, IL-12A, IL-12B, IL- 12RB1, IL-12RB2, IL-13, IL13RA1, IL13RA2, IL14, IL15, IL15RA, IL16, IL17, IL17A, IL17B, IL17C, IL17R, IL18, IL18BP, IL18R1, IL18RAP, IL19, ILIA, ILIB, ILIF10, ILIF5, IL1F6, ILIF7, IL1F8, DL1F9, ILIHYI, ILIR1, ILIR2, ILIRAP, ILIRAPLI, ILIRAPL2, ILIRL1, IL1RL2, ILIRN, IL2, IL20, IL20RA, IL21R, IL22, IL22R, IL22RA2, IL23, DL24, IL25, IL26, IL27, IL28A, IL28B, IL29, IL2RA, IL2RB, IL2RG, IL3, IL30, IL3RA, IL4, IL4, IL6ST (glycoprotein 130), ILK, INHA, INHBA, INSL3, INSL4, IRAKI, IRAK2, ITGA1, ITGA2, ITGA3, ITGA6 (.alpha.6 integrin), ITGAV, ITGB3, ITGB4 ( beta.4 integrin), ITGB6 (beta.6 integrin), JAG1, JAK1, JAK3, JTB, JUN, K6HF, KAI1, KDR, KITLG, KLF5 (GC Box BP), KLF6, KLK10, KLK12, KLK13, KLK14, KLK15, KLK3, KLK4, KLK5, KLK6, KLK9, KRT1, KRT19 (Keratin 19), KRT2A, KRTHB6 (hair-specific type II keratin), LAMA5, LEP (leptin), Lingo-p75, Lingo-Troy, LIV-1, LPS, LRRC15, LTA (TNF-b)), LTB, LTB4R (GPR16), LTB4R2, LTBR, MACMARCKS, MAG or OMgp, MAP2K7 (c-Jun), MCP-1, MDK, MIB I, midkine, MIF, MISRII, MJP-2, MK, MKI67 (Ki-67), MMP2, MMP9, MS4A1, MSMB, MT3 (metallothionectin-UI), mTOR, MTSS1, MUC1 (mucin), MUC16, MYC, MYD88, NCK2, neurocan, Nectin-4, NFKBI, NFKB2, NGFB (NGF), NGFR, NgR-Lingo, NgRNogo66, (Nogo), NgR-p75, NgR-Troy, NMEI (NM23A), NOTCH, NOTCH1, N0X5, NPPB, NR0B1, NR0B2, NRID1, NR1D2, NR1H2, NR1H3, NR1H4, NR112, NR113, NR2C1 , NR2C2, NR2E1, NR2E3, NR2F1, NR2F2, NR2F6, NR3C1 , NR3C2, NR4A1, NR4A2, NR4A3, NR5A1, NR5A2, NR6A1, NRP1, NRP2, NT5E, NTN4, ODZI, OPRDI, P2RX7, PAP, PARTI, PATE, PAWR, PCA3, PCDGF, PCNA, PDGFA, PDGFB, PDGFRA, PDGFRB, PECAMI, peg-asparaginase, PF4 (CXCL4), PGF, PGR, phosphacan, PIAS2, PI3 Kinase, PIK3CG, PLAU (uPA), PLG, PLXDCI, PKC, PKC-beta, PPBP (CXCL7), PPID, PR1, PRKCQ, PRKD1, PRL, PROC, PROK2, PSAP, PSCA, PSMA, PTAFR, PTEN, PTGS2 (COX-2), PEST, RAC2 (P21Rac2), RANK, RANK ligand, RARB, RGS1, RGS13, RGS3, RNFI1O (ZNF144), Ron, ROBO2, RXR, S100A2, SCGB 1D2 (lipophilin B), SCGB2A1 (mammaglobin 2), SCGB2A2 (mammaglobin 1), SCYE1 (endothelial Monocyte-activating cytokine), SDF2, SERPENA1, SERPINA3, SERPINB5 (maspin), SERPINEI (PALI), SERPINFI, SHIP-1, SHIP-2, SHB1, SHB2, SHBG, SfcAZ, SLC2A2, SLC33A1, SLC43A1, SLIT2, SPP1, SPRR1B (Sprl), ST6GAL1, STAB1, STATE, STEAP, STEAP2, TB4R2, TBX21, TCP1O, TDGF1, TEK, TGFA, TGFB1, TGFB1I1, TGFB2, TGFB3, TGFBI, TGEBR1, TGFBR2, TGFBR3, THIL, THBS1 (thrombospondin- 1), THBS2, THBS4, THPO, TIE (Tie-1), TIMP3, tissue factor, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, TLR11, TNF, TNF-a, TNFAIP2 (B94), TNFAIP3, TNFRSF11A, TNFRSF1A, TNFRSF1B, TNFRSF21, TNFRSF5, TNFRSF6 (Fas), TNFRSF7, TNFRSF8, TNFRSF9, TNFSF1O (TRAIL), TNFSF11 (TRANCE), TNFSF12 (APO3L), TNFSF13 (April), TNFSF13B, TNSF14 (HVEM-L), TNFRSF14 (HVEM), TNFSF15 (VEGI), TNFSF18, TNFSF4 (0X40 ligand), TNFSF5 (CD40 ligand). TNFSF6 (FasL), TNFSF7 (CD27 ligand), TNFSF8 (CD30 ligand), TNFSF9 (4-1BB ligand), TOLLLP, Toll-like receptors, TOP2A (topoisomerase lia), TP53, TPM1, TPM2, TRADD, TRAF1, TRAF2, TRAF3, TRAF4, TRAF5, TRAF6, TRKA, TREM1, TREM2, TROP2, TRPC6, TSLP, TWEAK, Tyrosinase, uPAR, VEGF, VEGFB, VEGFC, versican, VHL C5, VLA-4, Wnt-1, XCL1 (tymphotactin), XCL2 (SCM-Ib), XCRI (GPR5/CCXCR1), YYI, ZFPM2, CLEC4C (BDCA-2, DLEC, CD303, CLECSF7), CLEC4D (MCL, CLECSF8), CLEC4E (Mincle), CLEC6A (Dectin-2). CLEC5A (MDL-1, CLECSF5), CLEC1 B (CLEC-2), CLEC9A (DNGR-1), CLEC7A (Dectin-1), PDGFRa, SLAMF7, GP6 (GPVI), LILRA1 (CD85I), LILRA2 (CD85H, ILT1), LILRA4 (CD85G, ILT7), LILRA5 (CD85F, ILT11), LILRA6 (CD85b, ILT8), NCR1 (CD335, LY94, NKp46), NCR3 (CD335, LY94, NKp46), NCR3 (CD337, NKp30), OSCAR, TARM1, CD300C, CD300E, CD300LB (CD300B), CD300LD (CD300D), KIR2DL4 (CD158D), KIR2DS, KLRC2 (CD159C, NKG2C), KLRK1 (CD314, NKG2D), NCR2 (CD336, NKp44), PILRB, SIGLEC1 (CD169, SN), SIGLEC14, SIGLEC15 (CD33L3), SIGLEC16, SIRPB1 (CD172B), TREM1 (CD354), Tissue Factor (CD142), TREM2, and KLRFl (NKp80).
In some embodiments, the antibody binds to an antigen selected from CDH1, CD19, CD20, CD29, CD30, CD38, CD40, CD47, EpCAM, MUC1 , MUC16, EGFR, HER2, SLAMF7, and gp75.
In some embodiments, the antibody of an antibody conjugate composition of the invention is capable of binding to one or more tumor-associated antigens (TAA), cell-surface receptors, and immune-specific antigens to confer specificity to the targeting of the conjugate and enable safe and systemic delivery of an active drug moiety. C6rtain tumor-associated antigens are known in the art, and can be prepared for use in generating antibodies using methods and information which are well known in the art. In attempts to discover effective cellular targets for cancer diagnosis and therapy, researchers have sought to identify transmembrane or otherwise tumor-associated polypeptides that are specifically expressed on the surface of one or more particular type(s) of cancer cell as compared to on one or more normal non-cancerous cell(s). Often, such tumor-associated polypeptides are more abundantly expressed on the surface of the cancer cells as compared to on the surface of the non-cancerous cells. The identification of such tumor-associated cell surface antigen polypeptides allows more specificity in targeting cancer cells for destruction via antibody -based therapies.
Examples of TAAs include, but are not limited to, those listed below including (l)-(54). For convenience, information relating to these antigens, all of which are known in the art, is listed below and includes names, alternative names, Genbank accession numbers and primary reference(s), following nucleic acid and protein sequence identification conventions of the National C6nter for Biotechnology Information (NCBI). Nucleic acid and protein sequences corresponding to TAAs listed below including (l)-(54) are available in public databases such as GenBank. TAAs targeted by antibodies include all amino acid sequence variants and isoforms possessing at least about 70%, 80%, 85%, 90%, or 95% sequence identity relative to the sequences identified in the cited references, and/or which exhibit substantially the same biological properties or characteristics as a TAA having a sequence found in the cited references. For example, a TAA having a variant sequence generally is able to bind specifically to an antibody that binds specifically to the TAA with the corresponding sequence listed. The sequences and disclosure in the reference specifically recited herein are expressly incorporated by reference. The disclosure in the references specifically recited herein are expressly incorporated by reference.
(1) BMPR1B (bone morphogenetic protein receptor-type IB, Genbank accession no. NM_001203) ten Dijke, P., et al. Science 264 (5155): 101-104 (1994), Oncogene 14 (11): 1377- 1382 (1997)); W02004063362 (Claim 2); W02003042661 (Claim 12); US2003134790-Al (Page 38-39); W02002102235 (Claim 13, Page 296), W02003055443 (Page 91-92), WO200299122 (Example 2; Page 528-530); W02003029421 (Claim 6); W02003024392 (Claim 2; Fig 112); WO200298358 (Claim 1; Page 183); W0200254940 (Page 100-101); WO200259377(Page 349-350), W0200230268 (Claim 27; Page 376); W0200148204 (Example; Fig 4) NP 001194 bone morphogenetic protein receptor, type IB /pid=NP_001194. 1 - Cross-references: MIM:603248; NP_001194 1; AY065994.
(2) E16 (LAT1, SLC7A5, Genbank accession no. NM_003486) Biochem. Biophys. Res. Commun. 255 (2), 283-288 (1999), Nature 395 (6699):288-291 (1998), Gaugitsch, H.W., et al. (1992) J. Biol. Chem. 267 (16): 11267-11273); W02004048938 (Example 2); W02004032842 (Example IV); W02003042661 (Claim 12); W02003016475 (Claim 1); WO200278524 (Example 2); W0200299074 (Claim 19; Page 127-129); WO200286443 (Claim 27; Pages 222, 393); W02003003906 (Claim 10; Page 293); WO200264798 (Claim 33; Page 93-95); W0200014228 (Claim 5; Page 133-136); US2003224454 (Fig 3); W02003025138 (Claim 12; Page 150); NP_003477 solute carrier family 7 (cationic amino acid transporter, y+ system), member 5 /pid=NP_003477.3 - Homo sapiens Cross-references: MZM:600182; NP_003477.3; NM_015923 ; NM_003486_l .
(3) STEAP1 (six transmembrane epithelial antigen of prostate, Genbank accession no. NM 012449) Cancer Res. 61 (15), 5857-5860 (2001), Hubert, R.S., et al. (1999) Proc. Natl. Acad. Sci. U.S.A. 96 (25): 14523-14528); W02004065577 (Claim 6); W02004027049 (Fig IL); EP1394274 (Example 11); W02004016225 (Claim 2); W02003042661 (Claim 12); US2003157089 (Example 5); US2003185830 (Example 5); US2003064397 (Fig 2); WO200289747 (Example 5; Page 618-619); W02003022995 (Example 9; Fig 13A, Example 53; Page 173, Example 2; Fig 2A); NP_036581 six transmembrane epithelial antigen of the prostate Cross-references: MIM:604415; NP 036581.1; NM_012449_l.
(4) 0772P (CA125, MUC16, Genbank accession no. AF361486) J. Biol. Chem. 276 (29):27371-27375 (2001)); W02004045553 (Claim 14); WO200292836 (Claim 6; Fig 12); WO200283866 (Claim 15; Page 116-121); US2003124140 (Example 16); US 798959. Cross- references: GL34501467; AAK74120.3; AF361486J.
(5) MPF (MPF, MSLN, SMR, megakaryocyte potentiating factor, mesothelin, Genbank accession no. NM_005823) Yamaguchi, N., et al. Biol. Chem. 269 (2), 805-808 (1994), Proc. Natl. Acad. Sci. U.S.A. 96 (20): 11531-11536 (1999), Proc. Natl. Acad. Sei. U.S.A. 93 (1): 136- 140 (1996), J. Biol. Chem. 270 (37)21984-21990 (1995)); W02003101283 (Claim 14); (W02002102235 (Claim 13; Page 287-288); W02002101075 (Claim 4; Page 308-309); WO200271928 (Page 320-321); WO9410312 (Page 52-57); Cross-references: MIM:601051; NP_005814.2; NM_005823_l.
(6) Napi3b (NAPI-3B, NPTIIb, SLC34A2, solute carrier family 34 (sodium phosphate), member 2, type II sodium-dependent phosphate transporter 3b, Genbank accession no. NM_006424) J. Biol. Chem. 277 (22): 19665-19672 (2002), Genomics 62 (2)281-284 (1999), Field, J A , et al (1999) Biochem. Biophys. Res. Commun 258 (3):578-582); W02004022778 (Claim 2); EP1394274 (Example 11); W02002102235 (Claim 13; Page 326); EP875569 (Claim 1; Page 17-19); W0200157188 (Claim 20; Page 329); W02004032842 (Example IV); W0200175177 (Claim 24; Page 139-140); Cross-references: MIM:604217; NP_006415.1; NM_006424_l.
(7) Serna 5b (FLJ10372, KIAA1445, Mm.42015, SEMA5B, SEMAG, Semaphorin 5b Hlog, sema domain, seven thrombospondin repeats (type 1 and type 1 -like), transmembrane domain (TM) and short cytoplasmic domain, (30emaphoring) 5B, Genbank accession no AB040878) Nagase T., et al. (2000) DNA Res. 7 (2): 143-150); W02004000997 (Claim 1); W02003003984 (Claim 1); W0200206339 (Claim 1; Page 50); W0200188133 (Claim 1; Page 41-43, 48-58); W02003054152 (Claim 20); W02003101400 (Claim 11); Accession: Q9P283; EMBL; AB040878; BAA95969.1. Genew; HGNC: 10737.
(8) PSCA hlg (2700050C12Rik, C530008016Rik, RIKEN cDNA 2700050C12, RIKEN cDNA 2700050C12 gene, Genbank accession no. AY358628); Ross et al. (2002) Cancer Res. 62:2546-2553; US2003129192 (Claim 2); US2004044180 (Claim 12); US2004044179 (Claim 11); US2003096961 (Claim 11); US2003232056 (Example 5); W02003105758 (Claim 12); US2003206918 (Example 5); EP1347046 (Claim 1); W02003025148 (Claim 20); Cross- references: GI:37182378; AAQ88991.1; AY358628 1.
(9) ETBR (Endothelin type B receptor, Genbank accession no. AY275463), Nakamuta M., et al. Biochem. Biophys. Res. Commun. 177, 34-39, 1991; Ogawa Y., et al. Biochem. Biophys. Res. Commun. 178, 248-255, 1991; Arai H., et al. Jpn. Circ. J. 56, 1303-1307, 1992; Arai H., et al. J. Biol. Chem. 268, 3463-3470, 1993; Sakamoto A., Yanagisawa M., et al. Biochem. Biophys. Res. Commun. 178, 656-663, 1991; Elshourbagy N.A., et al. J. Biol. Chem. 268, 3873-3879, 1993; Haendler B., et al. J. Cardiovasc. Pharmacol. 20, sl-S4, 1992; Tsutsumi M., et al. Gene 228, 43-49, 1999; Strausberg R.L., et al. Proc. Natl. Acad. Sci. U.S.A 99, 16899- 16903, 2002; Bourgeois C., et al. J. Clin. Endocrinol. Metab. 82, 3116-3123, 1997; Okamoto Y , et al. Biol. Chem. 272, 21589-21596, 1997; Verheij J.B., et al. Am. J. Med. Genet. 108, 223-225, 2002; Hofstra R.M.W., et al. Eur. J. Hum. Genet 5, 180-185, 1997; Puffenberger E G., et al. Cell 79, 1257-1266, 1994; Attie T., et al., Hum. Mol. Genet. 4, 2407-2409, 1995; Auricchio A., et al. Hum. Mol. Genet. 5:351-354, 1996, Amiel J., et al. Hum. Mol. Genet. 5, 355-357, 1996; Hofstra R.M.W., et al. Nat. Genet. 12, 445-447, 1996; Svensson P.J., et al. Hum. Genet. 103, 145-148, 1998; Fuchs S., et al. Mol. Med. 7, 115-124, 2001; Pingault V., et al. (2002) Hum. Genet. I l l, 198-206; W02004045516 (Claim 1), W02004048938 (Example 2);
W02004040000 (Claim 151); W02003087768 (Claim 1); W02003016475 (Claim 1); W02003016475 (Claim 1); W0200261087 (Fig 1); W02003016494 (Fig 6); W02003025138 (Claim 12; Page 144), W0200198351 (Claim 1; Page 124-125); EP522868 (Claim 8; Fig 2); W0200177172 (Claim 1; Page 297-299); US2003109676; US6518404 (Fig 3); US5773223 (Claim la; Col 31-34); W02004001004.
(10) MSG783 (RNF124, hypothetical protein FLJ20315, Genbank accession no. NM_017763); W02003104275 (Claim 1); W02004046342 (Example 2); W02003042661 (Claim 12); W02003083074 (Claim 14; Page 61); WG2003018621 (Claim 1); W02003024392 (Claim 2; Fig 93); WO200166689 (Example 6); Cross-references: LocusID:54894; NP_060233.2; NM_017763_l.
(11) STEAP2 (HGNC_8639, IPCA-1, PCANAP1, STAMP1, STEAP2, STMP, prostate cancer associated gene 1, prostate cancer associated protein 1, six transmembrane epithelial antigen of prostate 2, six transmembrane prostate protein, Genbank accession no. AF455138) Lab. Invest. 82 (11): 1573-1582 (2002)); W02003087306; US2003064397 (Claim 1; Fig 1); WO200272596 (Claim 13; Page 54-55); WO200172962 (Claim 1; Fig 4B); W02003104270 (Claim 11); W02003104270 (Claim 16); US2004005598 (Claim 22); W02003042661 (Claim 12); US2003060612 (Claim 12; Fig 10); WG200226822 (Claim 23; Fig 2); WO200216429 (Claim 12; Fig 10); Cross-references: GL22655488; AAN04080.1; AF455138_1.
(12) TrpM4 (BR22450, FLJ20041, TRPM4, TRPM4B, transient receptor potential cation channel, subfamily M, member 4, Genbank accession no. NM_017636) Xu, X.Z., et al Proc. Natl. Acad. Set. U.S.A. 98 (19): 10692-10697 (2001), Cell 109 (3):397-407 (2002), J. Biol. Chem. 278 (33)30813-30820 (2003)); US2003143557 (Claim 4); W0200040614 (Claim 14; Page 100-103); W0200210382 (Claim 1; Fig 9A); W02003042661 (Claim 12); W0200230268 (Claim 27; Page 391); US2003219806 (Claim 4); WO200162794 (Claim 14; Fig 1A-D); Cross- references: MIM:606936; NP_060106.2; NM_017636_l.
(13) CRIPTO (CR, CR1, CRGF, CRIPTO, TDGF1, teratocarcinoma-derived growth factor, Genbank accession no. NP_003203 or NM_003212) Ciccodicola, A., et al. EMBO J. 8 (7): 1987-1991 (1989), Am. J. Hum. Genet. 49 (3):555-565 (1991)); US2003224411 (Claim 1); W02003083041 (Example 1); W02003034984 (Claim 12); W0200288170 (Claim 2; Page 52- 53); W02003024392 (Claim 2; Fig 58); W0200216413 (Claim 1; Page 94-95, 105); W0200222808 (Claim 2; Fig 1); US5854399 (Example 2; Col 17-18); US5792616 (Fig 2); Cross-references: MIM: 187395; NP_003203.1, NM_003212_l.
(14) CD21 (CR2 (Complement receptor 2) or C3DR (C3d/Epstein Barr virus receptor) or Hs.73792 Genbank accession no. M26004) Fujisaku et al. (1989) J. Biol. Chem. 264 (4):2118- 2125); Weis J. J., et al. J. Exp. Med. 167, 1047-1066, 1988; Moore M , et al. Proc. Natl. Acad. Sci. U.S.A. 84, 9194-9198, 1987; Barel M., et al. Mol. Immunol. 35, 1025-1031, 1998; Weis J.J., et al. Proc. Natl. Acad. Sci. U.S.A. 83, 5639-5643, 1986; Sinha S.K., et al. (1993) J. Immunol. 150, 5311-5320; W02004045520 (Example 4); US2004005538 (Example 1); W02003062401 (Claim 9); W02004045520 (Example 4); WO9102536 (Fig 9. 1-9.9); W02004020595 (Claim 1); Accession: P20023; Q13866; Q14212; EMBL; M26004; AAA35786.1.
(15) CD79b (CD79B, CD790, Igb (immunoglobulin-associated beta), B29, Genbank accession no. NM_000626 or 11038674) Proc. Natl. Acad. Sci. U.S.A. (2003) 100 (7):4126- 4131, Blood (2002) 100 (9):3068-3076, Muller et al. (1992) Eur. J. Immunol. 22 (6): 1621-1625); W02004016225 (claim 2, Fig 140); W02003087768, US2004101874 (claim 1, page 102); W02003062401 (claim 9); WO200278524 (Example 2); US2002150573 (claim 5, page 15); US5644033; W02003048202 (claim 1, pages 306 and 309); WO 99/558658, US6534482 (claim 13, Fig 17A/B); W0200055351 (claim 11, pages 1145-1146); Cross-references: MIM:147245; NP_000617.1; NM_000626_l .
(16) FcRH2 (IFGP4, IRTA4, SPAP1A (SH2 domain containing phosphatase anchor protein la), SPAP1B, SPAP1C, Genbank accession no. NM_030764, AY358130) Genome Res. 13 (10):2265-2270 (2003), Immunogenetics 54 (2):87-95 (2002), Blood 99 (8):2662-2669 (2002), Proc. Natl. Acad. Sci. USA. 98 (17):9772-9777 (2001), Xu, M.J., et al. (2001) Biochem. Biophys. Res. Commun. 280 (3):768-775; W02004016225 (Claim 2); W02003077836; W0200138490 (Claim 5; Fig 18D-1-18D-2); W02003097803 (Claim 12); W02003089624 (Claim 25); Cross-references: MDM606509; NP_110391.2; NM_030764_l.
(17) HER2 (ErbB2, Genbank accession no. Ml 1730) Coussens L., et al. Science (1985) 230(4730):l 132-1139); Yamamoto T., et al. Nature 319, 230-234, 1986; Semba K., et al. Proc. Natl. Acad. Sci. U.S.A. 82, 6497-6501, 1985; Swiercz J.M., et al. J. Cell Biol. 165, 869-880, 2004; Kuhns J.J., et al. J. Biol. Chem. 274, 36422-36427, 1999; Cho H.-S., et al. Nature 421, 756-760, 2003; Ehsani A., et al. (1993) Genomics 15, 426-429; W02004048938 (Example 2); W02004027049 (Fig II); W02004009622; W02003081210; W02003089904 (Claim 9); W02003016475 (Claim 1); US2003118592; W02003008537 (Claim 1); W02003055439 (Claim 29; Fig 1A-B); W02003025228 (Claim 37; Fig 5C); WO200222636 (Example 13, Page 95-107); W0200212341 (Claim 68; Fig 7); WO200213847 (Page 71-74); W0200214503 (Page 114-117); WO200153463 (Claim 2; Page 41-45); W0200141787 (Page 15); W0200044899 (Claim 52; Fig 7); W0200020579 (Claim 3; Fig 2); US5869445 (Claim 3; Col 31-38); WO9630514 (Claim 2; Page 56-61); EP1439393 (Claim 7); W02004043361 (Claim 7); W02004022709; W0200100244 (Example 3; Fig 4); Accession: P04626; EMBL; Ml 1767; AAA35808.1. EMBL; Ml 1761; AAA35808.1.
(18) NCA (CEACAM6, Genbank accession no. Ml 8728); Barnet T ., et al. Genomics 3, 59-66, 1988; Tawaragi Y., et al. Biochem. Biophys. Res. Commun. 150, 89-96, 1988; Strausberg R.L., et al. Proc. Natl. Acad. Sci. U.S.A. 99:16899-16903, 2002; W02004063709; EP1439393 (Claim 7), W02004044178 (Example 4), W02004031238, W02003042661 (Claim 12); WO200278524 (Example 2); WO200286443 (Claim 27; Page 427); W0200260317 (Claim 2); Accession: P40199; Q14920; EMBL; M29541; AAA59915.1. EMBL; M18728.
(19) MDP (DPEP1, Genbank accession no. BC017023) Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899-16903 (2002)); W02003016475 (Claim 1); WO200264798 (Claim 33; Page 85-87); JP05003790 (Fig 6-8); WO9946284 (Fig 9); Cross-references: MIM:179780; AAH17023.1; BC017023 1.
(20) IL20Roc (IL20Ra, ZCYTOR7, Genbank accession no AF184971); Clark H F , et al. Genome Res. 13, 2265-2270, 2003; Mungall A.J., et al. Nature 425, 805-811, 2003; Blumberg H., et al. Cell 104, 9-19, 2001; Dumoutier L., et al. J. Immunol. 167, 3545-3549, 2001; Parrish- Novak J., et al. J. Biol. Chem. 277 , 47517-47523, 2002; Pletnev S., et al. (2003) Biochemistry 42: 12617-12624; Sheikh F., et al. (2004) 7 Immunol. 172, 2006-2010; EP1394274 (Example 11); US2004005320 (Example 5); W02003029262 (Page 74-75); W02003002717 (Claim 2; Page 63); WO200222153 (Page 45-47); US2002042366 (Page 20-21); W0200146261 (Page 57- 59); WO200146232 (Page 63-65); WO9837193 (Claim 1; Page 55-59); Accession: Q9UHF4; Q6UWA9; Q96SH8; EMBL; AF184971; AAF01320.1.
(21) Brevican (BCAN, BEHAB, Genbank accession no. AF229053) Gary S.C , et al. Gene 256, 139-147, 2000; Clark H.F., et al. Genome Res. 13, 2265-2270, 2003; Strausberg R.L., et al. Proc. Natl. Acad. Sci. U.S.A. 99, 16899-16903, 2002; US2003186372 (Claim 11); US2003186373 (Claim 11); US2003119131 (Claim 1; Fig 52); US2003119122 (Claim 1; Fig 52); US2003119126 (Claim 1); US2003119121 (Claim 1; Fig 52); US2003119129 (Claim 1); US2003119130 (Claim 1); US2003119128 (Claim 1; Fig 52); US2003119125 (Claim 1); W02003016475 (Claim 1); W0200202634 (Claim 1).
(22) EphB2R (DRT, ERK, Hek5, EPHT3, Tyro5, Genbank accession no. NM_004442) Chan, J. and Wat, V.M., Oncogene 6 (6), 1057-1061 (1991) Oncogene 10 (5):897-905 (1995), Annu. Rev. Neurosci. 21:309-345 (1998), Int. Rev. Cytol. 196: 177-244 (2000)); W02003042661 (Claim 12); W0200053216 (Claim 1; Page 41); W02004065576 (Claim 1); W02004020583 (Claim 9); W02003004529 (Page 128-132); W0200053216 (Claim 1; Page 42); Cross- references: MIM:600997; NP_004433.2; NM_004442_l.
(23) ASLG659 (B7h, Genbank accession no. AX092328) US20040101899 (Claim 2); W02003104399 (Claim 11); W02004000221 (Fig 3); US2003165504 (Claim 1);
US2003124140 (Example 2); US2003065143 (Fig 60); W02002102235 (Claim 13; Page 299); US2003091580 (Example 2); W0200210187 (Claim 6; Fig 10); W0200194641 (Claim 12, Fig 7b); W0200202624 (Claim 13; Fig 1A-1B); US2002034749 (Claim 54; Page 45-46);
W0200206317 (Example 2; Page 320-321, Claim 34; Page 321-322); WO200271928 (Page 468-469); W0200202587 (Example 1; Fig 1); W0200140269 (Example 3; Pages 190-192); W0200036107 (Example 2; Page 205-207); W02004053079 (Claim 12); W02003004989 (Claim 1); WO200271928 (Page 233-234, 452-453); WO 0116318.
(24) PSCA (Prostate stem cell antigen precursor, Genbank accession no. AJ297436) Reiter R.E., et al. Proc. Natl. Acad. Sci. U.S.A. 95, 1735-1740, 1998; Gu Z ., et al. Oncogene 19, 1288-1296, 2000; Biochem. Biophys. Res. Commun. (2000) 275(3):783-788; W02004022709; EP1394274 (Example 11); US2004018553 (Claim 17); W02003008537 (Claim 1); WO200281646 (Claim 1; Page 164); WO 2003003906 (Claim 10; Page 288); WO 200140309 (Example 1; Fig 17); US 2001055751 (Example 1; Fig lb); WO 200032752 (Claim 18; Fig 1); WO 1998/51805 (Claim 17; Page 97); WO 1998/51824 (Claim 10; Page 94); WO 1998/40403 (Claim 2; Fig IB); Accession: 043653; EMBL; AF043498; AAC39607.1.
(25) GEDA (Genbank accession No. AY260763); AAP14954 lipoma HMGIC fusionpartner-like protein /pid=AAP 14954.1 - Homo sapiens Species: Homo sapiens (human) W02003054152 (Claim 20); W02003000842 (Claim 1); W02003023013 (Example 3, Claim 20); US2003194704 (Claim 45); Cross-references: GL30102449; AAP14954.1; AY260763 1.
(26) BAFF-R (B cell -activating factor receptor, BlyS receptor 3, BR3, Genbank accession No. AF116456); BAFF receptor /pi d=NP_443177.1 - Homo sapiens Thompson, J.S., et al. Science 293 (5537), 2108-2111 (2001); W02004058309; W02004011611;
W02003045422 (Example; Page 32-33); W02003014294 (Claim 35; Fig 6B); W02003035846 (Claim 70; Page 615-616); WO200294852 (Col 136-137); WO200238766 (Claim 3; Page 133); W0200224909 (Example 3; Fig 3); Cross-references: MIM:606269; NP_443177.1;
NM_052945_l; AF132600.
(27) CD22 (B-cell receptor CD22-B isoform, BL-CAM, Lyb-8, Lyb8, SIGLEC-2, FLJ22814, Genbank accession No. AK026467); Wilson et al. (1991) J. Exp. Med. 173 :137-146; W02003072036 (Claim 1; Fig 1); Cross-references: MIM: 107266; NP_001762.1; NM_001771_l. (28) CD79a (CD79A, CD79oc, immunoglobulin-associated alpha, a B cell-specific protein that covalently interacts with Ig beta (CD79B) and forms a complex on the surface with Ig M molecules, transduces a signal involved in B-cell differentiation), pl: 4.84, MW: 25028 TM: 2 [P] Gene Chromosome: 19ql3.2, Genbank accession No NP 001774.10) W02003088808, US20030228319; W02003062401 (claim 9); US2002150573 (claim 4, pages 13-14), WO9958658 (claim 13, Fig 16); WO9207574 (Fig 1); US5644033; Ha et al. (1992) J. Immunol. 148(5): 1526- 1531; Mueller et al. (1992) Eur. J. Biochem. 22: 1621-1625; Hashimoto et al. (1994) Immunogenetics 40(4):287-295; Preud’homme et al. (1992) Clin. Exp. Immunol. 90(1): 141-146; Yu et al. (1992) J. Immunol. 148(2) 633-637; Sakaguchi et al. (1988) EA/BO J. 7(11):3457-3464.
(29) CXCR5 (Burkitt’s lymphoma receptor 1, a G protein-coupled receptor that is activated by the CXCL13 chemokine, functions in lymphocyte migration and humoral defense, plays a role in HIV-2 infection and perhaps development of AIDS, lymphoma, myeloma, and leukemia); 372 aa, pl: 8.54 MW: 41959 TM: 7 [P] Gene Chromosome: 1 lq23.3, Genbank accession No. NP_001707.1) WO 2004040000; W02004/015426; US2003105292 (Example 2); US6555339 (Example 2); WO 2002/61087 (Fig 1); W0200157188 (Claim 20, page 269); W0200172830 (pages 12-13); WO 2000/22129 (Example 1, pages 152-153, Example 2, pages 254-256); WO 199928468 (claim 1, page 38); US 5440021 (Example 2, col 49-52); WO9428931 (pages 56-58); WO 1992/17497 (claim 7, Fig 5); Dobner et al. (1992) Eur. J. Immunol. 22-.2795-2I99,- Barella et al. ( \ 995) Biochem. J. 3Q9CT3-I79.
(30) HLA-DOB (Beta subunit of MHC class II molecule (la antigen) that binds peptides and presents them to CD4+ T lymphocytes); 273 aa, pl: 6.56 MW: 30820 TM: 1 [P] Gene Chromosome: 6p21.3, Genbank accession No. NP_002111.1) Tonnelle et al. (1985) EMBO J. 4(11):2839-2847; Jonsson et al. (1989) Immunogenetics 29(6):411-413; Beck et al. (1992) J. Mol. Biol. 228:433-441; Strausberg et al. (2002) Proc. Natl. Acad. Sci USA 99: 16899-16903; Servenius et al. (1987) J. Biol. Chem. 262:8759-8766; Beck et al. (1996) J. Mol. Biol. 255: 1-13; Naruse et al. (2002) Tissue Antigens 59:512-519; WO9958658 (claim 13, Fig 15); US6153408 (Col 35-38); US5976551 (col 168-170); US6011146 (col 145-146); Kasahara et al. (1989) Immunogenetics 30(l):66-68; Larhammar et al. (1985) J. Biol. Chem. 260(26): 14111-14119.
(31) P2X5 (Purinergic receptor P2X ligand-gated ion channel 5, an ion channel gated by extracellular ATP, may be involved in synaptic transmission and neurogenesis, deficiency may contribute to the pathophysiology of idiopathic detrusor instability); 422 aa), pl: 7.63, MW: 47206 TM: 1 [P] Gene Chromosome: 17p 13.3, Genbank accession No. NP_002552.2) Le et al. (1991) FEBS Lett. 418(1-2): 195-199, W02004047749, W02003072035 (claim 10); Touchman et al. (2000) Genome Res. 10: 165-173; W0200222660 (claim 20); W02003093444 (claim 1); W02003087768 (claim 1); W02003029277 (page 82).
(32) CD72 (B-cell differentiation antigen CD72, Lyb-2), pl: 8.66, MW: 40225 TM: 1 [P] Gene Chromosome: 9pl3.3, Genbank accession No. NP 001773.1) W02004042346 (claim 65); WO 2003/026493 (pages 51-52, 57-58); WO 2000/75655 (pages 105-106); Von Hoegen et al. (1990) J. Immunol. 144(12):4870-4877; Strausberg et al. (2002) Proc. Natl. Acad. Sci USA 99: 16899-16903.
(33) LY64 (Lymphocyte antigen 64 (RP105), type I membrane protein of the leucine rich repeat (LRR) family, regulates B-cell activation and apoptosis, loss of function is associated with increased disease activity in patients with systemic lupus erythematosus); 661 aa, pl: 6.20, MW: 74147 TM: 1 [P] Gene Chromosome: 5ql2, Genbank accession No. NP_005573.1) US2002193567; WO9707198 (claim 11, pages 39-42); Miura et al. (1996) Genomics 38(3):299- 304; Miura et al. (1998) Blood 92:2815-2822; W02003083047; WO9744452 (claim 8, pages 57-61); W0200012130 (pages 24-26).
(34) FcRHl (Fc receptor-like protein 1, a putative receptor for the immunoglobulin Fc domain that contains C2 type Ig-like and ITAM domains, may have a role in B-lymphocyte differentiation); 429 aa, pl: 5.28, MW: 46925 TM: 1 [P] Gene Chromosome: Iq21-lq22, Genbank accession No NP_443170 1) W02003077836; W0200138490 (claim 6, Fig 18E-1- 18-E-2); Davis et al. (2001) Proc. Natl. Acad. Sci USA 98(17):9772-9777; W02003089624 (claim 8); EP1347046 (claim 1); W02003089624 (claim 7).
(35) IRTA2 (Immunoglobulin superfamily receptor translocation associated 2, a putative immunoreceptor with possible roles in B cell development and lymphomagenesis; deregulation of the gene by translocation occurs in some B cell malignancies); 977 aa, pl: 6.88 MW: 106468 TM: 1 [P] Gene Chromosome: lq21, Genbank accession No. Human: AF343662, AF343663, AF343664, AF343665, AF369794, AF397453, AK090423, AK090475, AL834187, AY358085; Mouse: AK089756, AY158090, AY506558; NP_112571.1. W02003024392 (claim 2, Fig 97); Nakayama et al. (2000) Biochem. Biophys. Res. Commun. 277(1): 124-127; W02003077836; W0200138490 (claim 3, Fig 18B-1-18B-2).
(36) TENB2 (TMEFF2, tomoregulin, TPEF, HPP1, TR, putative transmembrane proteoglycan, related to the EGF/heregulin family of growth factors and follistatin); 374 aa, NCBI Accession: AAD55776, AAF91397, AAG49451, NCBI RefSeq: NP_057276; NCBI Gene: 23671; OMIM: 605734; SwissProt Q9UIK5; Genbank accession No. AF179274; AY358907, CAF85723, CQ782436 WO 2004074320; JP 2004113151; WO 2003042661; W02003009814; EP1295944 (pages 69-70); WO 200230268 (page 329); WO 200190304; US2004249130; US 2004022727; WO 2004063355; US 2004197325; US2003232350; US2004005563; US 2003124579; Hone et al. (2000) Genomics 67: 146-152; Uchida et al. (1999) Biochem. Biophys. Res. Commun. 266:593-602; Liang et al. (2000) Cancer Res 60:4907- 12; Glynne-Jones et al. (2001) Int J Cancer. Oct 15;94(2): 178-84.
(37) PMEL17 (silver homolog; SILV; D12S53E; PMEL17; SI; SIL); ME20; gplOO) BC001414; BT007202; M32295; M77348; NM_006928; McGlinchey, R.P. et al. (2009) Proc. Natl. Acad. Sci. U.S.A. 106 (33), 13731-13736; Kummer, M.P. et al. (2009) J Biol. Chem. 284 (4), 2296-2306.
(38) TMEFF1 (transmembrane protein with EGF-Iike and two follistatin-like domains 1; Tomoregulin-1); H7365; C9orf2; C9ORF2; U19878; X83961; NM 080655; NM_003692; Harms, P.W. (2003) Genes Dev. 17 (21), 2624-2629; Gery, S. et al. (2003) Oncogene 22 (18):2723-2727.
(39) GDNF-Ral (GDNF family receptor alpha 1; GFRA1; GDNFR; GDNFRA, RETL1; TRNR1; RET1L; GDNFR-alphal; GFR-ALPHA-1); U95847; BC014962; NM_145793 NM_005264; Kim, M.H. et al. (2009) Mol. Cell. Biol. 29 (8), 2264-2277; Treanor, J. J. et al. (1996) Nature 382 (6586):80-83.
(40) Ly6E (lymphocyte antigen 6 complex, locus E; Ly67,RIG-E,SCA-2,TSA-l); NP_002337.1; NM_002346.2; de Nooij-van Dalen, A.G. et al. (2003) Int. J. Cancer 103 (6), 768-774; Zammit, D J. et al (2002) Mol. Cell. Biol. 22 (3):946-952
(41) TMEM46 (shisa homolog 2 (Xenopus laevis); SHISA2); NP_001007539.1; NM_001007538.1; Furushima, K. et al. (2007) Bev. Biol. 306 (2), 480-492; Clark, H.F. et al. (2003) Genome Res. 13 (10):2265-2270.
(42) Ly6G6D (lymphocyte antigen 6 complex, locus G6D; Ly6-D, MEGT1);
NP 067079.2; NM 021246.2; Mallya, M. et al. (2002) Genomics 80 (1):113-123; Ribas, G. et al. (1999) J. Immunol. 163 (l):278-287.
(43) LGR5 (leucine-rich repeat-containing G protein-coupled receptor 5; GPR49, GPR67); NP_003658.1; NM_003667.2; Salanti, G. et al. (2009) Am. J. Epidemiol. 170 (5):537- 545; Yamamoto, Y. et al. (2003) Hepatology 37 (3):528-533.
(44) RET (ret proto-oncogene; MEN2A; HSCR1; MEN2B; MTC1 ; PTC; CDHF12; Hs.168114; RET51; RET-ELE1); NP 066124.1; NM_020975.4; Tsukamoto, H. et al. (2009) Cancer Sci. 100 (10): 1895-1901; Narita, N. et al. (2009) Oncogene 28 (34):3058-3068.
(45) LY6K (lymphocyte antigen 6 complex, locus K; LY6K; HSJ001348; FLJ35226); NP 059997.3; NM 017527.3; Ishikawa, N. et al. (2007) Cancer Res. 67 (24): 11601-11611; de Nooij -van Dalen, A.G. et al (2003) Int. J. Cancer 103 (6):768-774. (46) GPR19 (G protein-coupled receptor 19; Mm.4787); NP 006134.1; NM_006143.2; Montpetit, A. and Sinnett, D. (\999) Hum. Genet. 105 (1-2): 162-164; O’Dowd, B.F. et al. (\996) FEBS Lett 394 (3):325-329.
(47) GPR54 (KISSI receptor; KISS1R; GPR54; HOT7T175; AX0R12); NP_115940.2; NM_032551.4; Navenot, J M. et al. (2009) Mol. Pharmacol. 75 (6): 1300-1306; Hata, K. et al. (2009) Anticancer Res 29 (2):617-623.
(48) ASPHD1 (aspartate beta-hydroxylase domain containing 1; LOC253982); NP_859069.2; NM_181718.3; Gerhard, D.S. et al. (2004) Genome Res. 14 (10B):2121-2127.
(49) Tyrosinase (TYR; OCAIA; OCA1A; tyrosinase; SHEP3); NP 000363 1; NM_000372.4; Bishop, D.T. et al. (2009) Nat. Genet. 41 (8):920-925; Nan, H. et al. (2009) Int. J. Cancer 125 (4): 909-917
(50) TMEM118 (ring finger protein, transmembrane 2, RNFT2; FLJ14627);
NP_001103373.1; NM_001109903.1; Clark, H.F. et al. (2003) Genome Res. 13 (10):2265-2270; Scherer, S.E. et al. (2006) Nature 440 (7082):346-351.
(51) GPR172A (G protein-coupled receptor 172A; GPCR41; FLJ11856; D15Ertd747e); NP 078807.1; NM_024531.3; Ericsson, T.A. et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100
(1 l):6759-6764; Takeda, S. et al. (2002) FEBS Lett. 520 (l-3):97-101.
(52) CD33, a member of the sialic acid binding, immunoglobulin-like lectin family, is a 67-kDa glycosylated transmembrane protein. CD33is expressed on most myeloid and monocytic leukemia cells in addition to committed myelomonocytic and erythroid progenitor cells. It is not seen on the earliest pluripotent stem cells, mature granulocytes, lymphoid cells, or nonhematopoietic cells (Sabbath et al., (1985) J. Clin. Invest. 75:756-56; Andrews et al., (1986) Blood 68: 1030-5). CD33 contains two tyrosine residues on its cytoplasmic tail, each of which is followed by hydrophobic residues similar to the immunoreceptor tyrosine-based inhibitory motif (ITIM) seen in many inhibitory receptors.
(53) CLL-1 (CLEC12A, MICE, and DCAL2), encodes a member of the C-type lectin/C- type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signaling, glycoprotein turnover, and roles in inflammation and immune response. The protein encoded by this gene is a negative regulator of granulocyte and monocyte function. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. This gene is closely linked to other CTL/CTLD superfamily members in the natural killer gene complex region on chromosome 12p 13 (Drickamer K (1999) Curr. Opin. Struct. Biol. 9 (5):585-90; van Rhenen A, et al , (2007) Blood 110 (7):2659-66; Chen CH, et al. (2QQ6) Blood 107 (4):1459-67; Marshall AS, et al. (2006) Eur. J. Immunol. 36 (8):2159-69; Bakker AB, et al. (2005) Cancer Res. 64 (22):8443-50; Marshall AS, , et al. (2004) J. Biol. Chem. 279 (15): 14792-802). CLL-1 has been shown to be a type II transmembrane receptor comprising a single C-type lectin-like domain (which is not predicted to bind either calcium or sugar), a stalk region, a transmembrane domain and a short cytoplasmic tail containing an ITIM motif.
(54) TROP2 (tumor-associated calcium signal transducer 2) is a transmembrane glycoprotein encoded by the TACSTD2 gene (Linnenbach AJ, et al (1993) Mol Cell Biol. 13(3): 1507—15; Calabrese G, et al (2001) Cytogenet Cell Genet. 92(1-2): 164-5). TROP2 is an intracellular calcium signal transducer that is differentially expressed in many cancers It signals cells for seif-renewal, proliferation, invasion, and survival. It has stem cell -like qualities. TROP2 is expressed in many normal tissues, though in contrast, it is overexpressed in many cancers (Ohmachi T, et al., (2006) Clin. Cancer Res., 12(10):3057-3063; Muhlmann G, et al., (2009) 7. Clin. Pathol., 62(2): 152-158; Fong D, et al., (2008) Br. J. Cancer, 99(8): 1290-1295; Fong D, et al., (2008) Afc>7 Pathol., 21(2): 186-191; Ning S, et al., (2013) Neurol. Sci., 34(10): 1745-1750). Overexpression of TROP2 is of prognostic significance. Several ligands have been proposed that interact with TROP2. TROP2 signals the cells via different pathways and it is transcriptionally regulated by a complex network of several transcription factors.
Human TROP2 (TACSTD2: tumor-associated calcium signal transducer 2, GA733-1, EGP-1, Ml SI; hereinafter, referred to as hTROP2) is a single-pass transmembrane type 1 cell membrane protein consisting of 323 amino acid residues. While the presence of a cell membrane protein involved in immune resistance, which is common to human trophoblasts and cancer cells (Faulk W P, et al. (1978), Proc. Natl. Acad. Sci. 75(4): 1947-1951), has previously been suggested, an antigen molecule recognized by a monoclonal antibody against a cell membrane protein in a human choriocarcinoma cell line was identified and designated as TROP2 as one of the molecules expressed In human trophoblasts (Lipinski M, et al. (1981), Proc. Natl. Acad. Sci. 78(8), 5147-5150). This molecule was also designated as tumor antigen GA733-1 recognized by a mouse monoclonal antibody GA733 (Linnenbach A J, et al., (1989) Proc. Natl. Acad. Sci. 86(1), 27-31) obtained by immunization with a gastric cancer cell line or an epithelial glycoprotein (EGP-1; Basu A, et al., Int. J. Cancer, 62 (4), 472-479 (1995)) recognized by a mouse monoclonal antibody RS7-3G11 obtained by immunization with non-small cell lung cancer cells. In 1995, however, the TROP2 gene was cloned, and all of these molecules were confirmed to be identical molecules (Fornaro M, et al., (1995) Int. J. Cancer, 62(5), 610-618). The DNA sequence and amino acid sequence of hTROP2 are available on a public database and can be referred to, for example, under Accession Nos. NM_002353 and NP_002344 (NCBI). ISOINDOLINONE-GLUTARIMIDE COMPOUNDS
The antibody conjugate composition of the invention comprises an isoindolinone- glutarimide moiety (IG). The antibody conjugate composition of the present disclosure may be prepared from an isoindolinone-glutarimide (IG) compound selected from Formula III:
Figure imgf000041_0001
or a pharmaceutically acceptable salt, stereoisomer, mixture of stereoisomers, tautomer, or isotopic analog thereof, wherein: m is 0, 1 or 2;
X1 is selected from the group consisting of CH2, C(=O) and N=N;
X2 is independently selected from the group consisting of F, Cl, Br, I, -CN, C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), ( C1-C6 alkyldiyl)-(C6-C20 aryl), -(C1-C6 alkyldiyl)-NRaRb, -( C1-C6 alkyldiyl)-ORa, (C1-C6 alkyldiyl)-(Ca-C20 carbocyclyl), (C1-C6 alkyldiyl)-(C2-C20 heterocyclyl), (C1-C6 alkyldiyl)-( C1-C20 heteroaryl), C6-C20 aryl, C3-C20 carbocyclyl, C2-C20 heterocyclyl, C1-C20 heteroaryl, -C(=NH)NH(0H), -C(=NH)NH2, -C(=O)NRaRb, -C(=0)NRa-NRaRb, -C(=O)NH(C1-C6 alkyldiyl)-NRaRb, -C(=O)ORa, -NRaRb, -NO2, -ORa, -OC(=O)Ra, -SRa, -S(O)Ra, -S(O)2Ra, -S(O)2NRa, and -S(O)3H;
Ra is independently selected from H, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl;
Rb is independently selected from H, OH, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl; n is 0, 1, 2, 3, or 4; and
X4 is selected from the group consisting of H, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl); wherein each alkyl, alkyldiyl, alkenyl, alkenyldiyl, alkynyl, alkynyldiyl, heteroalkyl, heteroalkyl diyl, aryl, aryldiyl, carbocyclyl, carbocyclyldiyl, heterocyclyl, heterocyclyldiyl, heteroaryl, and heteroaryl diyl is independently and optionally substituted with one or more groups selected from F, Cl, Br, I, -CN, -CH3, -CH2CH3, -CH=CH2, -C=CH, -C=CCH3, - CH2CH2CH3, -CH(CH3)2, -CH2CH(CH3)2, -CH2OH, -CH2OCH3, -CH2CH2OH, -C(CH3)2OH, -CH(OH)CH(CH3)2, -C(CH3)2CH2OH, -CH2CH2SO2CH3, -CH2OP(O)(OH)2, -CH2F, -CHF2, -CF3, -CH2CF3, -CH2CHF2, -CH(CH3)CN, -C(CH3)2CN, -CH2CN, -CH2NH2, - CH2NHSO2CH3, -CH2NHCH3, -CH2N(CH3)2J -CO2H, -COCH3, -CO2CH3, -CO2C(CH3)3, - COCH(OH)CH3, CONH2, -CONHCHS, -CON(CH3)2, -C(CH3)2CONH2, -NH2, NHCH3, - N(CH3)2, -NHCOCH3, -N(CH3)COCH3, -NHS(O)2CH3, -N(CH3)C(CH3)2CONH2, - N(CH3)CH2CH2S(O)2CH3, -NHC(=NH)H, -NHC(=NH)CH3, -NHC(=NH)NH2, - NHC(=O)NH2, -NO2, =0, -OH, -OCH3, -OCH2CH3, -OCH2CH2OCH3, -OCH2CH2OH, - OCH2CH2N(CH3)2, -0CH2F, -0CHF2, -OCF3, -OP(O)(OH)2J -S(O)2N(CH3)2J -SCH3, - S(O)2CH3, and -S(O)3H.
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein m is 0.
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein m is 1.
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein m is 2.
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X1 is CH2.
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X1 is C(=O).
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X1 is N=N.
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X2 comprises a -NHC(=0)NH- group.
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X2 is selected from the group consisting of C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), and -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl).
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X2 is — (C1 — C12 heteroalkyldiyl)-(C6-C20 aryl). An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X2 is -CH2NHC(=O)NH-(CS-C20 aryl).
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X2 is:
Figure imgf000043_0001
where ** indicates the point of attachment.
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X4 is H.
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X4 is selected from the group consisting of C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), and -(C1-C12 heteroalkyldiyl )-(C6-C20 aryldiyl)-0-(C2-C20 heterocyclyl).
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X4 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-0-(C2-C20 heterocyclyl), and C2-C20 heterocyclyl is a glucuronide.
An exemplary embodiment of the isoindolinone-glutarimide compound includes wherein X4 of formula la is selected from the formulae:
Figure imgf000043_0002
wherein R is selected from H, C1-C6 alkyl, and O-(C1-C6 alkyl); and * indicates the point of attachment. Exemplary isoindolinone-glutarimide (IG) compounds of Table la, lb and 1c were prepared and characterized according to the Examples herein. C6rtain exemplary IG compounds of Table la were tested for their effects in inhibiting cellular proliferation, including CAL51,; WSU-DLCL2, NCI-N87 and SKBR3. CAL51 is a human breast adenocarcinoma cell line with triple-negative status for expression of estrogen, progesterone and HER2 receptors. WSU- DLCL2 is a human B-C6ll non-Hodgkin lymphoma cell line that expresses high levels of CD22. NCI-N87 is a human epithelial cell line established from a gastric carcinoma; SKBR3 is a human epithelial cell line established from a breast adenocarcinoma; both NCI-N87 and SKBR3 cell lines express high levels of HER2 receptor Table la Isoindolinone-glutarimide (IG) compounds
Figure imgf000044_0001
Figure imgf000045_0001
Figure imgf000046_0001
Figure imgf000047_0001
Figure imgf000048_0001
Figure imgf000049_0001
Figure imgf000050_0001
Figure imgf000051_0001
Table lb C6ll killing by Isoindolinone-glutarimide (IG) compounds of Table la
Figure imgf000051_0002
Figure imgf000052_0001
Figure imgf000053_0001
Table 1c Isoindolinone-glutarimide (IG) compounds
Figure imgf000053_0002
Figure imgf000054_0001
Figure imgf000055_0001
LINKER UNITS
In certain embodiments, the present disclosure provides branched phenyl maleimide compounds (e.g., compounds of Structure (I)) enable the formation of a covalent bond between an isoindolinone-glutarimide linker compound (IG-L) and an antibody (Ab).
Accordingly, some embodiments provide a compound having the following Structure (I):
Figure imgf000056_0001
wherein: one of Y1, Y2, Y3, Y4 and Y5 is C-L'-R1, another one of Y1, Y2, Y3, Y4 and Y5 is C-L2- R2, and the remaining three of Y1, Y2, Y3, Y4 and Y5 are each independently N, C-R3, or C-L3- R3a;
R1, R2, and R3a each independently comprise one or more moieties selected from an amino acid element, a charged element, a heteroalkylene element, a hydrophilic element, a trigger element, an immolative unit, a polar cap, an isoindolinone-glutarimide moiety, and combinations thereof; provided that at least one of R1 and R2 comprises a isoindolinone-glutarimide moiety; each occurrence of R3 is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, aminyl, amidyl, aldehyde, hydroxyl, cyano, nitro, thiol, carboxy, carboxyalkyl, alkyl-S(O)3H, alkyl-O-P(O)sH, alkyl- P(O)3H, -O-carboxyalkyl, -O-alkyl-S(O)3H, -O-alkyl-O-P(O)3H, -O-alkyl-P(O)3H, -S(O)3H, - OP(O)3H, -P(O)3H, alkyl-O-P(O)3-alkyl, alkyl-P(O)3-alkyl, -O-alkyl-S(O)3-alkyl, -O-alkyl-O- P(O)3-alkyl, -O-alkyl-P(O)3-alkyl, -S(O)3-alkyl, -OP(O)3-alkyl, -P(O)3-alkyl, sulfamide, sulfinimide, and a carbohydrate;
R4a and R4b are each independently hydrogen, deuterium, halo, or -S-R4c wherein R4c is substituted or unsubstituted C6-C10 aryl or substituted or unsubstituted 5-12 membered heteroaryl; and
L1, L2, and L3 are each independently a linker comprising an optionally substituted alkylene, an optionally substituted alkenylene, an optionally substituted alkynylene, an optionally substituted heteroalkylene, an optionally substituted heteroalkenylene, an optionally substituted heteroalkynylene, a heteroatomic linker, an optionally substituted cycloalkylene, an optionally substituted arylene, an optionally substituted heterocyclylene, an optionally substituted heteroarylene, or combinations thereof; as a stereoisomer, enantiomer or tautomer thereof or a mixture thereof; or a pharmaceutically acceptable salt, solvate or prodrug thereof. C6rtain embodiments provide a compound having the following Structure (la):
Figure imgf000057_0001
wherein: one of Y1, Y2, Y3, Y4 and Y5 is C-L'-R1, another one of Y1, Y2, Y3, Y4 and Y5 is C-L2- R2, and the remaining three of Y1, Y2, Y3, Y4 and Y5 are each independently N, C-R3, or C-L3- R3a;
R1, R2, and R3a each independently comprise one or more moieties selected from an amino acid element, a charged element, a heteroalkylene element, a hydrophilic element, a trigger element, an immolative element, a polar cap, a payload, and combinations thereof; provided that at least one of R1 and R2 comprises a payload; each occurrence of R3 is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, aminyl, amidyl, aldehyde, hydroxyl, cyano, nitro, thiol, carboxy, carboxyalkyl, alkyl-S(O)3H, alkyl-O-P(O)3H, alkyl- P(O)3H, -O-carboxyalkyl, -O-alkyl-S(O)3H, -O-alkyl-O-P(O)3H, -O-alkyl-P(O)3H, -S(O)3H, - OP(O)3H, -P(O)3H, alkyl-O-P(O)3-alkyl, alkyl-P(O)3-alkyl, -O-alkyl-S(O)3-alkyl, -O-alkyl-O- P(O)3-alkyl, -O-alkyl-P(O)3-alkyl, -S(O)3-alkyl, -OP(O)3-alkyl, -P(O)3-alkyl, sulfamide, sulfinimide, and a carbohydrate;
R4a and R4b are each independently hydrogen, deuterium, halo, or -S-R4c wherein R4c is substituted or unsubstituted C6-C10 aryl or substituted or unsubstituted 5-12 membered heteroaryl; and
L1, L2, and L3 are each independently direct bond or a linker comprising an optionally substituted alkylene, an optionally substituted alkenylene, an optionally substituted alkynylene, an optionally substituted heteroalkylene, an optionally substituted heteroalkenylene, an optionally substituted heteroalkynylene, a heteroatomic linker, an optionally substituted cycloalkylene, an optionally substituted arylene, an optionally substituted heterocyclylene, an optionally substituted heteroarylene, or combinations thereof; as a stereoisomer, enantiomer or tautomer thereof or a mixture thereof; or a pharmaceutically acceptable salt, solvate or prodrug thereof.
In some embodiments, R4a and R4b are both hydrogen. In some embodiments, R4a is halo or R4b is halo. In some embodiments, R4a, R4b, or both have one of the following structures:
Figure imgf000058_0001
In some embodiments, R1 R2, and/or R3a comprises elements selected from an amino acid element, a charged element, a heteroalkylene element, a hydrophilic element, a trigger element, an immolative element, a polar cap, a payload, and combinations thereof. It is understood that these elements can be connected in any order and be connected in a linear manner or via a branched connection. In some embodiments, R1 R2, and/or R3a comprises multiple occurrences of an element (e.g, two or more heteroalkylene elements, two or more hydrophilic elements, two or more polar caps, etc.).
In some embodiments, R1, R2, or R3a comprises a branch point as part of an amino acid element (e.g., lysine) wherein additional elements are attached via an epsilon amine of the lysine and other additional elements are linked to the amino acid element via one or more peptide bonds to the alpha carbon of a lysine. A similar motif could be utilized with a glutamic acid of an amino acid element. In some embodiments, an amino acid element comprises one of the following structures:
Figure imgf000058_0002
In some embodiments, a compound of Structure (I) comprises one of the following structures:
Figure imgf000059_0001
In certain embodiments, R1 has the following structure:
Figure imgf000060_0001
wherein:
Llais an amino acid element;
Llb is a charged element;
Llc is a heteroalkylene element;
Lld is a hydrophilic element;
Lle is a trigger element; and
Llf is an immolative unit; wherein one or more occurrence of Lla, Llh, Llc, Lld, Lle, and Llf optionally joins with one or more of another of Lla, Llb, Llc, Lld, Lle, and Llf to form one or more ring; each occurrence of nl, n2, n3, n4, n5, and n6 is independently an integer from 0-3, provided that nl + n2 + n3 + n4 + n5 + n6 = 1 or more; n7 is 1, 2, 3, 4, 5, or 6; and
Rla is a isoindolinone-glutarimide moiety that is covalently bound to one occurrence of
Lla, Llb, Llc, Lld, Lle, or Llf and the isoindolinone-glutarimide moiety is optionally substituted with a polar cap.
In some embodiments, n7 is 1, 2, or 3. In some embodiments, n7 is 1 or 2. In some embodiments, n7 is 1 .
In some embodiments, R1 has the following structure:
Figure imgf000060_0002
wherein:
Llais an amino acid element;
Llb is a charged element;
Llc is a heteroalkylene element;
Lld is a hydrophilic element;
Lle is a trigger element; and
Llf is an immolative unit; wherein one or more occurrence of Lla, Llh, Llc, Lld, Lle, and Llf optionally joins with one or more of another of Lla, Llb, Llc, Lld, Lle, and Llf to form one or more ring; each occurrence of nl, n2, n3, n4, n5, and n6 is independently an integer from 0-3, provided that nl + n2 + n3 + n4 + n5 + n6 = 1 or more; n7 is 1, 2, 3, 4, 5, or 6; and
Rla is a isoindolinone-glutarimide moiety optionally substituted with a polar cap.
In more embodiments, R2 has the following structure:
Figure imgf000061_0001
wherein:
L2ais an amino acid element;
L2b is a charged element;
L2C is a heteroalkylene element;
L2d is a hydrophilic element;
L2e is a trigger element; each occurrence of ml, m2, m3, m4, and m5 is independently an integer from 0-3, provided that ml + m2 + m3 + m4 + m5 = 1 or more; m6 is 1, 2, 3, 4, or 5; and
R2a is hydrogen, alkyl, a isoindolinone-glutarimide moiety, or a polar cap
In some embodiments, m6 is 1, 2, or 3. In some embodiments, m6 is 1 or 2. In some embodiments, m6 is 1.
In still more embodiments, R3a has the following structure:
Figure imgf000061_0002
wherein:
L3ais an amino acid element; b is a charged element;
L3C is a heteroalkylene element;
L3d is a hydrophilic element;
L3e is a trigger element; each occurrence of pl, p2, p3, p4, and p5 is independently an integer from 0-3, provided that pl + p2 + p3 + p4 + p5 = 1 or more; p6 is 1, 2, 3, 4, or 5; and
R3b is hydrogen, alkyl, or a polar cap. In some embodiments, p6 is 1, 2, or 3. In some embodiments, p6 is 1 or 2. In some embodiments, p6 is 1 .
In certain embodiments, n7 is 1 and each of nl through n6 are 1. In some embodiments, n7 is 1 and each of nl through n4 are 0, n5 is 1, and nb is 1. In certain embodiments, n7 is 1 and nl is 0, n2 is 0, n3 is 1, n4 is 0, n5 is 1, and n6 is 1. In certain embodiments, n7 is 1 and nl is 1, n2 is 0, n3 is 1, n4 is 0, n5 is 1, and n6 is 1. In certain embodiments, n7 is 1 and nl is 1, n2 is 1, n3 is 1, n4 is 0, n5 is 1, and n6 is 1. In certain embodiments, n7 is 1 and nl is 1, n2 is 1, n3 is 1, n4 is 1, n5 is 1, and n6 is I In certain embodiments, n7 is 1 and nl is 1, n2 is 0, n3 is 1, n4 is 0, n5 is 1, and n6 is 1 In certain embodiments, n7 is 2 In certain embodiments, n7 is 3
In some embodiments, m6 is 1 and each of ml through m5 are 1. In some embodiments, m6 is 1, ml is 1, m2 is 0, m3 is 0, m4 is 1, and m5 is 0. In some embodiments, m6 is 1, ml is 1, m2 is 1, m3 is 0, m4 is 1, and m5 is 0. In some embodiments, m6 is 1, ml is 1, m2 is 0, m3 is 1, m4 is 1, and m5 is 0. In some embodiments, mb is 1, ml is 1, m2 is 0, m3 is 0, m4 is 1, and m5 is 1. In some embodiments, m6 is 2. In certain embodiments, m6 is 3.
In some embodiments, p6 is 1 and each of pl through p5 is 1. In certain embodiments, p6 is 1, pl is 1, p2 is 0, p3 is 0, p4 is 1, and p5 is 0. In some embodiments, p6 is 1, pl is 1, p2 is 1, p3 is 0, p4 is 1, and p5 is 0. In some embodiments, p6 is 1, pl is 1, p2 is 0, p3 is 1, p4 is 1, and p5 is 0 In some embodiments, p6 is 1, pl is 1, p2 is 0, p3 is 0, p4 is 1, and p5 is 1 In some embodiments, p6 is 2 and at least one occurrence of pl is 1, p2 is 1, p3 is 0, p4 is 1, and p5 is 0. In some embodiments, pb is 2. In certain embodiments, pb is 3.
In some embodiments, an amino acid element comprises one or more amino acids selected from the group consisting of glycine, alanine, serine, threonine, cysteine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tyrosine, tryptophan, aspartic acid, glutamic acid, asparagine, glutamine, histidine, lysine, arginine, sarcosine, and beta-alanine.
In certain embodiments, an amino acid element is selected from the group consisting of glycine, sarcosine, beta-alanine, and glutamic acid.
In some embodiments, an amino acid element comprises a dipeptide, a tripeptide, a tetrapeptide, or a pentapeptide.
In more embodiments, an amino acid element has one of the following structures:
Figure imgf000062_0001
wherein: each occurrence of R5a is independently hydrogen, alkyl, hydroxyalkyl, or alkoxyalkyl. In some embodiments, a charged element comprises moieties with a negative charge at about pH 7.4 (i.e., a range from 6.3 to 8 5). In certain embodiments, a charged element comprises moieties with a positive charge at about pH 7.4 (i.e., a range from 6.3 to 8 5). In some embodiments, a charged element comprises one or more charged amino acid, one or more carboxylic acid, one or more sulfonic acid, one or more sulfonamide, one or more sulfate, one or more phosphate, one or more quaternary amine, one or more sulfamide, one or more sulfinimide, or combinations thereof.
In certain embodiments, a charged amino acid is aspartic acid, glutamic acid, histidine, lysine, or arginine.
In some embodiments, R1, R2, or R3a comprises a non-cleavable linker (e.g, a linker, or segment thereof, that does not include a trigger element or immolative unit).
In some embodiments, R1, R2, or R3a comprises one of the following structures:
Figure imgf000063_0001
Figure imgf000064_0001
wherein: each occurrence of R5b, R5c R5d, and R5e is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, hydroxyl, cyano, nitro, thiol, carboxyalkyl, alkyl-S(O)3H, alkyl-O-P(O)3H, alkyl-P(O)3H, -O-carboxyalkyl, -O-alkyl-S(O)3H, -O-alkyl-O-P(O)3H, -O-alkyl-P(O)3H, -S(O)3H, -OP(O)3H, -P(O)3H, alkyl-O- P(O)3-alkyl, alkyl-P(O)3-alkyl, -O-alkyl-S(O)3-alkyl, -O-alkyl-O-P(O)3-alkyl, -O-alkyl-P(O)3- alkyl, -S(O)3-alkyl, -OP(O)3-alkyl, -P(O)3-alkyl, sulfamide, sulfmimide; each occurrence of R5f is independently hydrogen, alkyl, hydroxyalkyl, or alkoxyalkyl; each occurrence of R9 is independently hydrogen or alkyl; each occurrence of q2 is independently an integer from 1-25; and each occurrence of q3 is independently an integer from 5-15.
In some embodiments, a hydrophilic element comprises polyethylene glycol, poly sarcosine, cyclodextrin, c-glycosides, or combinations thereof. In some embodiments, a hydrophilic element comprises one of the following structures:
Figure imgf000065_0001
wherein: each occurrence of R5b, R5c R5d, and R5e is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, hydroxyl, cyano, nitro, thiol, carboxyalkyl, alkyl-S(O)3H, alkyl-O-P(O)3H, alkyl-P(O)3H, -O-carboxyalkyl, -O-alkyl-S(O)3H, -O-alkyl-O-P(O)3H, -O-alkyl-P(O)3H, -S(O)3H, -OP(O)3H, and -P(O)3H, each occurrence of R5g is independently hydrogen, alkyl, hydroxyalkyl, or alkoxyalkyl; and each occurrence of q4 is, independently an integer from 1-24.
In some embodiments, a hydrophilic element comprises one of the following structures:
Figure imgf000065_0002
In some embodiments, a hydrophilic element comprises one of the following structures:
Figure imgf000066_0001
Figure imgf000067_0001
In some embodiments, a hydrophilic element has one of the following structures:
Figure imgf000067_0002
Figure imgf000068_0001
In some embodiments, a hydrophilic element has the following structure:
Figure imgf000068_0002
10 In some embodiments, a hydrophilic element has one of the following structures:
Figure imgf000068_0003
Figure imgf000069_0001
In some embodiments, a hydrophilic element comprises a polysarcosine. In some embodiments, a hydrophilic element is a polysarcosine comprising the following structure:
Figure imgf000070_0001
In some embodiments, a hydrophilic element is a polysarcosine with one of the following structures:
Figure imgf000070_0002
In some embodiments, a hydrophilic element has a molecular weight greater than 150 g/mole, greater than 200 g/mole, greater than 300 g/mole, greater than 400 g/mole, greater than 500 g/mole, greater than 600 g/mole, greater than 700 g/mole, greater than 800 g/mole, greater than 900 g/mole, or greater than 1000 g/mole In some embodiments, a hydrophilic element has a molecular weight less than 150 g/mole, less than 200 g/mole, less than 300 g/mole, less than 400 g/mole, less than 500 g/mole, less than 600 g/mole, less than 700 g/mole, less than 800 g/mole, less than 900 g/mole, or less than 1000 g/mole.
In certain embodiments, L1 is alkylene. In some embodiments, L1 is C1-C6 alkylene. In certain embodiments, L2 is alkylene. In some embodiments, L2 is C1-C6 alkylene. In certain embodiments, I? is alkylene. In some embodiments, L3 is C1-Cg alkylene.
In certain embodiments, L1 is heteroalkylene. In some embodiments, L1 is C1-C6 heteroalkylene (i.e., contains from 1-6 carbon atoms and one or more heteroatoms). In certain embodiments, L2 is heteroalkylene In some embodiments, L2 is C1-Cg heteroalkylene In certain embodiments, I? is heteroalkylene. In some embodiments, L3 is C1-Cg heteroalkylene.
In more embodiments, L1, L2, or L3 are C1-Cg heteroalkylene and contain heteroatoms selected form O and N. In some embodiments, I? is a direct bond.
In more embodiments, L1, L2, or L3 have one of the following structures:
Figure imgf000070_0003
In some embodiments, a trigger element comprises a dipeptide, a tripeptide, a tetrapeptide, a pentapeptide, a glucuronide, a disulfide, a phosphate, a diphosphate, a triphosphate, a hydrazone, or combinations thereof. In some other embodiments, a trigger element comprises beta-glucuronic acid. In certain embodiments, a trigger element comprises a dipeptide, a tripeptide, a tetrapeptide, or a pentapeptide In some embodiments, a trigger element comprises two or more amino acids selected from the group consisting of valine, citrulline, alanine, glycine, phenylalanine, lysine, or combinations thereof. In certain embodiments, a trigger element comprises a sequence of amino acids selected from the group consisting of valine-citrulline, valine-alanine, glycine-glycine-phenylalanine-glycine, and combinations thereof. In some embodiments, a trigger element comprises one of the following structures, including combinations thereof
Figure imgf000071_0001
In some embodiments, a trigger element has a molecular weight greater than 150 g/mole, greater than 200 g/mole, greater than 300 g/mole, greater than 400 g/mole, greater than 500 g/mole, greater than 600 g/mole, greater than 700 g/mole, greater than 800 g/mole, greater than 900 g/mole, or greater than 1000 g/mole. In some embodiments, a trigger element has a molecular weight less than 150 g/mole, less than 200 g/mole, less than 300 g/mole, less than 400 g/mole, less than 500 g/mole, less than 600 g/mole, less than 700 g/mole, less than 800 g/mole, less than 900 g/mole, or less than 1000 g/mole.
In some embodiments, a trigger element has the following structure:
Figure imgf000072_0001
In some embodiments, a trigger element is specifically cleaved by an enzyme. For example, a trigger element can be cleaved by a lysosomal enzyme. A trigger element can be peptide-based or can include peptidic regions that can act as substrates for enzymes. Peptide based trigger elements can be more stable in plasma and extracellular milieu than chemically labile linkers. Exemplary disulfide-containing trigger elements can include the following structures:
Figure imgf000072_0002
wherein D is a isoindolinone-glutarimide moiety and R is independently selected at each occurrence from, for example, hydrogen or C1-C6 alkyl. Increasing steric hindrance adjacent to the disulfide bond can increase the stability of the linker. The above structures can result in increased in vivo stability when one or more R groups is selected from a lower alkyl, such as methyl.
Peptide bonds can have good serum stability, as lysosomal proteolytic enzymes can have very low activity in blood due to endogenous inhibitors and the unfavorably high pH value of blood compared to lysosomes. Release of a isoindolinone-glutarimide moiety from conjugate of Structure (II) can occur due to the action of lysosomal proteases, e.g., cathepsin and plasmin. These proteases can be present at elevated levels in certain tumor tissues. A trigger element can be cleavable by a lysosomal enzyme. The lysosomal enzyme can be, for example, cathepsin B, P-glucuronidase, or P-galactosidase.
A cleavable peptide of a trigger element can be selected from tetrapeptides such as Gly- Phe-Leu-Gly, Ala-Leu-Ala-Leu, tripeptides such as Glu-Val-Cit, or dipeptides such as Val-Cit, Vai-Ala, Ala-Ala, and Phe-Lys. Dipeptides can have lower hydrophobicity compared to longer peptides
In some embodiments, a trigger element may be a single amino acid residue. In some embodiments, the trigger element comprises asparagine, Asn as a legumain cleavable element (Miller, J.T. et al (2021) Bioconjugate Chem. 32(4):842-858
Enzymatically cleavable trigger elements be combined with an immolative unit and provide additional spatial separation between a isoindolinone-glutarimide moiety and the site of enzymatic cleavage. The direct attachment of isoindolinone-glutarimide moiety to a peptidic trigger element can result in proteolytic release of a isoindolinone-glutarimide moiety or of an amino acid adduct of a isoindolinone-glutarimide moiety thereby impairing its activity. The use of an immolative unit can allow for the release of the fully active, chemically unmodified isoindolinone-glutarimide moiety upon amide bond hydrolysis.
A trigger element can contain a chemically labile group such as hydrazone and/or disulfide groups. A trigger element comprising chemically labile group or groups can exploit differential properties between the plasma and some cytoplasmic compartments. The intracellular conditions that can facilitate release of a isoindolinone-glutarimide moiety for hydrazone containing trigger elements can be the acidic environment of endosomes and lysosomes, while the disulfide containing trigger elements can be reduced in the cytosol, which can contain high thiol concentrations, e.g., glutathione. The plasma stability of a trigger element containing a chemically labile group can be increased by introducing steric hindrance using substituents near the chemically labile group
Acid-labile groups, such as hydrazone, can remain intact during systemic circulation in the blood’s neutral pH environment (pH 7.3-7.5) and can undergo hydrolysis and can release a isoindolinone-glutarimide moiety once the conjugate of Structure (II) is internalized into mildly acidic endosomal (pH 5.0-6.5) and lysosomal (pH 4.5-5.0) compartments of the cell. This pH dependent release mechanism can be associated with non-specific release of a isoindolinone- glutarimide moiety. To increase the stability of a hydrazone group of a trigger element, a trigger element can be varied by chemical modification, e.g., substitution, allowing tuning to achieve more efficient release in the lysosome with a minimized loss in circulation.
In some embodiments, a trigger element comprises a hydrazone moiety having one of the following structures:
Figure imgf000074_0001
wherein R is selected from C1-C6 alkyl, aryl, and -O-C1-C6 alkyl
Hydrazone-containing trigger elements can contain additional cleavage sites, such as additional acid-labile cleavage sites and/or enzymatically labile cleavage sites (e.g., a disulfide). Conjugates and compounds including exemplary hydrazone-containing trigger elements can include, for example, the following structure:
Figure imgf000074_0002
wherein R is selected from C1-C6 alkyl, aryl, and -O-C1-C6 alkyl
Other acid-labile groups that can be included in trigger elements include c/.v-aconityl- containing linkers. rv.s-Aconityl chemistry can use a carboxylic acid juxtaposed to an amide bond to accelerate amide hydrolysis under acidic conditions.
Trigger elements can also include a disulfide group. Disulfides can be thermodynamically stable at physiological pH and release a isoindolinone-glutarimide moiety upon internalization of the conjugate of Structure (II) into cells, wherein the cytosol can provide a significantly more reducing environment compared to the extracellular environment. Scission of disulfide bonds can require the presence of a cytoplasmic thiol cofactor, such as (reduced) glutathione (GSH), such that disulfide-containing trigger element can be reasonably stable in circulation, selectively releasing a isoindolinone-glutarimide moiety in the cytosol. The intracellular enzyme protein disulfide isomerase, or similar enzymes capable of cleaving disulfide bonds, can also contribute to the preferential cleavage of disulfide bonds inside cells. GSH can be present in cells in the concentration range of 0.5-10 mM compared with a significantly lower concentration of GSH or cysteine, the most abundant low-molecular weight thiol, in circulation at approximately 5 pM. Tumor cells, where irregular blood flow can lead to a hypoxic state, can result in enhanced activity of reductive enzymes and therefore even higher glutathione concentrations. The in vivo stability of a disulfide-containing trigger element can be enhanced by chemical modification of a trigger element, e.g., use of steric hindrance adjacent to the disulfide bond.
A trigger element can also be a B-glucuronic acid-based linker. Facile release of a isoindolinone-glutarimide moiety, can be realized through cleavage of the B-glucuronide glycosidic bond by the lysosomal enzyme B-glucuronidase. This enzyme can be abundantly present within lysosomes and can be overexpressed in some tumor types, while the enzyme activity outside cells can be low. B-Glucuronic acid-based linkers can be used to circumvent the tendency of a conjugate to undergo aggregation due to the hydrophilic nature of B-glucuronides. In some embodiments, a trigger element comprises a B-glucuronic acid
The following scheme depicts the release of a isoindolinone-glutarimide moiety (D) from a conjugate of Structure (II) containing a B-glucuronic acid-based trigger element:
Figure imgf000075_0001
A variety of cleavable 0 -glucuronic acid-based linkers useful for linking drugs such as auristatins, camptothecin analogues, doxorubicin analogues, CBI minor-groove binders, and psymberin to antibodies have been described. Accordingly, these P-glucuronic acid-based trigger elements are used in the conjugates of Structure (II). In some embodiments, a trigger element comprises a P-galactoside-based linker. 0-Galactoside is present abundantly within lysosomes, while the enzyme activity outside cells is low.
A trigger element may include one or more peptides. In some embodiments, a peptide can be selected to contain natural amino acids, unnatural amino acids, or any combination thereof. In some embodiments, a peptide can be a tripeptide or a dipeptide. In particular embodiments, a dipeptide comprises L-amino acids, such as Val-Cit; Cit-Val; Ala-Ala; Ala-Cit; Cit-Ala; Asn-Cit; Cit-Asn; Cit-Cit; Val-Glu; Glu-Val; Ser-Cit; Cit-Ser; Lys-Cit, Cit-Lys; Asp- Cit; Cit-Asp; Ala-Vai; Vai-Ala; Phe-Lys; Lys-Phe; Val-Lys; Lys-Val; Ala-Lys; Lys-Ala; Phe- Cit; Cit-Phe; Leu-Cit; Cit-Leu; Ile-Cit; Cit-Ile; Phe-Arg; Arg-Phe; Cit-Trp; and Trp-Cit, or salts thereof.
Trigger elements and immolative groups are known (WO 2022/076905) which is hereby incorporated by reference in their entirety. One immolative unit can be a bifunctional para- aminobenzyl alcohol group, which can link to a trigger element through an amino group, forming an amide bond, while an amine containing isoindolinone-glutarimide moiety can be attached through carbamate functionalities to the benzylic hydroxyl group of the para- aminobenzyl alcohol (to give a //-amidobenzyl carbamate. The resulting pro-compound can be activated upon protease-mediated cleavage, leading to a 1,6-elimination reaction releasing the unmodified isoindolinone-glutarimide moiety and remnants of the antibody-linker.
In some embodiments, an immolative unit (IM) comprises paraaminobenzyloxycarbonyl, an aminal, a hydrazine, a disulfide, an amide, an ester, a hydrazine, a phosphotriester, a diester, a P-glucuronide, a double bond, a triple bond, an ether bond, a ketone, a diol, a cyano, a nitro, a quaternary amine, or combinations thereof In certain embodiments, an immolative unit comprises a paramethoxybenzyl, a dialkyldialkoxysilane, a diaryldialkoxysilane, an orthoester, an acetal, an optionally substituted p-thiopropionate, a ketal, a phosphorami date, a hydrazone, a vinyl ether, an imine, an aconityl, a trityl, a polyketal, a bis- arylhydrazone, a diazobenzene, a vivinal diol, a pyrophosphate diester, or combinations thereof.
In certain embodiments, an immolative unit (IM) comprises one of the following structures:
Figure imgf000076_0001
In some embodiments, an immolative unit comprises the following structure:
Figure imgf000077_0001
wherein:
R6a, R6b, R6C, and R6d are independently hydrogen, an optionally substituted alkyl, an optionally substituted aryl, or optionally substituted heteroaryl, or
R6a and R6c together with the nitrogen and carbon atoms to which they are attached form azetidinyl, pyrrolodinyl, piperidinyl, or homopiperidinyl and R6d is hydrogen; and
Y1 is -O-, -S-, or -NR6b-;
In certain embodiments, an immolative unit comprises the following structure:
Figure imgf000077_0002
wherein:
R6e, R6f, R6g, and R511 are independently hydrogen, an optionally substituted alkyl, an optionally substituted aryl, or optionally substituted heteroaryl, or
R6a and R6c together with the nitrogen and carbon atoms to which they are attached form azetidinyl, pyrrolodinyl, piperidinyl, or homopiperidinyl and R6d is hydrogen; and
Y2 is -O-, -S-, or -NR6f-;
In some embodiments, an immolative unit comprises the following structure:
Figure imgf000077_0003
wherein: each occurrence of R10 is independently alkyl, alkoxy, or halo;
R11 is hydrogen, alkyl, or -(CH2CH2O)Z3-CH3;
R12 is hydrogen or alkyl;
R13 is hydrogen or alkyl; zl is 0 or 1; z2 is 0, 1, 2, 3, or 4; and z3 is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; or
In some embodiments, an immolative unit comprises one of the following structures:
Figure imgf000078_0001
wherein:
R14a, R14b, R14C, R14d, R14e, and R14f are each independently hydrogen, alkyl, hydroxyalkyl, or alkoxyalkyl; z4, z5, z6, and z7 are each independently 1, 2, 3, 4, 5, or 6;
In some embodiments, an immolative unit comprises one of the following structures:
Figure imgf000078_0003
wherein: z8 and z9 are each independently 1, 2, 3, 4, 5, or 6; or
In certain embodiments, an immolative unit comprises one of the following structures:
Figure imgf000078_0002
Figure imgf000079_0001
wherein: each occurrence of R15 is independently H, methyl, ethyl, isopropyl, tert-butyl, or phenyl;
Y3 is O or CH2; and q5 is an integer ranging from 1-5.
In some embodiments, an immolative unit has a molecular weight greater than 150 g/mole, greater than 200 g/mole, greater than 300 g/mole, greater than 400 g/mole, greater than 500 g/mole, greater than 600 g/mole, greater than 700 g/mole, greater than 800 g/mole, greater than 900 g/mole, or greater than 1000 g/mole. In some embodiments, an immolative unit has a molecular weight less than 150 g/mole, less than 200 g/mole, less than 300 g/mole, less than 400 g/mole, less than 500 g/mole, less than 600 g/mole, less than 700 g/mole, less than 800 g/mole, less than 900 g/mole, or less than 1000 g/mole.
In some embodiments, an immolative unit and a trigger element together have the following structure:
Figure imgf000079_0002
wherein a trigger element is denoted with “peptide” and comprises from one to ten amino acids, and * represents the point of attachment to a isoindolinone-glutarimide moiety. In some embodiments, the peptide comprises Val-Cit or Val-Ala. Heterocyclic variants (e.g., pyridinyl, pyrimidinyl, etc.) of this immolative unit may also be used.
In some embodiments, an immolative unit contains a phenol group that is covalently bound to the remainder of the molecule through the phenolic oxygen. One such immolative unit relies on a methodology in which a diamino-ethane “Space Link” is used in conjunction with traditional “PABO”-based immolative unit to deliver phenols.
In some embodiments, a trigger element can include non-cleavable portions or segments. Polyethylene glycol (PEG) and related polymers can be included with cleavable groups such as a disulfide, a hydrazone or a dipeptide to form an immolative group and/or trigger element.
Other degradable linkages that can be included in immolative units can include esters. Esters can be formed by the reaction of PEG carboxylic acids or activated PEG carboxylic acids with alcohol groups on a isoindolinone-glutarimide moiety such ester groups can hydrolyze under physiological conditions to release a isoindolinone-glutarimide moiety Other hydrolytically degradable linkages can include carbonate linkages, imine linkages resulting from reaction of an amine and an aldehyde; phosphate ester linkages formed by reacting an alcohol with a phosphate group; acetal linkages that are the reaction product of an aldehyde and an alcohol; orthoester linkages that are the reaction product of a formate and an alcohol; and oligonucleotide linkages formed by a phosphoramidite group, including at the end of a polymer, and a 5’ hydroxyl group of an oligonucleotide.
In some embodiments, a trigger element, immolative unit (IM), and isoindolinone- glutarimide moiety (IG) together have the following structure:
Figure imgf000080_0001
Figure imgf000081_0001
wherein
Figure imgf000081_0002
indicates an attachment site to the remainder of the molecule (i.e., a compound of Structure (I) or conjugate of Structure (II)) and an isoindolinone-glutarimide moiety (IG) . Amino acids of embodiments above may be replaced or used in addition to other amino acids, in some embodiments, a trigger element is Asn-Cit, Arg-Cit, Val-Glu, Ser-Cit, Lys- Cit, Asp-Cit, Phe-Lys, Glu-Val-Cit, Glu-Val-Cit, Glu-Glu-Val-Cit, or Glu-Glu-Glu-Val-Cit, and an immolative unit is PABC.
In some embodiments, the phenyl portion of the PABC is substituted with one or more substituents. In some embodiments, the substituents have one of the following structures:
Figure imgf000081_0003
In some embodiments, an immolative group comprises one of the following structures:
Figure imgf000081_0004
In some embodiments, a trigger element, an immolative unit (IM), and isoindolinone- glutarimide moiety (IG) together have one of the following structures:
Figure imgf000082_0001
In some embodiments, an immolative unit (IM) has a structure selected from the following:
Figure imgf000083_0001
The structures above show a substitution pattern of 1, 3, 4 on the phenyl ring of an immolative unit (IM). In some embodiments, a substitution pattern may be 1, 2, 4 (i.e., 1 being a linkage to an IG, 2 being a linkage to the remainder of the molecule and 4 being a linkage to the carbohydrate) or 1, 3, 5 (i.e., 1 being a linkage to an IG, 3 being a linkage to the remainder of the molecule and 4 being a linkage to the carbohydrate).
Although cleavable linkers (e.g., linkers with trigger elements or immolative unit) can provide certain advantages, linkers need not be cleavable. For non-cleavable linkers, an IG release may not depend on the differential properties between the plasma and some cytoplasmic compartments. The release of an IG can occur after internalization of the conjugate of Structure (II) via antigen-mediated endocytosis and delivery to lysosomal compartment, where the targeting moiety (or binding fragment thereof) can be degraded to the level of amino acids through intracellular proteolytic degradation. This process can release a isoindolinone- glutarimide moiety or isoindolinone-glutarimide moiety derivative. A isoindolinone-glutarimide moiety or isoindolinone-glutarimide moiety derivative can be more hydrophilic and less membrane permeable, which can lead to less bystander effects and less non-specific toxicities compared to conjugates with a cleavable linker. Conjugates with non-cleavable linkers can have greater stability in circulation than conjugates with cleavable linkers Non-cleavable linkers can include alkylene chains, or can be polymeric, such as, for example, based upon polyalkylene glycol polymers, amide polymers, or can include segments of alkylene chains, poly alkylene glycols and/or amide polymers. The linker can contain a polyethylene glycol segment having from 1 to 6 ethylene glycol units. In some embodiments, -L1-R.1 or L2-R2 comprises a linker that is non-cleavable in vivo.
In some embodiments, a trigger element and an immolative unit (IM) together comprise one of the following structures:
Figure imgf000084_0001
Figure imgf000085_0001
In some embodiments, a heteroalkylene element comprises polyethylene glycol or polypropylene glycol. In some embodiments, a heteroalkylene element comprises one of the following structures:
Figure imgf000086_0001
wherein: each occurrence of R5b, R5c R5d, and R5e is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, hydroxyl, cyano, nitro, thiol, carboxyalkyl, alkyl-S(O)3H, alkyl-O-P(O)3H, alkyl-P(O)3H, -O-carboxyalkyl, -O-alkyl-S(O)3H, -O-alkyl-O-P(O)3H, -O-alkyl-P(O)3H, -S(O)3H, -OP(O)3H, and -P(O)3H, each occurrence of ql is, independently an integer from 1-24. In some embodiments, R5b, R5c R5d, and R5e are all hydrogen.
In some embodiments, a polar cap comprises one or more charged amino acid, one or more polyol, or combinations thereof. In certain embodiments, a polar cap comprises a diol, a triol, a tetraol, or combinations thereof. In some embodiments, a polar cap comprises glycerol, trimethylolpropane, pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof. In certain embodiments, a polar cap comprises one or more natural amino acids. In some embodiments, a polar cap comprises one or more non-natural amino acids. In some embodiments, a polar cap comprises one or more non-natural amino acids and one or more natural amino acids. In certain embodiments, a polar cap comprises serine, threonine, cysteine, proline, asparagine, glutamine, lysine, arginine, histidine, aspartate, glutamate, 4- hydroxyproline, 5-hydroxylysine, homoserine, homocysteine, ornithine, beta-alanine, statine, or gamma aminobutyric acid In certain embodiments, a polar cap comprises aspartic acid, serine, glutamic acid, serine-beta-glucose, or combinations thereof.
In some embodiments, a polar cap comprises one of the following structures:
Figure imgf000087_0001
In more embodiments, a polar cap has one of the following structures, including combinations thereof:
Figure imgf000087_0002
Figure imgf000088_0001
In more embodiments, L1, L2, or L3 comprise a linker selected from the group alkylene, alkylene-!/-, alkenylene, alkenylene-I?-, alkynylene, alkynylene-La-, -La-, -La-alkylene-La-, -La- alkenylene-La-, -La-alkynylene-La-, and combinations thereof, wherein each alkylene, alkenylene, and alkynylene is optionally substituted and each occurrence of La is independently selected from -O-, -S-, -N(R7)-, -C(O)-, -C(S)-, -C(O)O-, -OC(O)-, -OC(O)O-, -C(O)N(R7)-, -N(R7)C(O)-, -C(O)N(R7)C(O)-, -C(O)N(R7)C(O)N(R7), -N(R7)C(O)N(R7)-, -N(R7)C(O)O-, -OC(O)N(R7)-, -C(NR7)-, -N(R7)C(NR7)-, -C(NR7)N(R7)-,
-N(R7)C(NR7)N(R7)-, -S(O)2- -OS(O)-, -S(O)O-, -S(O), -OS(O)2-, -S(O)2O, -N(R7)S(O)2-, -S(O)2N(R7)-, -N(R7)S(O)-, -S(O)N(R7)-, -N(R7)S(O)2N(R7)-, and -N(R7)S(O)N(R7)- and R7 is independently selected at each occurrence from hydrogen, -NH2, -C(O)OCH2C6Hs; and Cnio alkyl, C2 10 alkenyl, C2-10 alkynyl, C3-12 cycloalkyl, and 3- to 12-membered heterocycle, each of which is optionally substituted with one or more substituents independently selected from halo, hydroxyl, cyano, nitro, amino, oxo, thioxo, -C(O)OCH2C6H5, -NHC(O)OCH2C6H5, Cnio alkyl, C1-10 haloalkyl, C1-10 alkoxy, C2-10 alkenyl, C2-10 alkynyl, C3-12 cycloalkyl, and 3- to 12- membered heterocyclyl.
In some embodiments, each L1, L2, or L3 is optionally substituted with one or more substituents selected from alkyl, alkenyl, alkynyl, halo, hydroxyl, cyano, -OR8, -SR8, amino, aminyl, amido, cycloalkyl, aryl, heterocyclyl, heteroaryl, cycloclkylalkyl, arylalkyl, heterocyclylalkyl, heteroarylalkyl, -C(O)R8, -C(O)N(R8)2, -N(R8)C(O)R8, -C(O)OR8, -OC(O)R8, -S(O)R8, -S(O)2R8, -P(O)(OR8)2, -OP(O)(OR8)2, nitro, oxo, thioxo, =N(R8), or cyano, and R8 is hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heterocyclyl, heteroaryl, cycloclkylalkyl, arylalkyl, heterocyclylalkyl, or heteroarylalkyl.
In some embodiments, L1, L2, or L3 are independently selected from the following structures:
Figure imgf000089_0001
wherein:
Ra is hydrogen or alkyl; each occurrence of Lb is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or a combination thereof; and each occurrence of Lc is independently an optionally substituted alkylene linker and provided that at least one of L1, L2, or L3 has the following structure:
Figure imgf000089_0002
In some embodiments, L1 and L2 are independently selected from the following structures:
Figure imgf000089_0003
wherein:
Ra is hydrogen or alkyl; each occurrence of Lb is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or a combination thereof; each occurrence of Lc is independently an optionally substituted alkylene linker; provided that at least one of L1 or L2has the following structure:
Figure imgf000089_0004
In more embodiments, L2 has the following structure:
Figure imgf000090_0001
In some embodiments, Lc is unsubstituted. In some embodiments, Lc is a C1-Cg alkylene.
In some more embodiments, Lc is a C2-C4 alkylene. In some embodiments, Lc is a straight C1-C6 alkylene. In more embodiments, Lc is a straight, unsubstituted C1-C6 alkylene. In more embodiments, Lc is a straight, unsubstituted C2-C4 alkylene.
In some embodiments, the isoindolinone-glutarimide linker compound has one of the following structures (la- 1), (la-2), (la-3), (la-4), (Ia-5),or (la-6):
Figure imgf000090_0002
each occurrence of Lb is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or combinations thereof; and q6 is 0, 1, or 2. In some embodiments, q6 is 1 and Lb is gly-gly.
In certain embodiments, the isoindolinone-glutarimide linker compound has one of the following Structures (Ic-1), (Ic-2), (Ic-3), or (Ic-4):
Figure imgf000091_0001
(Ic-3) (Ic-4) wherein: each occurrence of Lb is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or combinations thereof; and q7 is 1, 2, or 3.
In some embodiments, q7 is 2.
In some embodiments, the isoindolinone-glutarimide linker compound has the following Structure (Id), (le), (If), or (Ig):
Figure imgf000092_0001
(If) (Ig) wherein: each occurrence of Lb is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or combinations thereof; q8 is 0, 1, or 2; and q9 is 0, 1, or 2.
In some embodiments, q9 is 0 and q8 is 1.
In some embodiments, the isoindolinone-glutarimide linker compound has one of the following Structures (Ih) or (li):
Figure imgf000092_0002
wherein: each occurrence of Lb is independently a direct bond, an optionally substituted alkylene linker, an optionally substituted heteroalkylene linker, a heteroatomic linker, or combinations thereof.
In some embodiments, Lb is a direct bond, an optionally substituted alkylene linker or an optionally substituted heteroalkylene linker.
In some embodiments, Lb is a direct bond or has one of the following structures:
Figure imgf000093_0001
wherein: each occurrence of Rb is independently hydrogen, alkyl, hydroxyalkyl, or alkoxyalkyl.
In some embodiments, each occurrence of Rb is -CH3.
In some embodiments, L1 or L2 has the following structure:
Figure imgf000093_0002
wherein:
** shows a bond to X1, X2, X3, X4 or X5
In certain embodiments, X2 is C-L^R1 and X3 is C-L2-R2. In some embodiments, X3 is C-L'-R1 and X2 is C-L2-R2. In some embodiments, X1, X4, and X5 are all CR3. In some embodiments, X1, X4, and X3 are all CH.
ISOINDOLINONE-GLUTARIMIDE LINKER COMPOUNDS
The conjugates of the invention are prepared by conjugation of an antibody with an isoindolinone-glutarimide linker compound, IG-L.
An isoindolinone-glutarimide linker compound is selected from Formulae Ila and Hb :
Figure imgf000094_0001
wherein: m is 1 or 2;
X1 is selected from the group consisting of CH2, C(=O) and N=N;
X2 is independently selected from the group consisting of F, Cl, Br, I, -CN, C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), -(C1-C12 heteroalkyldiyl)-(C6-Czo aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), (C1-C6 alkyl diyl)-(C6-C20 aryl), -(C1-C6 alkyl diyl)-NRaRb, -(C1-C6 alkyldiyl)-ORa, (C1-C6 alkyldiyl)-(C3-C20 carbocyclyl), (C1-C6 alkyldiyl)-(C2-C20 heterocyclyl), (C1-C6 alkyldiyl)-(C1-C20 heteroaryl), C6-C20 aryl, C3-C20 carbocyclyl, C2-C20 heterocyclyl, C1-C20 heteroaryl, -C(=NH)NH(OH), -C(=NH)NH2, -C(=O)NRaRb, -C(=O)NRa-NRaRh, -C(=O)NH(C1-C6 alkyldiyl)-NRaRb, -C(=O)ORa, -NRaRb, -NO2, -ORa, -OC(=O)Ra, -SRa, -S(O)Ra, -S(O)2Ra, -S(O)2NRa, and -S(O)3H;
Ra is independently selected from H, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl;
Rb is independently selected from H, OH, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl; n is 0, 1, 2, 3, or 4,
X3 is selected from the group consisting of a bond, O, C1-C12 alkyldiyl, C2-C12 alkenyldiyl, C2-C12 alkynyldiyl, C1-C12 heteroalkyldiyl, -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl)-, -(C1-C6 alkyl diyl)NRa-, -(C1-C6 alkyldiyl)O-, -(C1-C6 alkyldiyl)-(C3-C20 carbocyclyldiyl)-, -(C1-C6 alkyl diyl)-(C2-C20 heterocyclyldiyl)-, -(C1-C6 alkyldiyl)-(C1-C20 heteroaryldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl)-, C6-C20 aryldiyl, C3-C20 carb ocyclyl diyl, C2-C20 heterocyclyldiyl, and C1-C20 heteroaryl diyl;
X4 is selected from the group consisting of H, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl);
X5 is selected from the group consisting of C1-C12 alkyldiyl, C2-C12 alkenyldiyl, C2-C12 alkynyldiyl, C1-C12 heteroalkyldiyl, -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl), -(C1-C6 alkyldiyl)-(C6-C20 atyldiyl)-O-(C2-C20 heterocyclyl), -(C1-C6 alkyldiyl)NRa-, -(C1-C6 alkyldiyl)O-, -(C1-C6 alkyldiyl)-(C3-C20 carb ocyclyl diyl), -C1-C6 alkyl diyl)-(C2-C20 heterocyclyldiyl), -(C1-C6 alkyldiyl)-(C1-C20 heteroaryldiyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl), -(C1-C12 heteroalkyl diyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl), C6-C20 aryldiyl, C3-C20 carbocyclyldiyl, C2-C20 heterocyclyldiyl, and C1-C20 heteroaryldiyl;
L is the antibody linker; and
Z is:
Figure imgf000095_0001
where the wavy line is the attachment to L; wherein each alkyl, alkyldiyl, alkenyl, alkenyldiyl, alkynyl, alkynyldiyl, heteroalkyl, heteroalkyldiyl, aryl, aryldiyl, carbocyclyl, carbocyclyldiyl, heterocyclyl, heterocyclyldiyl, heteroaryl, and heteroaryl diyl is independently and optionally substituted with one or more groups selected from F, Cl, Br, I, -CN, -CH3, -CH2CH3, -CH=CH2, -C=CH, -C =CCI I3, - CH2CH2CH3, -CH(CH3)2, -CH2CH(CH3)2, -CH2OH, -CH2OCH3, -CH2CH2OH, -C(CH3)2OH, -CH(OH)CH(CH3)2, -C(CH3)2CH2OH, -CH2CH2SO2CH3, -CH2OP(O)(OH)2, -CH2F, -CHF2, -CF3, -CH2CF3, -CH2CHF2, -CH(CH3)CN, -C(CH3)2CN, -CH2CN, -CH2NH2, - CH2NHSO2CH3, -CH2NHCH3, -CH2N(CH3)2, -CO2H, -COCH3, -CO2CH3, -CO2C(CH3)3, - COCH(OH)CH3, -CONH2, -CONHCH3, -CON(CH3)2, -C(CH3)2CONH2, -NH2, -NHCH3, - N(CH3)2, -NHCOCH3, -N(CH3)COCH3, -NHS(O)2CH3, -N(CH3)C(CH3)2CONH2, - N(CH3)CH2CH2S(O)2CH3, -NHC(=NH)H, -NHC(=NH)CH3, -NHC(=NH)NH2, - NHC(=O)NH2, -NO2, =0, -OH, -OCH3, -OCH2CH3, -OCH2CH2OCH3, -OCH2CH2OH, - OCH2CH2N(CH3)2, -OCH2F, -OCHF2, -OCF3, -OP(O)(OH)2, -S(O)2N(CH3)2, -SCH3, - S(O)2CH3, and -S(O)3H.
An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein L has the formula:
-Str'-(PEP)„-(IM)m- wherein:
Str1 is a stretcher unit covalently attached to Z;
PEP is a protease-cleavable, peptide unit covalently attached to Str1 and IM;
IM is an immolative unit covalently attached the isoindolinone-glutarimide moiety; n is 0 or 1; and m is 0 or 1
An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein PEP-IM is selected from the structures:
Figure imgf000096_0001
wherein ** indicates the point of attachment to the isoindolinone-glutarimide moiety.
An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein Z-Str1 has the structure:
Figure imgf000097_0001
wherein:
** indicates the point of attachment to PEP or the isoindolinone-glutarimide moiety;
R1 is selected from the group consisting of C1-C12 alkyldiyl, C1-C12 alkyldiyl-C(=O), C1- C12 alkyldiyl-NH, (CH2CH2O)r, (CH2CH2O)r-C(=O), (CH2CH2O)r-CH2, C6-C20 aryldiyl, (C6- C20 aryldiyl)-(C1-C12 alkyldiyl), and (C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl); r is an integer ranging from 1 to 10; and alkyldiyl, heteroalkyldiyl, and aryldiyl are independently and optionally substituted with one or more groups selected from F, Cl, -CN, -NH2, -CH2NH2, -OH, -OCH3, -OCH2CH3, - OCH2CH2OCH3, -OCH2CH2OH, -OCH2CH2N(CH3)2, -OCH2F, -OCHF2, -OCF3, - OP(O)(OH)2, -S(O)2N(CH3)2, -SCH3, -S(O)2CH3, -S(O)3H, and a solubilizing unit.
An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein R1 is selected from -(CH2)s-, and -CH2CH2-.
An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein R1 is selected from Cg-C20 aryldiyl, (C6-C20 aryldiyl)-(C1-C12 alkyldiyl), and (C6-C20 aryldiyl)-(C1-C12 heteroalkyl diyl).
An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein Z-Str1 has the structure:
Figure imgf000097_0002
wherein:
L1 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl;
Lla is selected from an amino acid, amino, hydroxyl, halide, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof; o is 0, 1, or 2;
L2 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl; and
** indicates the point of attachment to PEP or to the isoindolinone-glutarimide moiety. An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein L1 or L2 comprise a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C1-C40 heteroalkyl, and a glycoside, or combinations thereof.
An exemplary embodiment of the isoindolinone-glutarimide linker compound includes wherein L1 or L2 is selected from (N(CH3)CH2C(=O))q, (N(CH3)CH2CH2C(=O))q, N(CH3)CH2CH2OCH2CH2C(=O))q, (CH2CH2O)q, (CH2CH2O)q-C(=O), and (CH2CH2O)q-CH2, where q is an integer from 2 to 20.
The invention includes all reasonable combinations, and permutations of the features, of the Formula II embodiments.
The linker units comprise functional groups and subunits which affect stability, permeability, solubility, and other pharmacokinetic, safety, and efficacy properties of the antibody conjugates. The linker unit includes a reactive functional group which reacts, i e. conjugates, with a reactive functional group of the antibody. For example, a nucleophilic group such as a lysine side chain amino of the antibody reacts with an electrophilic reactive functional group of the isoindolinone-glutarimide-linker, IG-L compound to form the antibody conjugate. Also, for example, a cysteine thiol of the antibody reacts with a maleimide or bromoacetamide group of the IG-L compound to form the antibody conjugate.
Considerations for the design of the antibody conjugates of the invention include: (1) preventing the premature release of the isoindolinone-glutarimide (IG) moiety during in vivo circulation and (2) ensuring that a biologically active form of the IG moiety is released at the desired site of action at an adequate rate. The complex structure of the antibody conjugate together with its functional properties requires careful design and selection of every component of the molecule including antibody, conjugation site, linker structure, and the IG moiety. The linker determines the mechanism and rate of isoindolinone-glutarimide moiety release.
Generally, the linker unit (L) may be cleavable or non-cleavable. Cleavable linker units may include a peptide sequence which is a substrate for certain proteases such as Cathepsins which recognize and cleave the peptide linker unit, separating the isoindolinone-glutarimide moiety from the antibody (Caculitan NG, et al (2017) Cancer Res. 77(24):7027-7037).
Cleavable linker units may include labile functionality such as an acid-sensitive disulfide group (Kellogg, BA et al (2011) Bioconjugate Chem. 22, 717-727; Ricart, A. D. et al (2011) Clin. Cancer Res. 17, 6417-6427; Pillow, T., et al (2017) Chem. Sci. 8, 366-370, Zhang D, et al (2016) ACS Med Chem Lett. 7(1 l):988-993).
In some embodiments , the linker is non-cleavable under physiological conditions . As used herein , the term “physiological conditions” refers to a temperature range of 20-40 degrees C6lsius , atmospheric pressure ( i.e. , 1 atm) , a pH of about 6 to about 8 , and the one or more physiological enzymes, proteases, acids , and bases. One advantage of a non-cleavable linker between the antibody and IG moiety in an antibody conjugate is minimizing premature isoindolinone-glutarimide moiety release and corresponding toxicity.
In some embodiments, the linker comprises a trivalent, branch point as part of an amino acid unit (e.g., lysine) wherein additional linker units are attached via the side chain amine of lysine or linked to other sites of an amino acid unit (US 11, 173,214). A similar motif could be utilized with a glutamic acid of an amino acid unit. An exemplary additional linker unit is a monovalent solubilizing unit such as one or more units of polyglycine, poly sarcosine, polyethyleneoxy (PEG), C1-C40 heteroalkyl, and a glycoside, or combinations thereof. The solubilizing unit may bear a group at the terminus such as an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
In some embodiments, a solubilizing unit is a polysarcosine with one of the following structures:
Figure imgf000099_0001
In some embodiments, an amino acid unit or peptide unit comprises one or more amino acids selected from the group consisting of glycine, alanine, serine, threonine, cysteine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tyrosine, tryptophan, aspartic acid, glutamic acid, asparagine, glutamine, histidine, lysine, arginine, sarcosine, and beta-alanine.
In one embodiment, the invention includes an amino acid unit or a peptide linking unit, i.e. L or linker, between the antibody and the IG moiety, comprising a peptide comprising a linear sequence of specific amino acid residues which can be selectively cleaved by a protease such as a cathepsin, caspase, a tumor-associated elastase enzyme or an enzyme with proteaselike or elastase-like activity. The peptide radical may be two to about twelve amino acids. Enzymatic cleavage of a bond within the peptide linker releases an active form of the IG moiety. This leads to an increase in the tissue specificity of the antibody conjugates and thus to an additional decrease of toxicity of the conjugates according to the invention in other tissue types. Release of an active IG moiety from an antibody conjugate can occur due to the action of lysosomal proteases such as cathepsin and plasmin which may be present at elevated levels in certain tumor tissues. The lysosomal enzyme can be, for example, cathepsin B, P-glucuronidase, or P-galactosidase. A cleavable peptide of a peptide linker unit can be selected from tetrapeptides such as Gly-Phe-Leu-Gly, Ala-Leu-Ala-Leu, and Gly-Gly-Phe-Gly; tripeptides such as Glu-Val-Cit, and Ala- Ala-Ala; and dipeptides such as Val-Cit, Vai-Ala, Ala-Ala, and Phe-Lys.
The linker provides sufficient stability of the antibody conjugate in biological media, e.g. culture medium or serum and, at the same time, the desired intracellular action within tumor tissue as a result of its specific enzymatic or hydrolytic cleavability with release of the IG moiety, i.e. “isoindolinone-glutarimide moiety”.
The enzymatic activity of a protease, cathepsin, or elastase can catalyze cleavage of a covalent bond of the antibody conjugate under physiological conditions The enzymatic activity being the expression product of cells associated with tumor tissue The enzymatic activity on the cleavage site of the targeting peptide converts the antibody conjugate to an active IG drug free of targeting antibody and linking group. The cleavage site may be specifically recognized by the enzyme Cathepsin or elastase may catalyze the cleavage of a specific peptidic bond between the C-terminal amino acid residue of the specific peptide and the IG moiety of the antibody conjugate.
In one embodiment, the invention includes a linking unit, i.e. L or linker, between the antibody and the IG moiety, comprising a substrate for glucuronidase (Jeffrey SC, et al (2006) Bioconjug Chem. 17(3):831-40; US11,413,353; US11,173,214), or sulfatase (Bargh ID, et al (2020) Chem Sei. 1 1 (9):2375-2380) cleavage. In particular, L includes a Glue unit and comprises a formula selected from:
Figure imgf000100_0001
Specific cleavage of the antibody conjugate takes advantage of the presence of tumor infiltrating cells of the immune system and leukocyte- secreted enzymes, to promote the activation of an anticancer drug at the tumor site.
Reactive electrophilic reactive functional groups (Q in Formula II) suitable for the isoindolinone-glutarimide linker compound (IG-L) include, but are not limited to, N- hydroxysuccinimidyl (NHS) esters and N-hydroxysulfosuccinimidyl (sulfo-NHS) esters (amine reactive); carbodiimides (amine and carboxyl reactive); hydroxymethyl phosphines (amine reactive); mal eimides (thiol reactive); halogenated acetamides such as A'-iodoacetamides (thiol reactive); aryl azides (primary amine reactive); fluorinated aryl azides (reactive via carbon- hydrogen (C-H) insertion); pentafluorophenyl (PFP) esters (amine reactive); tetrafluorophenyl (TFP) and sulfotetrafluorophenyl (STP) esters (amine reactive); imidoesters (amine reactive); isocyanates (hydroxyl reactive); vinyl sulfones (thiol, amine, and hydroxyl reactive); pyridyl disulfides (thiol reactive); and benzophenone derivatives (reactive via C-H bond insertion). Further reagents include, but are not limited, to those described in Hermanson, Bioconjugate Techniques 2nd Edition, Academic Press, 2008.
Some linkers such as those comprising peptide units and substrates for protease may be labile in the blood stream, thereby releasing unacceptable amounts of the drug prior to internalization in a target cell (Khot, A et al (2015) Bioanafysis 7(13): 1633-1648) Other linkers may provide stability in the bloodstream, but intracellular release effectiveness may be negatively impacted. Linkers that provide for desired intracellular release may have poor stability in the bloodstream. In addition, in standard conjugation processes, the amount of adjuvant/drug moiety loaded on the antibody, i.e. drug loading, the amount of aggregate that is formed in the conjugation reaction, and the yield of final purified conjugate that can be obtained are interrelated. Aggregate formation may be correlated to the number of equivalents of drug moieties conjugated to the antibody. Under high drug loading, formed aggregates must be removed for therapeutic applications. As a result, drug loading-mediated aggregate formation decreases antibody conjugate yield and can render process scale-up difficult
The invention includes all reasonable combinations, and permutations of the features, of the Formula Ila and Hb embodiments.
In some embodiments, the isoindolinone-glutarimide linker compound has one of the following structures:
Figure imgf000101_0001
Figure imgf000102_0001
Figure imgf000103_0001
wherein.
Rlb is an isoindolinone-glutarimide moiety (IG); R2b has one of the following structures:
Figure imgf000104_0001
Llg has one of the following structures:
Figure imgf000105_0001
Figure imgf000106_0001
In some embodiments, the isoindolinone-glutarimide linker compound has one of the following structures:
Figure imgf000106_0002
Figure imgf000107_0001
Figure imgf000108_0001
Figure imgf000109_0001
In some embodiments, the isoindolinone-glutarimide linker compound has one of the following structures:
Figure imgf000109_0002
Figure imgf000110_0001
Figure imgf000111_0001
Figure imgf000112_0001
Figure imgf000113_0001
Figure imgf000114_0001
.0
Figure imgf000115_0001
Figure imgf000116_0001
In some embodiments, the isoindolinone-glutarimide linker compound has one of the following structures:
Figure imgf000116_0002
Figure imgf000117_0001
Figure imgf000118_0001
as a stereoisomer, enantiomer or tautomer thereof or a mixture thereof; or a pharmaceutically acceptable salt, solvate or prodrug thereof.
Exemplary embodiments of isoindolinone-glutarimide linker compounds (IG-L) are shown in Table 2. Each IG-L compound was prepared and characterized by mass spectrometry and shown to have the mass indicated. The IG-L compounds of Table 2 demonstrate the surprising and unexpected property of targeted protein degradation which may predict useful therapeutic activity to treat cancer and other disorders when conjugated to an antibody.
Table 2 Isoindolinone-glutarimide linker compounds (IG-L)
Figure imgf000118_0002
Figure imgf000119_0001
Figure imgf000120_0001
Figure imgf000121_0001
Figure imgf000122_0001
Figure imgf000123_0001
Figure imgf000124_0001
Figure imgf000125_0001
Figure imgf000126_0001
Figure imgf000127_0001
Figure imgf000128_0001
Figure imgf000129_0001
Figure imgf000130_0001
Figure imgf000131_0001
Figure imgf000132_0001
Figure imgf000133_0001
Figure imgf000134_0001
Figure imgf000135_0001
Figure imgf000136_0001
Figure imgf000137_0001
Figure imgf000138_0001
Figure imgf000139_0001
Figure imgf000140_0001
Figure imgf000141_0001
Figure imgf000142_0001
ISOINDOLINONE-GLUTARIMIDE ANTIBODY CONJUGATES
The isoindolinone-glutarimide antibody conjugates (IGAC) of the invention induce target-specific protein degradation. Tumor targeting brings specificity to minimize off-target effects
The isoindolinone-glutarimide antibody conjugates (IGAC) of the invention comprise an isoindolinone-glutarimide moiety covalently attached to an antibody by an antibody linker, wherein the antibody binds to a tumor-associated antigen or cell-surface receptor.
Exemplary embodiments of IGAC include Formula I:
Ab-[L-IG]P I or a pharmaceutically acceptable salt thereof, wherein:
Ab is the antibody;
L is the antibody linker;
IG is the isoindolinone-glutarimide moiety; and p is an integer from 1 to 12.
An exemplary embodiment of the IGAC of Formula I includes wherein a phenolic oxygen of the isoindolinone-glutarimide moiety is attached to the antibody linker.
An exemplary embodiment of the IGAC of Formula I includes wherein the nitrogen of the glutarimide group is attached to the antibody linker.
An exemplary embodiment of the IGAC of Formula I includes wherein a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C1-C40 heteroalkyl, and a glycoside, or combinations thereof is attached to: (1) a phenolic oxygen, or (2) the nitrogen of the glutarimide group of the isoindolinone-glutarimide moiety.
An exemplary embodiment of the IGAC of Formula I includes wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
An exemplary embodiment of the IGAC is selected from Formulae la and lb:
Figure imgf000143_0001
wherein: m is 0, 1 or 2;
X1 is selected from the group consisting of CH2, C(=O) and N=N;
X2 is independently selected from the group consisting of F, Cl, Br, I, -CN, C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), (C1-C6 alkyl diyl)-(C6-C20 aryl), -(C1-C6 alkyl diyl)-NRaRb, -(C1-C6 alkyldiyl)-ORa, (C1-C6 alkyldiyl)-( C3-C20 carbocyclyl), (C1-Cg alkyldiyl)-(C2-C20 heterocyclyl), (C1-C6 alkyldiyl)-(C1-C20 heteroaryl), C6-C20 aryl, C3-C20 carbocyclyl, C2-C20 heterocyclyl, C1-C20 heteroaryl, C(=NH)NH(OH), C(=NH)NH2, C(=O)NRaRb, -C(=O)NRa-NRaRb, -C(=O)NH(C1-C6 alkyldiyl)-NRaRb, -C(=O)ORa, -NRaRb, -NO2, -ORa, -OC(=O)Ra, -SRa, -S(O)Ra, -S(O)2Ra, -S(O)2NRa, and -S(O)3H; Ra is independently selected from H, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl;
Rb is independently selected from H, OH, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl; n is 0, 1, 2, 3, or 4;
X3 is selected from the group consisting of a bond, O, C1-C12 alkyldiyl, C2-C12 alkenyldiyl, C2-C12 alkynyldiyl, C1-C12 heteroalkyldiyl, -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl)-, -(C1-C6 alkyl diyl)NRa-, -(C1-C6 alkyldiyl)O-, -(C1-C6 alkyldiyl)-(C3-C20 carbocyclyldiyl)-, -(C1-C6 alkyl diyl)-(C2-C20 heterocyclyldiyl)-, -(C1-C6 alkyldiyl)-(C1-C20 heteroaryldiyl)- -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)— (C1— C 12 heteroalkyldiyl)-, -(C1- C12 heteroalkyldiyl)— (C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl)-, C6-C20 aryldiyl, C3-C20 carbocyclyldiyl, C2-C20 heterocyclyldiyl, and C1-C20 heteroaryl diyl;
X4 is selected from the group consisting of H, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl);
X5 is selected from the group consisting of a bond, C1-C12 alkyldiyl, C2-C12 alkenyldiyl, C2-C12 alkynyldiyl, C1-C12 heteroalkyldiyl, -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl), -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl)-0-(C2-C20 heterocyclyl), -(C1-C6 alkyldiyl)NRa-, -(C1-C6 alkyldiyl)O-, -(C1-C6 alkyldiyl)-(C3-C20 carbocyclyldiyl), -C1-C6 alkyl diyl)-(C2-C20 heterocyclyldiyl), -(C1-C6 alkyldiyl)-(C1-C20 heteroaryldiyl), -(C1-C12 heteroalkyldiyl)-( C6-C20 aryldiyl), -(C1-C12 heteroalkyl diyl )— (C.3— C20 aryldiyl)-(C1-C12 heteroalkyldiyl), C6-C20 aryldiyl, C3-C20 carbocyclyldiyl, C2-C20 heterocyclyldiyl, and C1-C20 heteroaryldiyl; and
L is the antibody linker; wherein each alkyl, alkyldiyl, alkenyl, alkenyldiyl, alkynyl, alkynyldiyl, heteroalkyl, heteroalkyl diyl, aryl, aryldiyl, carbocyclyl, carbocyclyldiyl, heterocyclyl, heterocyclyldiyl, heteroaryl, and heteroaryl diyl is independently and optionally substituted with one or more groups selected from F, Cl, Br, I, -CN, -CH3, -CH2CH3, CH~CH2, C=CH, C=CCH3, - CH2CH2CH3, -CH(CH3)2, -CH2CH(CH3)2, -CH2OH, -CH2OCH3, -CH2CH2OH, -C(CH3)2OH, -CH(OH)CH(CH3)2, -C(CH3)2CH2OH, -CH2CH2SO2CH3, -CH2OP(O)(OH)2, — CH2F, -CHF2, -CF3, -CH2CF3, -CH2CHF2, -CH(CH3)CN, -C(CH3)2CN, -CH2CN, -CH2NH2, - CH2NHSO2CH3, -CH2NHCH3, -CH2N(CH3)2, -CO2H, -COCH3, -CO2CH3, -CO2C(CH3)3, - COCH(OH)CH3, -CONH2, -CONHCH3, -CON(CH3)2, -C(CH3)2CONH2, -NH2, -NHCH3, - N(CH3)2, -NHCOCH3, -N(CH3)COCH3, -NHS(O)2CH3, -N(CH3)C(CH3)2CONH2, - N(CH3)CH2CH2S(O)2CH3, NHC(-NH)H, NHC(=NH)CH3, NHC(-NH)NH2, NHC(-O)NH2. NO2, -0, OH, OCH3, OCH2CH3, OCH2CH2OCH3, OCH2CH2OH, OCH2CH2N(CH3)2, -0CH2F, -0CHF2, -OCF3, -OP(O)(OH)2, -S(O)2N(CH3)2, -SCH3, - S(O)2CH3, and -S(O)3H.
An exemplary embodiment of the IGAC of Formula I includes wherein the antibody linker is covalently attached to a cysteine amino acid of the antibody.
An exemplary embodiment of the IGAC of Formula I includes wherein the antibody is a cysteine-engineered antibody.
An exemplary embodiment of the IGAC of Formulae la and lb includes wherein m is 0. An exemplary embodiment of the IGAC of Formulae la and lb includes wherein m is 1 . An exemplary embodiment of the IGAC of Formulae la and lb includes wherein m is 2. An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X1 is CH2.
An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X1 is C(=O).
An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X1 is N=N.
An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X2 comprises a -NHC(=0)NH- group.
An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X2 is selected from the group consisting of C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), and -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl).
An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X2 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl).
An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X2 is -CH2NHC(=0)NH-(C6-C2O aryl).
An exemplary embodiment of the IGAC of Formulae la and lb includes wherein X2 is:
Figure imgf000146_0001
wherein:
** indicates the point of attachment to the isoindolinone-glutarimide moiety.
An exemplary embodiment of the IGAC of Formulae la includes wherein X3 is O.
An exemplary embodiment of the IGAC of Formulae la b includes wherein X3 comprises a -NHC(=O)NH- group.
An exemplary embodiment of the IGAC of Formulae la includes wherein X3 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl).
An exemplary embodiment of the IGAC of Formulae la includes wherein X3 is -CH2NHC(=0)NH-(C6-C2O aryldiyl)-(C1-C12 heteroalkyldiyl).
An exemplary embodiment of the IGAC of Formulae la includes wherein X3 is selected from -(C1-C12 heteroalkyl diyl)-(C6-C20 aryldiyl)-O- -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-N(Ra)-, and -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl).
An exemplary embodiment of the IGAC of Formulae la includes wherein X3 is - CH2CH2CH2NHC(=O)NH- (C6-C20 aryldiyl)-O-.
An exemplary embodiment of the IGAC of Formulae la includes wherein X3 is selected from the structures:
Figure imgf000146_0002
and wherein:
* indicates the point of attachment to L;
** indicates the point of attachment to the phenyl glutarimide moiety; R6 is independently selected from F, Cl, Br, I, -CN, OH, -O-(C1-C12 alkyl), C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, C1-C12 heteroalkyl, C6-C20 aryl, C3-C20 carbocyclyl, C2-C20 heterocyclyl, and C1-C20 heteroaryl; nl is 1, 2, 3, or 4;
Y1 is selected from CF2 and NH; and
Y2 is selected from NH, O, and CH2.
An exemplary embodiment of the IGAC of Formulae la includes wherein X3 is selected from:
Figure imgf000147_0001
and wherein:
* indicates the point of attachment to L;
** indicates the point of attachment to the isoindolinone-glutarimide moiety;
R4 is selected from H and C1-C12 alkyl;
R6 is independently selected from F, Cl, Br, I, -CN, OH, C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, and C1-C12 heteroalkyl; and q is selected from 0, 1, 2, 3, and 4.
An exemplary embodiment of the IGAC of Formulae la includes wherein X3 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl).
An exemplary embodiment of the IGAC of Formulae la includes wherein X3 is selected from:
Figure imgf000147_0002
wherein:
* indicates the point of attachment to L;
** indicates the point of attachment to the isoindolinone-glutarimide moiety;
R6 is independently selected from F, Cl, Br, I, -CN, OH, C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, and C1-C12 heteroalkyl; and q is selected from 0, 1, 2, 3, and 4.
An exemplary embodiment of the IGAC of Formula I includes Formula la:
Figure imgf000148_0001
An exemplary embodiment of the IGAC of Formula la includes wherein X2 is -OH and n is 1 .
An exemplary embodiment of the IGAC of Formula la includes the structures:
Figure imgf000148_0002
Figure imgf000149_0001
An exemplary embodiment of the IGAC of Formula la includes wherein X4 is H.
An exemplary embodiment of the IGAC of Formula la includes wherein X4 is selected from the group consisting of C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), and -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-0-(C2-C20 heterocyclyl).
An exemplary embodiment of the IGAC of Formula la includes wherein X4 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-0-(C2-C20 heterocyclyl), and C2-C20 heterocyclyl is a glucuronide. An exemplary embodiment of the IGAC of Formula la includes wherein X4 of formula la is selected from the formulae:
Figure imgf000149_0002
Figure imgf000150_0001
wherein R is selected from H, C1-C6 alkyl, and O-( C1-C6 alkyl); and * indicates the point of attachment to IG. An exemplary embodiment of the IGAC of Formula I includes Formula lb:
Figure imgf000150_0002
An exemplary embodiment of the IGAC of Formula lb includes wherein n is 2, 3 or 4 and one of X2 is -OH.
An exemplary embodiment of the IGAC of Formula lb includes the structures:
Figure imgf000150_0003
Figure imgf000151_0001
An exemplary embodiment of the IGAC of Formula lb includes wherein X5 is selected from -(C1-C12 heteroalkyl diyl )-(C6-C20 aryldiyl) and -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl).
Exemplary embodiments of the IGAC of Formula I includes Formulae Ic-g:
Figure imgf000151_0002
le;
Figure imgf000152_0001
where R is independently selected from H, C1-C6 alkyl, and O-( C1-C6 alkyl); na is an integer from 1 to 5; and Y is CH2 or O. An exemplary embodiment of the IGAC of Formulas Ic-g includes wherein R is -CH3 and na is 1.
An exemplary embodiment of the IGAC of Formulas Ic-g includes X2 is -OH and n is 1. Exemplary embodiments of the IGAC of Formula I include Formulae Ih and li:
Figure imgf000152_0002
Figure imgf000153_0001
wherein R is selected from H, C1-C6 alkyl, and O-(C1-C6 alkyl); and X5a is -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl)-0-(C2-C20 heterocyclyl).
An exemplary embodiment of the IGAC of Formulas Ih and li includes wherein C2-C20 heterocyclyl of X5a is a glucuronide.
An exemplary embodiment of the IGAC of Formulas Ih and li includes wherein X5a is:
Figure imgf000153_0002
wherein * indicates the point of attachment.
An exemplary embodiment of the IGAC of Formulas Ih and li includes wherein L has the structure:
Figure imgf000153_0003
wherein:
L1 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl;
Lla is selected from an amino acid, amino, hydroxyl, halide, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof; o is 0, 1, or 2;
L2 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl; * indicates the point of attachment to a cysteine thiol of Ab; and
** indicates the point of attachment to the isoindolinone-glutarimide moiety.
Exemplary embodiments of the IGAC of Formula I include Formulae Ij-m:
Figure imgf000154_0001
Figure imgf000155_0001
where t is selected from 0, 1, 2, 3, and 4.
An exemplary embodiment of the IGAC of Formulae Ij-m includes wherein L1 is a bond and Lla is F.
An exemplary embodiment of the IGAC of Formula I includes wherein the antibody linker comprises an immolating group. An exemplary embodiment of the IGAC of Formula I includes wherein the antibody linker comprises a peptide unit.
An exemplary embodiment of the IGAC of Formula I includes wherein L has the formula:
-Str-(PEP)n-(IM)m- wherein:
Str is a stretcher unit covalently attached to the antibody;
PEP is a protease-cleavable, peptide unit covalently attached to Str and IM or IG;
IM is an immolative unit covalently attached to IG; n is 0 or 1 ; and m is 0 or 1 .
An exemplary embodiment of the IGAC of Formula I includes wherein IG is attached to L by Str.
An exemplary embodiment of the IGAC of Formula I includes wherein IG is attached to L by PEP.
An exemplary embodiment of the IGAC of Formula I includes wherein IG is attached to L by IM.
An exemplary embodiment of the IGAC of Formula I includes wherein Str is a branched linker covalently attached to: (i) the antibody; and (ii) a solubilizing unit comprising a group selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C1-C40 heteroalkyl, and a glycoside, or combinations thereof, wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
An exemplary embodiment of the IGAC of Formula I includes wherein the solubilizing unit and the terminus of the solubilizing unit covalently attached to Str are selected from the structures:
Figure imgf000156_0001
Figure imgf000157_0001
Figure imgf000158_0001
wherein * indicates the point of attachment to Str An exemplary embodiment of the IGAC of Formula I includes wherein L is a branched linker and PEP is covalently attached to: (i) Str and IM or IG; and (ii) a solubilizing unit comprises a group selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C1-C40 heteroalkyl, and a glycoside, or combinations thereof, wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
An exemplary embodiment of the IGAC of Formula I includes wherein L is a branched linker and IM is covalently attached to: (i) IG; and (ii) a solubilizing unit comprises a group selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C1-C40 heteroalkyl, and a glycoside, or combinations thereof, wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof. An exemplary embodiment of the IGAC of Formula I includes wherein Str has the structure:
Figure imgf000159_0001
wherein:
* indicates the point of attachment to a cysteine thiol of Ab;
** indicates the point of attachment to PEP or to the isoindolinone-glutarimide moiety;
R1 is selected from the group consisting of C1-C12 alkyldiyl, C1-C12 alkyldiyl-C(=O), C1- C12 alkyldiyl-NH, (CH2CH2O)r, (CH2CH2O)r-C(=O), (CH2CH2O)r-CH2, C6-C20 aryldiyl, (C6- C20 aryldiyl)-(C1-C12 alkyldiyl), and (C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl); r is an integer ranging from 1 to 10; and alkyldiyl, heteroalkyldiyl, and aryldiyl are independently and optionally substituted with one or more groups selected from F, Cl, -CN, -NH2, -CH2NH2, -OH, -OCH3, -OCH2CH3, - OCH2CH2OCH3, -OCH2CH2OH, -OCH2CH2N(CH3)2, -OCH2F, -OCHF2, -OCF3, - OP(O)(OH)2, -S(O)2N(CH3)2, -SCH3, -S(O)2CH3, -S(O)3H, and a solubilizing unit.
An exemplary embodiment of the IGAC of Formula I includes wherein R1 is selected from -(CH2)5-, and -CH2CH2-.
An exemplary embodiment of the IGAC of Formula I includes wherein R1 is selected from C6-C20 aryldiyl, (C6-C20 aryldiyl)-(C1-C12 alkyldiyl), and (C6-C20 aryldiyl)-(C1-C12 heteroalkyl diyl).
An exemplary embodiment of the IGAC of Formula I includes wherein Str is selected from the structure:
Figure imgf000159_0002
wherein: one of Y1, Y2, Y3, Y4 and Y5 is C-L’-R1, another one of Y1, Y2, Y3, Y4 and Y5 is C-L2- R2, and the remaining three of Y1, Y2, Y3, Y4 and Y5 are each independently N, C-R3, or C-L3- R3a;
R1, R2, and R3a each independently comprise one or more moieties selected from an amino acid element, a charged element, a heteroalkylene element, a hydrophilic element, a trigger element, an immolative unit, a polar cap, a isoindolinone-glutarimide moiety, and combinations thereof; provided that at least one of R1 and R2 comprises the isoindolinone-glutarimide moiety; each occurrence of R3 is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, aminyl, amidyl, aldehyde, hydroxyl, cyano, nitro, thiol, carboxy, carboxyalkyl, alkyl-S(O)3H, alkyl-O-P(O)3H, alkyl- P(O)3H, -O-carboxyalkyl, -O-alkyl-S(O)3H, -O-alkyl-O-P(O)3H, -O-alkyl-P(O)3H, -S(O)3H, - OP(O)3H, -P(O)3H, alkyl-O-P(O)3-alkyl, alkyl-P(O)3-alkyl, -O-alkyl-S(O)3-alkyl, -O-alkyl-O- P(O)3-alkyl, -O-alkyl-P(O)3-alkyl, -S(O)3-alkyl, -OP(O)3-alkyl, -P(O)3-alkyl, sulfamide, sulfinimide, and a carbohydrate;
R4a and R4b are each independently hydrogen, deuterium, halo, or -S-R4c wherein R4c is substituted or unsubstituted C6-C10 aryl or substituted or unsubstituted 5-12 membered heteroaryl; and
L1, L2, and L3 are each independently a linker comprising an optionally substituted alkylene, an optionally substituted alkenylene, an optionally substituted alkynylene, an optionally substituted heteroalkylene, an optionally substituted heteroalkenylene, an optionally substituted heteroalkynylene, a heteroatomic linker, an optionally substituted cycloalkylene, an optionally substituted arylene, an optionally substituted heterocyclylene, an optionally substituted heteroarylene, or combinations thereof; and
* indicates the point of attachment to a cysteine thiol of Ab
An exemplary embodiment of the IGAC of Formula I includes wherein Str is selected from the structure:
Figure imgf000160_0001
wherein:
L1 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl;
Lla is selected from an amino acid, amino, hydroxyl, halide, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof; o is 0, 1, or 2;
L2 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl;
* indicates the point of attachment to a cysteine thiol of Ab; and ** indicates the point of attachment to PEP or to the isoindolinone-glutarimide moiety.
An exemplary embodiment of the IGAC of Formula I includes wherein L1 or L2 comprise a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C1-C40 heteroalkyl, and a glycoside, or combinations thereof.
An exemplary embodiment of the IGAC of Formula I includes wherein L1 or L2 comprises glucuronic acid having the structure:
Figure imgf000161_0001
An exemplary embodiment of the IGAC of Formula I includes wherein L1 or L2 is selected from (N(CH3)CH2C(=O))q, (N(CH3)CH2CH2C(=O))q, N(CH3)CH2CH2OCH2CH2C(=O))q, (CH2CH2O)q, (CH2CH2O)q-C(=O), and (CH2CH2O)q-CH2, where q is an integer from 2 to 20.
An exemplary embodiment of the IGAC of Formula I is selected from formulas:
Figure imgf000161_0002
wherein * indicates the point of attachment to a cysteine thiol of Ab and ** indicates the point of attachment to IG. An exemplary embodiment of the IGAC of Formula I includes wherein n is 1, m is 1, and PEP-IM has the formula:
Figure imgf000162_0001
wherein * indicates the point of attachment to Str and ** indicates the point of attachment to IG;
AA is independently selected from a natural or unnatural amino acid side chain, or one or more of AA, and an adjacent nitrogen atom form a 5 -membered ring proline amino acid, and the wavy line indicates a point of attachment;
Cyc is selected from C6-C20 aryldiyl and C1-C20 heteroaryldiyl, optionally substituted with one or more groups selected from F, Cl, NO2, -OH, -OCH3, and glucuronic acid having the structure:
Figure imgf000162_0002
R7 is selected from the group consisting of -CH(R8)O-, -CH2-, -CH2N(R8)CH(R8)-, - CH(R8)OC(=O)-, -CH(R8)OC(=O)N(R8)CH(R8)-, -CH(R8)OP(=O)2OCH(R8)-, and - CH(R8)OC(=O)N(R8)-(C1-C6 alkyldiyl)-N(R8)C(=O)OCH(R8)-;
R8 is selected from H, C1-C6 alkyl, C(=O)-C1-C6 alkyl, and -C(=O)N(R9)2;
R9 is independently selected from the group consisting of H, C1-C12 alkyl, and - (CH2CH2O)n-(CH2)m-OH, where m is an integer from 1 to 5, and n is an integer from 2 to 50, or two R9 groups together form a 5- or 6-membered heterocyclyl ring; y is an integer from 2 to 12, and z is 0 or 1.
An exemplary embodiment of the IGAC of Formula I includes wherein AA is independently selected from the side chain of a naturally occurring amino acid.
An exemplary embodiment of the IGAC of Formula I includes wherein AA is independently selected from H, -CH3, -CH(CH3)2, -CFhlGeHs), -CH2C(O)NH2, -CH2CH2CO2H, -CH2CO2H, -CH2CH2CH2CH2NH2, -CH2CH2CH2NHC(NH)NH2, -CH2CH(CH3)2, -CH2SO3H, and -CH2CH2CH2NHC(O)NH2; or two AA form a 5-membered ring proline amino acid. An exemplary embodiment of the IGAC of Formula I includes wherein PEP-IM comprises at least one natural or unnatural amino acid side chain AA substituted with C1-C40 heteroalkyl.
An exemplary embodiment of the IGAC of Formula I includes wherein C1-C40 heteroalkyl comprises a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), and a glycoside, or combinations thereof
An exemplary embodiment of the IGAC of Formula I includes wherein the solubilizing unit is selected from (N(CH3)CH2C(=O))q, (N(CH3)CH2CH2C(=O))q, N(CH3)CH2CH2OCH2CH2C(=O))q, (CH2CH2O)q, (CH2CH2O)q-C(=O), and (CH2CH2O)q-CH2, where q is an integer from 2 to 20.
An exemplary embodiment of the IGAC of Formula I includes wherein y is 2, PEP is a dipeptide, and PEP-IM has the formula:
Figure imgf000163_0001
wherein AA1 and AA2 are independently selected from a side chain of a naturally- occurring amino acid.
An exemplary embodiment of the IGAC of Formula I includes wherein the dipeptide is selected from ala-ala, val-cit, and phe-ala.
An exemplary embodiment of the IGAC of Formula I includes wherein AA1 is - CH(CH3)2, and AA2 is -CH2CH2CH2NHC(O)NH2.
An exemplary embodiment of the IGAC of Formula I includes wherein AA1 and AA2 are each -CH3.
An exemplary embodiment of the IGAC of Formula I includes wherein y is 3, PEP is a tripeptide, and PEP-IM has the formula:
Figure imgf000163_0002
An exemplary embodiment of the IGAC of Formula I includes wherein y is 4, PEP is a tetrapeptide PEP-IM, and has the formula:
Figure imgf000164_0001
An exemplary embodiment of the IGAC of Formula I includes where z is 1 and IM has the formula:
*-Cyc-R7-** wherein:
* indicates the point of attachment to PEP; and
** indicates the point of attachment to IG.
An exemplary embodiment of the IGAC of Formula I includes where R7 has the formula:
Figure imgf000164_0002
wherein:
R8 is selected from H and C1-C6 alkyl;
* indicates the point of attachment to PEP; and
** indicates the point of attachment to IG.
An exemplary embodiment of the IGAC of Formula I includes where R8 is H. An exemplary embodiment of the IGAC of Formula I includes where R8 is -CH3.
An exemplary embodiment of the IGAC of Formula I includes wherein IM is selected from the formulae:
Figure imgf000165_0001
wherein:
* indicates the point of attachment to PEP; and
** indicates the point of attachment to IG. An exemplary embodiment of the IGAC of Formula I includes wherein IM is selected from the formulae:
Figure imgf000166_0001
wherein:
* indicates the point of attachment to PEP; and
** indicates the point of attachment to IG. The invention includes all reasonable combinations, and permutations of the features, of the Formula I embodiments
In certain embodiments, the isoindolinone-glutarimide antibody conjugates (IGAC) of the invention include those with anti-cancer activity. The IGAC selectively deliver an effective dose of an isoindolinone-glutarimide drug to tumor tissue or hematopoietic cell, whereby greater selectivity (z.e., a lower efficacious dose) may be achieved while increasing the therapeutic index (“therapeutic window”) relative to unconjugated isoindolinone-glutarimide drug.
Drug loading in Table 3 is represented as DAR, the number of isoindolinone-glutarimide (IG) moi eties per antibody in an IGAC of Formula I. Drug (IG) loading may range from 1 to about 8 drug moieties (D) per antibody. IGAC of Formula I include mixtures or collections of antibodies conjugated with a range of IG drug moieties, from 1 to about 8. In some embodiments, the number of IG drug moieties that can be conjugated to an antibody is limited by the number of reactive or available amino acid side chain residues such as lysine and cysteine. In some embodiments, free cysteine residues are introduced into the antibody amino acid sequence by the methods described herein. In such aspects, p may be 1, 2, 3, 4, 5, 6, 7, or 8, and ranges thereof, such as from 1 to 8 or from 2 to 5. Exemplary IGAC of Formula I include, but are not limited to, antibodies that have 1, 2, 3, or 4 engineered cysteine amino acids (Lyon, R. et al. (2012) Methods in Enzym. 502:123-138). In some embodiments, one or more free cysteine residues are already present in an antibody forming intra-chain and inter-chain disulfide bonds (native disulfide groups), without the use of engineering, in which case the existing free, reduced cysteine residues may be used to conjugate the antibody to a drug In some embodiments, an antibody is exposed to reducing conditions prior to conjugation of the antibody in order to generate one or more free cysteine residues.
For some antibody conjugates, p may be limited by the number of attachment sites on the antibody For example, where the attachment is a cysteine thiol, as in certain exemplary embodiments described herein, an antibody may have only one or a limited number of cysteine thiol groups, or may have only one or a limited number of sufficiently reactive thiol groups, to which the drug may be attached. In other embodiments, one or more lysine amino groups in the antibody may be available and reactive for conjugation with a IG-lmker compound of Formula II. In certain embodiments, higher drug loading, e.g. p >5, may cause aggregation, insolubility, toxicity, or loss of cellular permeability of certain antibody -drug conjugates. In certain embodiments, the average drug loading for an antibody conjugate ranges from 1 to about 8; from about 2 to about 6; or from about 3 to about 5 In certain embodiments, an antibody is subjected to denaturing conditions to reveal reactive nucleophilic groups such as lysine or cysteine.
The loading (drug/antibody ratio) of an antibody conjugate may be controlled in different ways, and for example, by: (i) limiting the molar excess of the IG-linker intermediate compound relative to antibody, (ii) limiting the conjugation reaction time or temperature, and (iii) partial or limiting reductive denaturing conditions for optimized antibody reactivity.
It is to be understood that where more than one nucleophilic group of the antibody reacts with a drug, then the resulting product is a mixture of antibody conjugate compounds with a distribution of one or more IG drug moieties attached to an antibody. The average number of drugs per antibody may be calculated from the mixture by a dual ELISA antibody assay, which is specific for antibody and specific for the drug. Individual IGAC molecules may be identified in the mixture by mass spectroscopy and separated by HPLC, for example hydrophobic interaction chromatography, HIC (McDonagh et al. (2006) Prot. Engr. Design & Selection 19(7):299-307; Hamblett et al. (2004) Clin. Cancer Res. 10:7063-7070; Hamblett, K J., et al. “Effect of drug loading on the pharmacology, pharmacokinetics, and toxicity of an anti-CD30 antibody-drug conjugate,” Abstract No. 624, American Association for Cancer Research, 2004 Annual Meeting, March 27-31, 2004, Proceedings of the AACR, Volume 45, March 2004; Alley, S.C., et al. “Controlling the location of drug attachment in antibody-drug conjugates,” Abstract No. 627, American Association for Cancer Research, 2004 Annual Meeting, March 27- 31, 2004, Proceedings of the AACR, Volume 45, March 2004). In certain embodiments, a homogeneous antibody conjugate with a single loading value may be isolated from the conjugation mixture by electrophoresis or chromatography.
Exemplary embodiments of the isoindolinone-glutarimide antibody conjugates (IGAC) of Formula I are compiled in Table 3. Assessment of IGAC biological activity and other properties may be conducted according to the methods of Example 102. In some instances, the C6ll proliferation dose response IC50 value is an average of repetitive assays C6rtain exemplary IGAC were tested for their effects in inhibiting cellular proliferation, including CAL51 ; WSU-DLCL2, NCI-N87 and SKBR3 cell lines. CAL51 is a human breast adenocarcinoma cell line with triple-negative status for expression of estrogen, progesterone and HER2 receptors. WSU-DLCL2 is a human B-C6ll non-Hodgkin lymphoma cell line that expresses high levels of CD22. NCI-N87 is a human epithelial cell line established from a gastric carcinoma; SKBR3 is a human epithelial cell line established from a breast adenocarcinoma; both NCI-N87 and SKBR3 cell lines express high levels of HER2 receptor.
Table 3 Isoindolinone-glutarimide antibody conjugates (IGAC)
Figure imgf000168_0001
Figure imgf000169_0001
Figure imgf000170_0001
Figure imgf000171_0001
Figure imgf000172_0001
Figure imgf000173_0001
Figure imgf000174_0001
PHARMACEUTICAL COMPOSITIONS OF ISOINDOLINONE-GLUTARIMIDE ANTIBODY CONJUGATES
The invention provides a composition, e g., a pharmaceutically or pharmacologically acceptable composition or formulation, comprising an isoindolinone-glutarimide antibody conjugate (IGAC) composition of the invention as described herein and a pharmaceutically acceptable diluent, vehicle, carrier or excipient.
The isoindolinone-glutarimide antibody conjugate (IGAC) composition can be the same or different in the pharmaceutical composition, i.e., the composition can comprise IGAC that have the same number of isoindolinone-glutarimide (IG) moieties linked to the same positions on the antibody and/or IGAC that have the same number of (IG) moieties linked to different positions on the antibody, that have different numbers of (IG) moieties linked to the same positions on the antibody, or that have different numbers of (IG) moieties linked to different positions on the antibody. In an exemplary embodiment, a pharmaceutical composition comprises a mixture of the IGAC, wherein the average drug (IG) loading per antibody in the mixture of antibody conjugate compounds is about 2 to about 8. An IGAC of the invention can have an average IG to antibody ratio (DAR) of about 0.4 to about 10. A skilled artisan will recognize that the number of IG moieties conjugated to the antibody may vary amongst IGAC in a composition comprising multiple IGAC of the invention and thus the DAR can be measured as an average which may be referred to as the drug to antibody ratio (DAR) which can be assessed by any suitable means, many of which are known in the art. The average number of IG moieties per antibody (DAR) in preparations of IGAC from conjugation reactions may be characterized by conventional means such as mass spectrometry, ELISA assay, and HPLC. The quantitative distribution of IGAC in a composition in terms of p may also be determined In certain instances, separation, purification, and characterization of homogeneous IGAC where p is a certain value from antibody drug conjugates (ADC) with other drug loadings may be achieved by purification means such as reverse phase HPLC or electrophoresis.
An isoindolinone-glutarimide antibody conjugate (IGAC) composition can be formulated for parenteral administration, such as intradermal, subcutaneous, intramuscular (IM), or intravenous (IV) injections, infusion, or administration into a body cavity or lumen of an organ. Alternatively, the IGAC as a pharmaceutical composition can be injected into otherwise placed into a specific site of the body, such as a tumor. Compositions for injection will commonly comprise a solution of the IGAC dissolved in a pharmaceutically acceptable carrier Among the acceptable vehicles and solvents that can be employed are water and an isotonic solution of one or more salts such as sodium chloride, e.g., Ringer's solution. In addition, sterile fixed oils can conventionally be employed as a solvent or suspending medium. For this purpose, any bland fixed oil can be employed, including synthetic monoglycerides or diglycerides. In addition, fatty acids such as oleic acid can likewise be used in the preparation of inj ectables. These pharmaceutical compositions desirably are sterile and generally free of undesirable matter. These pharmaceutical compositions can be made sterilized by conventional, well known sterilization techniques. The pharmaceutical compositions can contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents, e g., sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like.
The pharmaceutical composition may contain any suitable concentration of the IGAC . The concentration of the IGAC in the pharmaceutical composition can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight, and the like, in accordance with the particular mode of administration selected and the patient's needs. In certain embodiments, the concentration of IGAC in a solution formulation for injection will range from about 0.1% (w/w) to about 10% (w/w). METHODS OF TREATING CANCER WITH ISOINDOLINONE-GLUTARIMIDE ANTIBODY CONJUGATES
By inducing target-specific degradation of tumor-associated proteins and conferring specificity to minimize off-target toxicity effects, the isoindolinone-glutarimide antibody conjugate (IGAC) compositions of the invention may be useful in the treatment of diseases and disorders such as cancer. The IGAC direct a tumor-associated antigen-binding antibody to a cell that expresses the antigen and deliver a cereblon-degrading moiety to the target cell. A target protein such as GSPT1 is ubiquitinated and subsequently degraded
The invention provides a method for treating cancer with a pharmaceutical composition of the IGAC. The method includes administering a therapeutically effective amount of an antibody conjugate composition as described herein to a subject in need thereof, such as a patient that has cancer and is in need of treatment for the cancer. The method includes administering a therapeutically effective amount of an IGAC selected from Table 3.
In certain embodiments, the IGAC include those with anticancer activity (Figures 1-4). The IGAC selectively delivers an effective dose of an active form of the isoindolinone- glutarimide protein target degrader moiety to tumor tissue, whereby greater selectivity (i.e., a lower efficacious dose) may be achieved while increasing the therapeutic index (“therapeutic window”) relative to an unconjugated protein target degrader compound
It is contemplated that the IGAC may be used to treat various hyperproliferative diseases or disorders, e.g. characterized by the overexpression of a tumor antigen. Exemplary hyperproliferative disorders include benign or malignant solid tumors and hematological disorders such as leukemia and lymphoid malignancies.
Examples of cancer to be treated herein include, but are not limited to, carcinoma, lymphoma, blastoma, sarcoma, leukemia or lymphoid malignancies including acute myeloid leukemia, squamous cell cancer, epithelial squamous cell cancer, lung cancer including smallcell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung and squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, rectal cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, and head and neck cancer. In some embodiments, the IGAC may be useful in therapy to treat solid tumors such as lung cancer; non-small cell lung cancer, squamous cell lung cancer, small cell lung cancer, breast cancer, and neuroendocrine cancers such as neuroendocrine prostate cancer, castration-resistant neuroendocrine prostate cancer (NEPC) and lung neuroendocrine tumors. In some embodiments, the IGAC may be useful in therapy to treat blood-borne hematological cancers such as leukemias; acute myelogenous leukemia (AML) and myelomas; multiple myeloma (MM).
In another aspect, an IGAC for use as a medicament is provided. In certain embodiments, the invention provides an IGAC for use in a method of treating an individual comprising administering to the individual an effective amount of the antibody conjugate composition in a pharmaceutical composition. In one such embodiment, the method further comprises administering to the individual an effective amount of at least one additional therapeutic agent, e.g., as described herein
In a further aspect, the invention provides for the use of an IGAC in the manufacture or preparation of a medicament. In one embodiment, the medicament is for treatment of cancer, the method comprising administering to an individual having cancer an effective amount of the medicament. In one such embodiment, the method further comprises administering to the individual an effective amount of at least one additional therapeutic agent, e.g., as described herein.
Dosing can be by any suitable route, e.g. by injections, such as intravenous or subcutaneous injections, depending in part on whether the administration is brief or chronic. Various dosing schedules including but not limited to single or multiple administrations over various time-points, bolus administration, and pulse infusion are contemplated herein. The IGAC dose can range from about 5 mg/kg (body weight) to about 50 mg/kg, from about 10 pg/kg to about 5 mg/kg, or from about 100 pg/kg to about 1 mg/kg. The IGAC dose can be about 100, 200, 300, 400, or 500 pg/kg. The IGAC dose can be about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mg/kg. The IGAC dose can also be outside of these ranges, depending on the particular conjugate as well as the type and severity of the cancer or disorder being treated. Frequency of administration can range from a single dose to multiple doses per week, or more frequently. In some embodiments, the IGAC is administered from about once per month to about five times per week. In some embodiments, the IGAC is administered once per week.
The IGAC can be used either alone or in combination with other therapeutic agents in a therapy regimen. IGAC may be administered concurrently in a regimen with one or more other drugs during the same treatment cycle, on the same day of treatment as the one or more other drugs, and, optionally, at the same time as the one or more other drugs. For instance, for cancer therapies given every 3 weeks, the concurrently administered drugs are each administered on day-1 of a 3-week cycle. For instance, an IGAC may be co-administered with at least one additional therapeutic agent, such as a chemotherapeutic agent. Such combination therapies encompass combined administration (where two or more therapeutic agents are included in the same or separate formulations), and separate administration, in which case, administration of the IGAC can occur prior to, simultaneously, and/or following, administration of the additional therapeutic agent. IGAC can also be used in combination with radiation therapy.
EXAMPLES
General Synthetic Schemes and Examples
The following synthetic schemes are provided for purposes of illustration, not limitation The following examples illustrate the various methods of making compounds described herein. It is understood that one skilled in the art may be able to make these compounds by similar methods or by combining other methods known to one skilled in the art. It is also understood that one skilled in the art would be able to make, in a similar manner as described below by using the appropriate starting materials and modifying the synthetic route as needed. In general, starting materials and reagents can be obtained from commercial vendors or synthesized according to sources known to those skilled in the art of prepared as described herein.
EXAMPLE 1 Synthesis of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)- l-oxoisoindolin-5-yl)methyl)urea (Compound IG-1)
Figure imgf000178_0001
Int 1a
A mixture of methyl 4-bromo-2-(bromomethyl)benzoate (20.0 g, 64.9 mmol, 1.00 eq), 3- aminopiperidine-2, 6-dione (12.8 g, 78.0 mmol, 1.20 eq) and A/A'-diisopropylcthylaminc (33.6 g, 259 mmol, 45.2 mL, 4.00 eq) in dimethylsulfoxide (200 mL) was stirred at 100 °C for 12 h. The reaction mixture was poured into water (300 mL) and stirred for 10 min, filtered to give a filter cake, the filter cake was concentrated to give a residue. The residue was triturated with ethyl acetate (100 mL) at 20 °C for 10 min to afford 3-(5-bromo-l-oxoisoindolin-2-yl)piperidine-2,6- dione, Int la, (17.0 g, 52.6 mmol, 81% yield) as a purple solid. MS (ESI) m/z 325.0 [M+H+2]+ Step B. Preparation of Int lb
Figure imgf000179_0001
Int 1a Int 1b
A mixture of 3-(5-bromo-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int la, (500 mg, 1.55 mmol, 1.00 eq), zinc cyanide (110 mg, 936 umol, 59.0 uL, 0.600 eq) and tetrakis[triphenylphosphine]palladium(0) (178 mg, 154 umol, 0.100 eq) in dimethylformamide (10.0 mL) was stirred at 100 °C for 3 h under nitrogen atmosphere. The reaction mixture was cooled to 25 °C and then poured into water (100 mL) and extracted with ethyl acetate (3 x 50.0 mL). The combined organic phase was washed with brine (100 mL), dried over anhydrous sodium sulfate, filtered and concentrated in vacuum to give a residue. The residue was triturated with ethyl acetate (20.0 mL) at 25 °C for 30 min to afford 2-(2,6-dioxopiperidin-3-yl)-l- oxoisoindoline-5-carbonitrile, Int lb, (400 mg, crude) as a gray solid. H \MR (400 MHz, DMSO-<A) δ = 11.03 (s, 1H), 8.17 (s, 1H), 8.03 - 7.97 (m, 1H), 7.95 - 7.89 (m, 1H), 5.16 (dd, J = 5.1, 13.3 Hz, 1H), 4.61 - 4.52 (m, 1H), 4.49 - 4.38 (m, 1H), 2.98 - 2.86 (m, 1H), 2.68 - 2.59 (m, 1H), 2.46 - 2.37 (m, 1H), 2.09 - 1.98 (m, 1H). MS (ESI) m/z 270.2 [M+H]+ Step C. Preparation of Int AA
Figure imgf000179_0002
To a solution of 2-(2,6-di oxopiperi din-3 -yl)-l-oxoisoindoline-5-carbonitrile, Int lb, (400 mg, 1.49 mmol, 1.00 eq) in hydrochloric acid (12 M, 1.00 mL, 8.08 eq) and methanol (10.0 mL) was added platinum dioxide (170 mg, 748 umol, 0.500 eq) under nitrogen atmosphere, the mixture was stirred at 25 °C for 12 h under hydrogen atmosphere. The reaction was filtered to give a filtrate, the filtrate was concentrated to give a residue. The residue was triturated with ethyl acetate (30.0 mL) at 25 °C for 10 min to afford 3-(5-(aminomethyl)-l-oxoisoindolin-2- yl)piperidine-2, 6-dione, Int AA, (250 mg, 914 umol, 62% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-d6 ) δ = 11.00 (br s, 1H), 8.66 - 8.45 (m, 2H), 7.78 (br d, J= 6.4 Hz, 1H), 7.74 (br s, 1H), 7.64 (br d, J= 7.7 Hz, 1H), 5.21 - 5.06 (m, 1H), 4 54 - 4.46 (m, 1H), 4.39 - 4.31 (m, 1H), 4.16 (br d, J= 1.7 Hz, 2H), 2.90 (br s, 1H), 2.68 - 2.64 (m, 1H), 2.42 (br d, J= 12.1 Hz, 1H), 2.10 - 1.96 (m, 1H).
Step D. Preparation of Compound IG-1
Figure imgf000180_0001
To a solution of 3 -(5-(aminomethyl)-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Compound AA, (250 mg, 914 umol, 1.00 eq) and triethylamine (277 mg, 2.74 mmol, 382 uL, 3.00 eq) in dimethylformamide (2.00 mL) was added 2-chloro-4-isocyanato-l -methylbenzene (168 mg, 1.01 mmol, 1.10 eq) at 0 °C, the mixture was stirred at 25 °C for 1 h. The reaction mixture was poured into water (50.0 mL) and stirred for 10 min, then filtered to give a filter cake, the filter cake was concentrated to give a residue. The residue was purified by Prep- HPLC (column: Waters Xbridge 150*25mm* 5um;mobile phase: [water(FA)-ACN];B%: 11%- 41%,10min) to afford l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl)urea (119.12 mg, 267 umol, 29% yield, 99% purity) as a yellow solid. 1H NMR (400 MHz, DMSO-7,) 6 = 10.98 (br s, 1H), 8.77 (s, 1H), 7.73 - 7.64 (m, 2H), 7.52 (s, 1H), 7.45 (d, J = 8.1 Hz, 1H), 7.20 - 7.17 (m, 1H), 7.16 - 7.11 (m, 1H), 6.82 (t, 7= 5.9 Hz, 1H), 5.11 (dd, 7= 5.1, 13.3 Hz, 1H), 4.49 - 4.39 (m, 3H), 4.36 - 4.26 (m, 1H), 2.98 - 2.87 (m, 1H), 2.64 - 2.61 (m, 1H), 2.43 - 2.34 (m, 1H), 2.23 (s, 3H), 2.05 - 1.96 (m, 1H). MS (ESI) m/z 441.1 [M+H]+
EXAMPLE 2 Synthesis of l-(3-chloro-4-(2-(2-(methylamino)ethoxy)ethyl)phenyl)-3- ((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)urea (Compound IG-3)
Figure imgf000180_0002
To a solution of 2-(2-chloro-4-nitrophenyl)acetic acid (5.00 g, 23.2 mmol, 1.00 eq) in tetrahydrofuran (75.0 mL) was added borane dimethyl sulfide complex (10.0 M, 5.80 mL, 2.50 eq) dropwise at 0 °C under nitrogen atmosphere, the mixture was stirred at 70 °C for 2 h under nitrogen atmosphere. The reaction was quenched with methanol (30.0 mL) at 10 °C and concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®;80 g SepaFlash® Silica Flash Column, Eluent of 0-50% Ethyl acetate/Petroleum ether gradient @ 100 mL/mint) to afford 2-(2-chloro-4-nitrophenyl)ethan-l-ol, Int 1c, (4.20 g, 20.8 mmol, 90% yield) as a yellow solid. 1H NMR (400 MHz, CDCh-rf) δ = 8.27 (d, J= 2.4 Hz, 1H), 8.08 (dd, J= 2.4, 8.4 Hz, 1H), 7.51 (d, J= 8.4 Hz, 1H), 3.96 (t, J = 6.4 Hz, 2H), 3.12 (t, J= 6.4 Hz, 2H)
Step B. Preparation of Int Id
Figure imgf000181_0001
To a solution of 2-(2-chloro-4-nitrophenyl)ethan-l-ol, Int 1c, (200 mg, 992 umol, 1.00 eq) and tert-butyl 2-bromoacetate (1.50 g, 7.69 mmol, 1.14 mL, 7 75 eq) in toluene (10.0 mL) was added tetrabutylammonium hydrogensulfate (269 mg, 794 umol, 0.800 eq) at 0 °C. To the above mixture was added sodium hydroxide (390 mg, 9.74 mmol, 9.82 eq) in water (2.40 mL) dropwise at 0 °C. The mixture was stirred at 25 °C for 4 h. The mixture was diluted with water (10.0 mL) and extracted with ethyl acetate (3 x 15.0 mL). The combined organic layer was washed with brine (3 x 15.0 mL), dried over anhydrous sodium sulfate and filtered. The filtrate was concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®;40 g SepaFlash® Silica Flash Column, Eluent of 0-16% Ethyl acetate/Petroleum ether gradient @ 100 mL/mint) to afford tert-butyl 2-(2-chloro-4-nitrophenethoxy)acetate, Int Id, (300 mg, 950 umol, 96% yield) as yellow oil. 1H NMR (400 MHz, CDC13-d ) = 8.24 (br s, 1H), 8.18 - 8 01 (m, 1H), 7.60 (br d, J= 7.0 Hz, 1H), 4.38 - 4.05 (m, 2H), 4.05 - 3.93 (m, 2H), 3.83 (br dd, J= 1.2, 5.3 Hz, 2H), 1.48 (br dd, J= 0.8, 2.8 Hz, 9H).
Step C. Preparation of Int le
Figure imgf000181_0002
To a solution of tert-butyl 2-(2-chloro-4-nitrophenethoxy)acetate, Int Id, (300 mg, 950 umol, 1 00 eq) in dichloromethane (3 00 mL) was added trifluoroacetic acid (924 mg, 8.10 mmol, 0.600 mL, 8.53 eq) at 0 °C. The mixture was stirred at 25 °C for 4 h. The mixture was concentrated under reduced pressure to afford 2-(2-chloro-4-nitrophenethoxy)acetic acid, Int le, (240 mg, 924 umol, 97% yield) as a yellow solid 1H NMR (400 MHz, DMSO-d6 ) δ = 8 27 (d, J = 2.4 Hz, 1H), 8.15 (dd, J= 2.4, 8.5 Hz, 1H), 7.75 (d, J= 8.6 Hz, 1H), 4.03 (s, 2H), 3.77 (t, J = 6.4 Hz, 2H), 3.08 (t, ~ 6.4 Hz, 2H).
Step D. Preparation of Int If
Figure imgf000182_0001
Int 1e Int 1f
To a solution of 2-(2-chloro-4-nitrophenethoxy)acetic acid, Int le, (240 mg, 924 umol, 1.00 eq) and O-(7-azabenzotriazol-l-yl)-/V//,7V’,Af’-tetramethyluronium hexafluorophosphate (562 mg, 1.48 mmol, 1.60 eq) in dimethylformamide (5.00 mh) was added diisopropylethylamine (478 mg, 3.70 mmol, 644 uL, 4.00 eq) and methanamine;hydrochloride (74.9 mg, 1.11 mmol, 1 20 eq). The mixture was stirred at 25°C for 4 h. The mixture was diluted with water (10.0 mL) and extracted with ethyl acetate (3 * 5.00 mL). The combined organic layer was washed with brine (3 x 15.0 mL), dried over anhydrous sodium sulfate and filtered. The filtrate was concentrated to give a residue. The residue was purified by reversed- phase HPLC (C1 8, 80 g; condition: water/ acetonitrile = 1/0-0/1, 0.1% formic acid) and lyophilized to afford 2-(2-chloro-4-nitrophenethoxy)-JV-methylacetamide, Int If, (100 mg, 341 umol, 37% yield, 93% purity) as yellow oil.
Figure imgf000182_0002
NMR (400 MHz, DMSO-tfc) 3 = 8.27 (d, J= 2.4 Hz, 1H), 8.18 - 8.13 (m, 1H), 7.75 (d, J= 8.6 Hz, 1H), 3.87 (s, 2H), 3.73 (t, J= 6.8 Hz, 2H), 3.12 (t, J= 6.6 Hz, 2H), 2.61
Figure imgf000182_0003
4.8 Hz, 3H).
Step E. Preparation of Int 1g
Figure imgf000182_0004
Int 1f Int 1g
To a solution of 2-(2-chloro-4-nitrophenethoxy)-/V-methylacetamide, Int If, (3.00 g, 11.0 mmol, 1.00 eq) in tetrahydrofuran (30.0 mL) was added borane tetrahydrofuran (1.0 M, 55.0 mL, 5.00 eq) at 0 °C. The mixture was stirred at 70 °C for 2 h. Three parallel reaction mixture was combined. The mixture was quenched with methanol (150 mL) and concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®;80 g SepaFlash® Silica Flash Column, Eluent of 0-66% Ethylacetate/Petroleum ether gradient @ 100 mL/mint) to afford 2-(2-chloro-4-nitrophenethoxy)-7V-methylethan-l -amine, Int 1g, (5.40 g, 20.9 mmol, 63% yield) as yellow oil. ‘HNMR (400 MHz, DMSO-tfc) 3 = 8.20 (d, J= 2.0 Hz, 1H), 8.10 (dd, J= 2.4, 8.5 Hz, 1H), 7.68 (d, J= 8.4 Hz, 1H), 5.78 (br s, 1H), 3.67 (t, J= 6.8 Hz, 2H), 3.61 (dt, J= 2.0, 5.6 Hz, 2H), 3.05 (t, J= 6.8 Hz, 2H), 2.77 - 2.56 (m, 2H), 2.29 - 2.22 (m, 3H).
Step F. Preparation of Int Ih
Figure imgf000183_0001
Int 1g Int lh
To a solution of 2-(2-chloro-4-nitrophenethoxy)-/V-methylethan-l-amine, Int 1g, (5.40 g, 20 9 mmol, 1.00 eq) in di -tert-butyl dicarbonate (50 0 mL) was added tri ethylamine (6.54 g, 64.7 mmol, 9.00 mL, 3.10 eq) and 4-dimethylaminopyridin (510 mg, 4.17 mmol, 0.200 eq).
The mixture was stirred at 25 °C for 0.5 h. The mixture was concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 120 g SepaFlash® Silica Flash Column, Eluent of 0~20% ethyl acetate/Petroleum ether gradient @ 100 mL/mint) to afford tert- butyl (2-(2-chloro-4-nitrophenethoxy)ethyl)(methyl)carbamate, Int Ih, (5.50 g, 15.3 mmol, 73% yield) as a yellow solid. H NMR (400 MHz, DMSO-uf) δ = 8.26 (d, J= 2.4 Hz, IH), 8.13 (dd, J = 2.4, 8.5 Hz, IH), 7.67 (d, J= 8.6 Hz, IH), 3.68 (t, J= 6.4 Hz, 2H), 3.48 (t, J= 5.6 Hz, 2H), 3.30 - 3 24 (m, 2H), 3.06 (t, J= 6.4 Hz, 2H), 2.73 (s, 3H), 1.36 (s, 9H).
Step G. Preparation of Int li
„
Boc
Figure imgf000183_0002
oc
Int lh Int 11
To a solution of tert-butyl (2-(2-chloro-4-nitrophenethoxy)ethyl)(methyl)carbamate, Int Ih, (6.00 g, 16.7 mmol, 1 .00 eq) in ethyl alcohol (110 mb) were added saturated ammonium chloride (2.68 g, 50.2 mmol, 3.00 eq) in water (13.0 mb) and iron (4.67 g, 83.6 mmol, 5.00 eq). The mixture was stirred at 80 °C for 3 h. The mixture was diluted with water (100 mb) and extracted with ethyl acetate (3 x 50.0 mb). The combined organic layer was washed with brine (3 x 100 mb), dried over anhydrous sodium sulfate and filtered. The filtrate was concentrated to afford tert-butyl (2-(4-amino-2-chlorophenethoxy)ethyl)(methyl)carbamate, Int li, (5.00 g, 15.2 mmol, 91% yield) as yellow oil. 1H NMR (400 MHz, DMSO-<@) δ = 6.96 (d, J= 8.2 Hz, IH), 6.58 (d, J= 2.4 Hz, IH), 6.44 (dd, 2.4, 8.3 Hz, IH), 5.28 - 5.14 (m, 2H), 3.54 - 3.42 (m, 4H), 3.33 (s, IH), 3.31 - 3.25 (m, 2H), 2.80 - 2.75 (m, 3H), 2.75 - 2.68 (m, 2H), 1.39 (s, 9H).
Figure imgf000183_0003
Int 1i Int 1j
To a solution of tert-butyl (2-(4-amino-2-chlorophenethoxy)ethyl)(methyl)carbamate,
Int li, (2.50 g, 7.60 mmol, 1.00 eq) in dichloromethane (25.0 mL) was added triethylamine (2.31 g, 22.8 mmol, 3.17 mL, 3.00 eq) and phenyl carbonochloridate (1.79 g, 11.4 mmol, 1.43 mL, 1.50 eq). The mixture was stirred at 25 °C for 4 h. The mixture was concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®;60 g SepaFlash® Silica Flash Column, Eluent of 0-66% Ethylacetate/Petroleum ether gradient @ 100 mL/mint) to afford terLbutyl (2-(2-chloro-4-((phenoxycarbonyl)amino)phenethoxy)ethyl)(methyl) carbamate, Int Ij, (2.60 g, 5.79 mmol, 76% yield) as yellow oil. 1H NMR (400 MHz, DMSO-tfc) δ = 7.94 (d, J = 2.0 Hz, 1H), 7.45 - 7.41 (m, 3H), 7.32 - 7.27 (m, 2H), 7.21 - 7.19 (m, 3H), 3.69 - 3.56 (m, 2H), 3.48 (br t, J= 5.4 Hz, 2H), 3.26 (q, J= 5.6 Hz, 2H), 2.92 - 2.72 (m, 1H), 2.76 (br d, J = 2.0 Hz, 1H), 2.68 (s, 3H), 1.39 - 1.33 (m, 9H).
Step I. Preparation of Int Ik
Figure imgf000184_0001
To a solution of 3 -(5-(aminomethyl)-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int Ij, (609 mg, 2.23 mmol, 1.00 eq) in A(A'-dimethylformamide (10.0 mL) was added diisopropylethylamine (864 mg, 6.68 mmol, 1.16 mL, 3.00 eq), 4-dimethylaminopyridin (272 mg, 2 23 mmol, 1.00 eq) and tert-butyl (2-(2-chloro-4- ((phenoxycarbonyl)amino)phenethoxy)ethyl)(methyl)carbamate, Int AA, (1.00 g, 2.23 mmol, 1.00 eq). The mixture was stirred at 25 °C for 12 h. The mixture was concentrated to give a residue. The residue was purified by reversed-phase HPLC (C1 8,120 g; condition: water/acetonitrile=l/0-0/l,0. 1% formic acid) and lyophilized to afford tert-butyl(2-(2-chloro-4- (3-((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)ureido) phenethoxy)ethyl)(methyl)carbamate, Int Ik, (300 mg, 444 umol, 20% yield, 93% purity) as a yellow solid. H NMR (400 MHz, DMSO-tfc) δ = 8.78 (s, 1H), 7.72 - 7.64 (m, 2H), 7.51 (s, 1H), 7.44 (d, J= 7.6 Hz, 1H), 7.22 - 7.11 (m, 2H), 6.80 (t, J= 5.6 Hz, 1H), 5.10 (dd, J= 5.2, 13.3 Hz, 1H), 4.47 - 4.27 (m, 3H), 3.55 (br t, J= 6.8 Hz, 2H), 3.47 (br t, J= 5.2 Hz, 2H), 3.29 - 3.25 (m, 2H), 2.83 (br t, J= 7.0 Hz, 2H), 2.75 (br s, 3H), 2.61 (br d, J= 2.2 Hz, 1H), 2.57 (br s, 1H), 2.43
- 2.35 (m, 1H), 2.04 - 1.92 (m, 1H), 1.38 (s, 9H).
Step J. Preparation of Compound IG-3
Figure imgf000185_0001
Compound IG-3 To a solution of tert-butyl (2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3-yl)-l- oxoisomdolin-5-yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int Ik, (270 mg, 430 umol, 1.00 eq) in ethyl acetate (3.00 mL) was added hydrochloric acid / dioxane (4.00 M, 2.16 mL, 20.1 eq). The mixture was stirred at 25 °C for 2 h. The mixture was concentrated under reduced pressure to give a residue. The residue was triturated with ethyl acetate (10.0 mL) and filtered to afford l-(3-chloro-4-(2-(2-(methylamino)ethoxy)ethyl)phenyl)-3-((2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)urea, Compound IG-3, (81.8 mg, 153 umol, 36% yield, 99% purity, hydrochloride) as a yellow solid. 1H NMR (400 MHz, DMSO-<4) 3 = 10.98 (s, 1H), 9.12 (s, 1H), 8.61 (br s, 2H), 7.79 - 7.62 (m, 2H), 7.52 (s, 1H), 7.44 (br d, J= 7.6 Hz, 1H), 7.31 - 7.11 (m, 2H), 7.02 (br t, J= 5.6 Hz, 1H), 5.11 (br dd, J= 4.8, 13.0 Hz, 1H), 4.50 - 4.37 (m, 3H), 4.35 - 4.28 (m, 1H), 3.66 (br t, J= 4.8 Hz, 2H), 3.62 (br t, J= 7.0 Hz, 2H), 3.08
(br s, 2H), 2.93 - 2.86 (m, 3H), 2.62 (br s, 1H), 2.54 (br s, 3H), 2.40 (br s, 1H), 2.01 (br dd, ./~ 5.6, 10.7 Hz, 1H). MS (ESI) m/z 528.5 [M+H]+
The compounds in Table 4 were prepared in a manner similar to that described for Compound IG-3 using Int AA and the appropriately substituted phenyl carbamate.
Table 4
Figure imgf000186_0001
Figure imgf000187_0001
Figure imgf000188_0001
EXAMPLE 3 Synthesis of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-4- hydroxy-l-oxoisoindolin-5-yl)methyl)urea (Compound IG-15)
Figure imgf000189_0001
Int 11
To a solution of 2-methylpropan-2-amine (4. 18 g, 57.2 mmol, 6.01 mL, 1.90 eq) in toluene
(50 mL) was added a mixture of dibromine (4.57 g, 28.6 mmol, 1.47 mL, 0.95 eq) in di chloromethane (10 mL) at -78 °C for 1 h, then methyl 3-hydroxy-2-methylbenzoate (5.00 g, 30.1 mmol, 1 00 eq) in dichloromethane (50 mL) was added dropwise, the mixture was stirred at 25 °C for 5 h. The mixture was concentrated to give a residue. The residue was purified by column chromatography (SiOr, petroleum ether/ethyl acetate=10/l) to afford methyl 4-bromo-3-hydroxy-2- methylbenzoate, Int 11, (5.50 g, 22.4 mmol, 75% yield) as a white solid. H NMR (400 MHz, DMSO-^) <>' = 9.63 - 9.16 (m, 1H), 7.46 (d, J= 8 4 Hz, 1H), 7.17 (d, J = 8.4 Hz, 1H), 3.80 (s, 3H), 2.38 (s, 3H)
Step B. Preparation of Int Im
Figure imgf000189_0002
To a solution of methyl 4-bromo-3-hydroxy-2-methylbenzoate, Int 11, (5.50 g, 22.4 mmol, 1.00 eq) in ,N,N-dimethylformamide (30 mL) was added potassium carbonate (6.20 g, 44.9 mmol, 2.00 eq) and methyl iodide (9.56 g, 67.3 mmol, 4.19 mL, 3.00 eq), the mixture was stirred at 25 °C for 12 h. The mixture was diluted with water (30 mL) and extracted with ethyl acetate (3 x 30 mL). The combined organic layers were washed with brine (2 x 20 mL), dried over sodium sulfate and filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography ( Si O2, petroleum ether/ethyl acetate=3/l ) to afford methyl 4- bromo-3-methoxy-2-methylbenzoate, Int Im, (5.70 g, 22.0 mmol, 98% yield) as yellow oil. 1H NMR (400 MHz, CDCh-J) δ = 7.56 - 7.49 (m, 1H), 7.47 - 7.41 (m, 1H), 3.89 (s, 3H), 3.81 (s, 3H), 2.56 (s, 3H).
Step C. Preparation of Int In
Figure imgf000190_0001
To a solution of methyl 4-bromo-3-methoxy-2-methylbenzoate, Int Im, (5.70 g, 22.0 mmol, 1.00 eq) and //-bromosuccinimide (4.31 g, 24.2 mmol, 1.10 eq) in trichloromethane (2 00 mL) was added (E)-3, 3 -(diazene- l,2-diyl)bis(2 -methylpropanenitrile) (361 mg, 2.20 mmol, 0.10 eq), the mixture was stirred at 80 °C for 4 h. The mixture was filtered and the filtrate was concentrated to give a residue. The residue was purified by column chromatography (SiO2, petroleum ether/ethyl acetate=10/l) to afford methyl 4-bromo-2-(bromomethyl)-3-methoxybenzoate, Int In, (6.50 g, 19.2 mmol, 87% yield) as yellow oil. 1H NMR (400 MHz, CDCI3) δ = 7.67 - 7.58 (m, 2H), 5.09 (s, 2H), 4.03 (s, 3H), 3.95 (s, 3H).
Step D. Preparation of Int lo
Figure imgf000190_0002
To a solution of methyl 4-bromo-2-(bromomethyl)-3-methoxybenzoate, Int In, (6.50 g, 19.2 mmol, 1 00 eq) and 3 -aminopiperidine-2, 6-dione (4.75 g, 28.9 mmol, 1.50 eq, hydrochloride) in acetonitrile (60 mL) was added diisopropylethylamine (7.46 g, 57 7 mmol, 10.1 mL, 3.00 eq), the mixture was stirred at 90 °C for 4 h. The mixture was triturated with ethyl acetate/water=2/l (50 mL) and filtered , the filter cake was concentrated under reduced pressure to afford 3-(5-bromo-4- methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int lo, (5.00 g, 14.2 mmol, 74% yield) as a brown solid. ‘HNMR (400 MHz, DMSO-O δ = 11.01 (s, 1H), 7.76 (d, J= 8.0 Hz, 1H), 7 36 (d, J = 8.0 Hz, 1H), 5.11 (dd, 7= 5.2, 13.6 Hz, 1H), 4.81 - 4 67 (m, 1H), 4 62 - 4.50 (m, 1H), 3 99 (s, 3H), 2.99 - 2.85 (m, 1H), 2.66 - 2.56 (m, 1H), 2.47 - 2.38 (m, 1H), 2.01 (tdd, J= 2.8, 5.6, 12.6 Hz, 1H).
Figure imgf000191_0001
To a solution of 3-(5-bromo-4-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int lo, (1 00 g, 2.83 mmol, 1.00 eq) and (((tert-butoxy carbonyl )amino)methyl)trifluoroborate (873 mg, 3.68 mmol, 1 .30 eq) in dioxane (10 mL) and water (1 .00 mL) was added palladium(II) acetate (127 mg, 566 umol, 0.20 eq), cesium carbonate (1.85 g, 5.66 mmol, 2.00 eq) and di(adamantan-l- yl)(butyl)phosphane (406 mg, 1.13 mmol, 0.40 eq), the mixture was stirred at 100 °C for 12 h under nitrogen atmosphere. The mixture was filtered and the filtrate was concentrated to give a residue. The residue was purified by column chromatography (SiO2, petroleum ether/ethyl acetate=3/l) to afford tert-butyl ((2-(2,6-dioxopiperidin-3-yl)-4-methoxy-l-oxoisoindolin-5-yl)methyl)carbamate, Int Ip, (500 mg, 1 24 mmol, 44% yield) as a yellow solid H NMR (400 MHz, DMSO-cfe) δ = 11.00 (s, 1H), 7.43 - 7.38 (m, 1H), 7.38 - 7.29 (m, 2H), 5.11 (dd, J= 5.2, 13.6 Hz, 1H), 4.68 (d, J =
17.2 Hz, 1H), 4.50 (d, J= 16 8 Hz, 1H), 4.20 (br d, J= 5.9 Hz, 2H), 3.94 (s, 3H), 2.97 - 2 87 (m, 1H), 2.57 (br s, 1H), 2.36 (br s, 1H), 2.01 (br dd, J= 2.4, 5.6 Hz, 1H), 1.40 (s, 9H). MS (ESI) m/z
404.2 [M+H]
Figure imgf000191_0002
To a solution of tert-butyl ((2-(2,6-dioxopiperidin-3-yl)-4-methoxy-l-oxoisoindolin-5- yl)methyl)carbamate, Int Ip, (500 mg, 1.24 mmol, 1.00 eq) in ethyl acetate (10 mL) was added hydrochloric acid /ethyl acetate (4 M, 16.7 mL, 53 8 eq), the mixture was stirred at 25 °C for 1 h. The mixture was concentrated to afford 3-(5-(aminomethyl)-4-methoxy-l-oxoisoindolin-2- yl)piperidine-2, 6-dione, Int BB, (250 mg, 824 umol, 66% yield) as a yellow solid
Step G. Preparation of Int Iq
Figure imgf000192_0001
To a solution of 3-(5-(aminomethyl)-4-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int BB, (150 mg, 495 umol, 1.00 eq) and 2-chloro-4-isocyanato-l-methylbenzene (166 mg, 989 umol, 2.00 eq) in A',;V-dimethylforniamide (2.00 mL) was added diisopropylethylamine (150 mg, 1.16 mmol, 202 uL, 2.35 eq), the mixture was stirred at 25 °C for 12 h. The mixture was diluted with water (2.00 mL), acetonitrile (2 00 mL) and filtered. The filtrate was purified by reversed- phase (C18, 12 g; condition: water/acetonitrile = 1/0 -0/1, 0.1% formic acid) and lyophilized to afford l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-4-methoxy-l-oxoisoindolin-5- yl)methyl)urea, Int Iq, (60.0 mg, 127 umol, 26% yield) as a white solid. MS (ESI) m/z 471. 1 [M+H]+
Step G. Preparation of Compound IG-15
Figure imgf000192_0002
To a solution of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-4-methoxy-l- oxoisoindolin-5-yl)methyl)urea, Int Iq, (60.0 mg, 127 umol, 1.00 eq) in di chloromethane (5.00 mL) was added tribromoborane (319 mg, 1.27 mmol, 123 uL, 10.0 eq) at 0 °C, the mixture was stirred at 25 °C for 1 h. The mixture was quenched with water (5.00 mL) and concentrated under reduced pressure to removed dichloromethane (5.00 mL) to give a residue. The residue was purified by reversed-phase HPLC (C18, 12 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1% formic acid) and lyophilized to afford l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l- oxoisoindolin-5-yl)methyl)urea, Compound IG-15, (27.72 mg, 59.5 umol, 47% yield, 98% purity) as a white solid. ’H NMR (400 MHz, DMSO-C&) 3 = 10.98 (s, 1H), 10.05 (s, 1H), 8.82 (s, 1H), 7.62 (d, J= 1 6 Hz, 1H), 7.35 (d, J= 7.6 Hz, 1H), 7.24 - 7.16 (m, 2H), 7.14 - 7.08 (m, 1H), 6.77 (br t, J = 5.8 Hz, 1H), 5.09 (dd, J= 5.0, 13.2 Hz, 1H), 4.41 - 4.19 (m, 4H), 2.97 - 2.84 (m, 1H), 2.60 (br d, J = 18.2 Hz, 1H), 2.42 - 2.35 (m, 1H), 2.23 (s, 3H), 2.05 - 1.95 (m, 1H). MS (ESI) m/z 445.2[M+H]+ The compounds in Table 5 were prepared in a manner similar to that described for Compound IG-15 using Int BB and the appropriately substituted carboxylic acid, aryl isocyanate, or phenyl carbamate (c.f. Example 2).
Table 5
Figure imgf000194_0001
Figure imgf000195_0001
Figure imgf000196_0001
Figure imgf000197_0001
Figure imgf000198_0001
Figure imgf000199_0001
Figure imgf000200_0001
Figure imgf000201_0001
EXAMPLE 4 Synthesis of N-(3-chloro-4-(2-(2-(methylamino)ethoxy)ethyl)phenyl)-3-(2-
(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)propanamide (Compound IG-2)
Figure imgf000202_0002
int ir
A mixture of A-cyclohexyl-A-methylcyclohexanamine (1.93 g, 9.90 mmol, 2.10 mL, 1.60 eq), tri-tert-butylphosphonium;tetrafluoroborate (900 mg, 3.10 mmol, 5.00 eq) and tris(dibenzylideneacetone)dipalladium(0) (566 mg, 618 urnol, 0.100 eq) in dioxane (30.0 mL) was stirred at 25 °C for 0.5 h, then 3-(5-bromo-l-oxoisoindolin-2-yl)piperidine-2, 6-dione (2.00 g, 6.19 mmol, 1 00 eq) and tert-butyl acrylate (1.98 g, 15.4 mmol, 2.25 mL, 2.50 eq) was added. The mixture was stirred at 50 °C for 12 h. The reaction was diluted with water (100 mL) and extracted with ethyl acetate (3 x 100 mL). The combined organic layers were washed with brine (100 mL), dried over anhydrous sodium sulfate, fdtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiC>2, Petroleum ether/Ethyl acetate- 1/1 to 0/1) to afford tert-butyl 3-(2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)acrylate, Int Ir, (1.80 g, 4.86 mmol, 79% yield) as a brown solid. LH NMR (400 MHz, DMSO-tte) δ = 11.01 (br d, /= 1.6 Hz, 1H), 7.97 (s, 1H), 7.84 (d, J = 7 6 Hz, 1H), 7.74 (d, J= 7.6 Hz, 1H), 7.67 (d, J = 16.0 Hz, 1H), 6.67 (d, J= 16 0 Hz, 1H), 5.14 (dd, J= 5.2, 13.3 Hz, 1H), 4.55 - 4.44 (m, 1H), 4.41 - 4.28 (m, 1H), 2.92 (ddd, J ~ 5 2. 13.6, 17.4 Hz, 1H), 2.62 (br s, 1H), 2.46 - 2.41 (m, 1H), 2.07 - 2.00 (m, 1H), 1.50 (s, 9H).
Step B. Preparation of Int Is
Figure imgf000202_0001
Int 1r To a solution of fert-butyl 3-(2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)acrylate, Int Ir, (1.80 g, 4.86 mmol, 1.00 eq) in tetrahydrofuran (100 mL) and methanol (10.0 mL) was added palladium carbon (180 mg, 10% purity) at nitrogen atmosphere. The mixture was stirred under hydrogen atmosphere at 25 °C for 12 h. The reaction was filtered to give a filter cake. The filter cake was triturated with ethyl acetate (100 mL) for 10 min to afford /evV-butyl 3-(2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)propanoate, Int Is, (1.20 g, 3.22 mmol, 66% yield) as a white solid. H NMR (400 MHz, DMSO-c/e) δ = 11.00 (br s, 1H), 7.64 (d, J - 7.6 Hz, 1H), 7.46 (s, 1H), 7.38 (d, J = 7.6 Hz, 1H), 5.11 (dd, J= 4.8, 13 2 Hz, 1H), 4.47 - 4.36 (m, 1H), 4.35 - 4.21 (m, 1H), 2.93 (br t, J= 'll Hz, 3H), 2.62 (br s, 1H), 2.59 - 2.56 (m, 2H), 2.40 (br dd, J= 4.0, 13.3 Hz, 1H), 2.05 - 1.97 (m, 1H), 1.37 (d, J= 1.2 Hz, 9H).
Step C. Preparation of Int It
Figure imgf000203_0001
A mixture of /c/7-butyl 3-(2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)propanoate, Int Is, (1.20 g, 3.22 mmol, 1.00 eq) in di chloromethane (15.0 mL) and trifluoroacetic acid (3.00 mL) was stirred at 25 °C for 1 h. The reaction was concentrated under reduced pressure to afford 3-(2- (2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)propanoic acid, Int It, (1.00 g, 3.16 mmol, 98% yield) as a white solid. 1H NMR (400 MHz, DMSO4) δ =10.99 (s, 1H), 7.64 (d, J= 7.6 Hz, 1H), 7.48 (s, 1H), 7.39 (d, J = 7.6 Hz, 1H), 5.11 (dd, J= 5.2, 13.2 Hz, 1H), 4.48 - 4.38 (m, 1H), 4.33 - 4.23 (m, 1H), 2.95 (br t, J= 7.2 Hz, 3H), 2.63 - 2.58 (m, 3H), 2.40 (br dd, J= 4.4, 13.2 Hz, 1H), 2.09 - 1.92 (m, 1H).
Step D. Preparation of Int Is
Figure imgf000204_0001
To a solution of fert-butyl (2-(4-amino-2-chlorophenethoxy)ethyl)(methyl)carbamate, Int Ih, (1.14 g, 3.48 mmol, 1.10 eq) in dimethylformamide (10.0 mL) was added 3-(2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)propanoic acid, Int It, (1.00 g, 3.16 mmol, 1.00 eq), O- (7-azabenzotriazol-l-yl)-N,N,N,N -tetramethyluroniumhexafluorophosphate (1.20 g, 3.16 mmol, 1.00 eq) and N,N, -diisopropylethylamine (1.23 g, 9 48 mmol, 1.65 mL, 3.00 eq), the mixture was stirred at 25 °C for 12 h. The reaction was diluted with water (50.0 mL) and extracted with ethyl acetate (3 x 50.0 mL). The combined organic layer was washed with brine (50.0 mL) and dried over anhydrous sodium sulfate, filtered and concentrated to give a residue. The residue was purified by column chromatography (SiO2, Petroleum ether/Ethyl acetate=l/l to 0/1) to afford tert- butyl (2-(2-chloro-4-(3-(2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)propanamido)phenethoxy) ethyl)(methyl)carbamate, Int lu, (1 50 g, 2.39 mmol, 76% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-d6)δ d = 10.97 (s, IH), 10.05 (s, IH), 7.79 (s, IH), 7.64 (d, J= 8.0 Hz, IH), 7.48 (s, IH), 7.40 (d, J= 8.0 Hz, IH), 7.37 - 7.31 (m, IH), 7.30 - 7.22 (m, IH), 5.10 (dd, J = 5.2, 13.4 Hz, IH), 4.47 - 4.36 (m, IH), 4.33 - 4 24 (m, IH), 3.57 (br t, J= 6.6 Hz, 2H),
3.47 (br t, J= 5.6 Hz, 2H), 3.29 - 3.24 (m, 2H), 3.02 (br t, J= 7 A Hz, 2H), 2.88 - 2.83 (m, 2H), 2.70 - 2.69 (m, IH), 2.68 - 2.65 (m, 2H), 2.61 (br s, IH), 2.58 - 2.58 (m, IH), 2.58 - 2.58 (m, IH), 2.58 - 2.57 (m, IH), 2.38 (br dd, J= 4.4, 13.6 Hz, IH), 1.37 (s, 9H).
Step D. Preparation of Compound IG-2
Figure imgf000205_0001
Compound IG-2
To a solution of tert-butyl (2-(2-chloro-4-(3-(2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)propanamido)phenethoxy)ethyl)(methyl)carbamate, Int lu, (700 mg, 1.12 mmol, 1.00 eq) in ethyl acetate (10 0 mL) was added hydrochloric acid/dioxane (4 M, 10 0 mL, 35 8 eq), the mixture was stirred at 25 °C for 1 h. Two parallel reactions was combined. The mixture was concentrated to give a residue. The residue was trituration with methanol (2.00 mL) and filtered to give a residue, the residue was diluted with water (20.0 mL) and lyophilized to afford /V-(3-chloro-4-(2-(2- (methylamino)ethoxy)ethyl)phenyl)-3-(2-(2, 6-di ox opiperi din-3 -yl)-l -oxoisoindolin-5- yl)propenamide, Compound IG-2, (813.28 mg, 1.40 mmol, 63% yield, 97% purity, hydrochloride) as a white solid. 1H NMR (400 MHz, DMS0-<4) δ = 10.98 (br s, 1H), 10.21 (s, 1H), 8.60 (br s, 1H), 7.80 (d, J= 1.6 Hz, 1H), 7.64 (d, J= 8.0 Hz, 1H), 7.49 (s, 1H), 7.43 - 7 35 (m, 2H), 7.34 - 7.26 (m, 1H), 5.09 (dd, J= 5.2, 13.6 Hz, 1H), 4.48 - 4.36 (m, 1H), 4.33 - 4.23 (m, 1H), 3.70 - 3.58 (m, 4H), 3.10 - 2.98 (m, 4H), 2.97 - 2.84 (m, 3H), 2.69 (br t, J= 7.6 Hz, 2H), 2.63 - 2.56 (m, 1H), 2.52 (br s, 3H), 2.41 - 2.32 (m, 1H), 2.05 - 1.91 (m, 1H). MS (ESI) m/z 527.3 [M+H]+ The compounds in Table 6 were prepared in a manner similar to that described for
Compound IG-2 using Int It and the appropriate aniline (c.f. Example 2).
Table 6
Figure imgf000205_0002
Figure imgf000206_0002
EXAMPLE 5
Synthesis of (2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl (3-chloro-4-(2-(2-
(methylamino)ethoxy)ethyl)phenyl)carbamate (Compound IG-4)
Figure imgf000206_0001
A mixture of 3-(5-bromo-l-oxo-isoindolin-2-yl)piperidine-2, 6-dione (500 mg, 1.55 mmol, 1.00 eq), [l,l-bis(diphenylphosphino)ferrocene]dichloropalladium(II) (340 mg, 464 umol, 0.300 eq), A,A-diisopropylethylamine (1.00 g, 7.74 mmol, 1.35 mL, 5.00 eq), triethylsilane (1.80 g, 15.47 mmol, 2 47 mL, 10.0 eq) in dimethylformamide (5.00 mL) and acetonitrile (5.00 mL), the mixture was stirred at 80 °C for 12 h under carbonic oxide (45 psi) atmosphere. The mixture was filtered to give a filtrate. The filtrate was purified by reversed phase-HPLC (column: Shim-pack C18 150*25*10um, mobile phase: [water(0.1% formic acid)- acetonitrile]) to afford 2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindoline-5-carbaldehyde, Int Iv, (120 mg, 441 umol, 28% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-uf) d = 1 1.04 (s, 1H), 10.16 (s, 1H), 8.16 (s, 1H), 8.07 (d, ./ - 7.8 Hz, 1H), 7.95 (d, ./ - 7.8 Hz, 1H), 5.17 (br dd, ./ - 5,0, 13.4 Hz, 1H), 4.64 - 4.54 (m, 1H), 4.50 - 4.41 (m, 1H), 2.98 - 2.87 (m, 1H), 2.64 (br s, 1H), 2.46 - 2.35 (m, 1H), 2.05 (br dd, J= 4.8, 10.8 Hz, 1H) Step B. Preparation of Int CC
Figure imgf000207_0001
To a solution of 2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindoline-5-carbaldehyde, Int Iv, (115 mg, 422 umol, 1.00 eq) in dimethylformamide (1.00 mL) and dichloromethane (1.00 mL) was added sodium borohydride acetate (448 mg, 2.11 mmol, 5.00 eq) and acetic acid (127 mg, 2. 11 mmol, 120 uL, 5.00 eq), the mixture was stirred at 50 °C for 2 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by Prep-HPLC (column: Waters Atlantis T3 15O*3Omm*5iim, mobile phase: [water(formic acid)- acetonitrile] ;B%: 5%-35%,10min) to afford 3-(5-(hydroxymethyl)-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int CC, (50.0 mg, 219 umol, 52% yield) as a white solid. ’H NMR (400 MHz, DMSO4) 3 = 11.00 (s,
Figure imgf000207_0002
Int 1 w
To a solution of 3-(5-(hydroxymethyl)-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int Ij, (397 mg, 1.45 mmol, 1.00 eq) in A,A-dimethylformamide (8.00 mL) was added sodium hydride (116 mg, 2 90 mmol, 60% purity, 2 00 eq) were stirred at 0 °C for 5 min, followed by addition of tert-butyl (2-(2-chloro-4-((phenoxycarbonyl)amino)phenethoxy)ethyl)(methyl)carbamate, Int CC, (650 mg, 1.45 mmol, 1.00 eq) The mixture was stirred at 0 °C for 1 h under nitrogen atmosphere. The mixture was quenched with formic acid (10.0 mL), diluted with water (20.0 mL) and extracted with ethyl acetate (3 * 20.0 mL). The combined organic layers were washed with brine (2 * 10.0 mL), dried over sodium sulfate and filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC (Cl 8, 12 g; condition: water/acetonitrile=l/0-0/l, 0.1% formic acid) and lyophilized to afford tert-butyl (2-(2-chloro-4-
((((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)methoxy)carbonyl)amino)phenethoxy)ethyl)(methyl)carbamate, Int Iw, (410 mg, 450 umol, 31% yield, 69% purity) as a yellow solid. MS (ESI) m/z 529.0 [M-99]+
Step D. Preparation of Compound IG-4
Figure imgf000208_0001
Compound IG-4
To a solution of tert-butyl (2-(2-chloro-4-((((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)methoxy)carbonyl)amino)phenethoxy)ethyl)(methyl)carbamate, Int Iw, (500 mg, 795 umol, 1.00 eq) in ethyl acetate (5.00 mL) was added hydrochloric acid /dioxane (4.00 M, 5.00 mL, 25.2 eq). The mixture was stirred at 25 °C for 2 h. The mixture was concentrated under reduced pressure to give a residue. The residue was triturated with ethyl acetate (10.0 mL) and filtered to give a residue, the residue was purified by Erep-HPLC (column: 3_Phenomenex Luna C18 75*30mm*3um;mobile phase: [water(HCl)-ACN];B%: 12%-32%,8min ) and lyophilized to afford (2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl (3-chloro-4-(2-(2- (methylamino)ethoxy)ethyl)phenyl)carbamate, Compound IG-4, (242 mg, 452 umol, 57% yield, 99% purity) as a yellow solid ’H NMR (400 MHz, DMSO+DiO) δ = 7 74 (d, J= 7 6 Hz, 1 H), 7 61 (s, 1H), 7 57 - 7.51 (m, 2H), 7.27 (s, 2H), 5.23 (s, 2H), 5.02 (dd, J= 5.2, 13.3 Hz, 1H), 4 53 - 441 (m, 1H), 4.38 - 4.29 (m, 1H), 3.66 - 3.55 (m, 4H), 3.03 (t, J= 5.0 Hz, 2H), 2.94 - 2.77 (m, 3H), 2.62 (br dd, J= 2.4, 15.6 Hz, 1H), 2.52 (br s, 3H), 2.44 - 2.29 (m, 1H), 2.08 - 1 .96 (m, 1H). MS (ESI) m/z 529.1 [M+H]+ The compounds in Table 7 were prepared in a manner similar to that described for Compound IG-4 using Int CC and the appropriately substituted aryl isocyanate, or phenyl carbamate (c.f. Example 2).
Table 7
Figure imgf000209_0002
EXAMPLE 6
Synthesis of l-(3-chloro-4-(2-(2-(methylamino)ethoxy)ethyl)phenyl)-3-((2-(l-methyl-2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)urea (Compound IG-8)
Figure imgf000209_0001
Int 1x To a solution of tert-butyl (2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int lk, (100 mg, 159 umol, 1.00 eq) in jV//-dimethylformamide (1.00 mL) was added potassium carbonate (44.0 mg, 318 umol, 2 00 eq) and methyl iodide (22.6 mg, 159 umol, 9.91 uL, 1.00 eq) at 0 °C. The mixture was stirred at 25 °C for 12 h. The mixture was quenched with saturated ammonium chloride solution (5.00 mL) and concentrated to give a residue. The residue was purified by P/vp-HPLC (column: Phenomenex Luna C18 150*25mm*10um;mobile phase: [water(FA)-ACN];B%: 43%-73%,10min) and lyophilized to afford tert-butyl (2-(2-chloro-4-(3-((2-(l-methyl-2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int lx, (60.0 mg, 93.4 umol, 58% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) δ = 8.83 (s, 1H), 7.73 - 7.65 (m, 2H), 7.51 (s, 1H), 7.44 (d, J = 8.0 Hz, 1H), 7.23 - 7.12 (m, 2H), 6.86 (t, 7= 6.0 Hz, 1H), 5.17 (dd, J= 4.8, 13.4 Hz, 1H), 4.50 - 4.25 (m, 4H), 3.55 (br t, J= 6.8 Hz, 2H), 3.47 (t, J= 5.6 Hz, 2H), 3.30 - 3.25 (m, 4H), 2.99 - 2.93 (m, 1H), 2.76 (br d, J= 5.2 Hz, 5H), 2.52 (br s, 1H), 2.47 - 2.39 (m, 1H), 2.38 - 2.31 (m, 1H), 2.06 - 1.96 (m, 1H), 1.37 (s, 9H).
MS (ESI) m/z 542.2 [M-100+H]4
Step B. Preparation of Compound IG-8
Figure imgf000210_0001
Compound IG-8
To a solution of tert-butyl (2-(2-chloro-4-(3-((2-(l-methyl-2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int lx, (60.0 mg, 93.4 umol, 1.00 eq) in ethyl acetate (1 00 mL) was added hydrochloric acid/dioxane (4.00 M, 23.4 uL, 1.00 eq). The mixture was stirred at 25 °C for 1 h. The mixture was concentrated to afford l-(3- chloro-4-(2-(2-(methylamino)ethoxy)ethyl)phenyl)-3-((2-( 1 -methyl -2, 6-dioxopiperi din-3 -yl)-l- oxoisoindolin-5-yl)methyl)urea, Compound IG-8, (34. 1 mg, 62.9 umol, 67% yield) as a yellow solid. H NMR (400 MHz, DMSO-d6 ) d = 9.18 - 8.96 (m, 1H), 8.81 - 8 37 (m, 2H), 7.75 - 7 62 (m, 2H), 7.51 (s, 1H), 7.44 (d, 7= 7.6 Hz, 1H), 7.28 - 7.16 (m, 2H), 7.05 - 6.92 (m, 1H), 5.17 (dd, J= 5.2, 13.5 Hz, 1H), 4.51 - 4.25 (m, 4H), 3.69 - 3.56 (m, 4H), 3.08 (br s, 2H), 3.04 - 2.93 (m, 4H), 2.89 (br t, J= 6.8 Hz, 2H), 2.81 - 2.69 (m, 1H), 2.54 (s, 3H), 2.39 (br dd, J= 4.0, 13 3 Hz, 1H), 2.07 - 1.94 (m, 1H). MS (ESI) m/z 542.2 [M+H]+ EXAMPLE 7
Synthesis of N-(2-(2,6-dioxopiperidin-3-yl)-l,3-dioxoisoindolin-5-yl)-2-
(trifluoromethoxy (benzenesulfonamide (Compound IG-9)
Figure imgf000211_0001
Step A. Preparation of Compound IG-9
Figure imgf000211_0002
Compound IG-9
A mixture of 5-amino-2-(2,6-dioxopiperidin-3-yl)isoindoline- 1,3-dione (500 mg, 1.83 mmol, 1 00 eq) and 2-(trifluoromethoxy (benzene- 1 -sulfonyl chloride (954 mg, 3.66 mmol, 2.00 eq) in pyridine (8 mL) was stirred at 80 °C for 12 h The mixture was concentrated to give a residue. The residue was purified by Prep-HPLC (column: Phenomenex luna Cl 8 150*25mm* 10um;mobile phase: [water(FA)-ACN];B%: 36%-66%,10min) and lyophilized to afford A-(2-(2,6- dioxopiperidin-3-yl)-l,3-dioxoisoindolin-5-yl)-2-(tri fluoromethoxy (benzenesulfonamide, Compound IG-9, (409.01 mg, 814 umol, 44% yield, 99% purity) as an off-white solid. 1H NMR (400 MHz, DMSO-r/e) 11.60 (s, 1H), 11.10 (s, 1H), 8.10 (dd, J= 1.6, 8.0 Hz, 1H), 7.91 - 7.76 (m, 2H), 7.70 - 7.56 (m, 2H), 7.55 - 7.46 (m, 2H), 5.09 (dd, J= 5.6, 12.8 Hz, 1H), 2.93 - 2.80 (m, 1H), 2.60 (br d, J= 2.4 Hz, 1H), 2.43 (br d, J= 4.4 Hz, 1H), 2.07 - 1.96 (m, 1H) MS (ESI) m/z 498.2 [M4-H]+
The compounds in Table 8 were prepared in a manner similar to that described for Compound IG-9 using 5-amino-2-(2,6-dioxopiperidin-3-yl)isoindoline-l, 3-dione and the appropriately substituted aryl sulfonyl chloride (c f. Example 2). Table 8
Figure imgf000211_0003
Figure imgf000212_0003
EXAMPLE 8
Synthesis of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-3-oxoisoindolin-5- yl)methyl)urea (Compound IG-16)
Figure imgf000212_0002
Int 1y
A solution of methyl 5-cyano-2-methylbenzoate (5.00 g, 28.5 mmol, 1.00 eq) and benzoyl peroxide (BPO) (691 mg, 2.85 mmol, 0.10 eq) in trichloromethane (50.0 mL) was added N- bromosuccinimide (6.10 g, 34.3 mmol, 1 .20 eq), the mixture was stirred at 80 °C for 12 h The reaction mixture was poured into water (50.0 ml) and extracted with ethyl acetate (3 x 50 mL ), the combined organic phase was washed with brine (50.0 mL), dried with anhydrous sodium sulfate, filtered and concentrated in vacuum to afford methyl 2-(bromomethyl)-5 -cyano-benzoate, Int ly, (7 20 g, crude) as yellow oil.
Figure imgf000212_0001
To a solution of methyl 2-(bromomethyl)-5-cyanobenzoate, Int ly, (7.20 g, 28.3 mmol, 1.00 eq) and 3-aminopiperidine-2,6-dione;hydrochloride (4.66 g, 28.3 mmol, 1.00 eq)) in acetonitrile (100 mL) was added N,N-diisopropylethylamine (11 .0 g, 85.0 mmol, 14.8 mL, 3.00 eq), the mixture was stirred at 100°C for 12 h The mixture was filtered to give a residue. The residue was wash with citric acid (20 mL) to afford 2-(2,6-dioxopiperidin-3-yl)-3-oxoisoindoline-5-carbonitrile, Int Iz, (5.50 g, 20.4 mmol, 72% yield) as a purple solid. 1H NMR (400 MHz, DMSO-d6) 3 = 11 .02 (s, 1H), 8.21 (s, 1H), 8.10 (dd, J = 1.5, 7.9 Hz, 1H), 7.85 (d, J = 7.9 Hz, 1H), 5.15 (dd, J = 5.1, 13.3 Hz, 1H), 4.73 - 4.38 (m, 2H), 2.97 - 2.85 (m, 1H), 2.64 - 2.56 (m, 1H), 2.41 (br dd, J = 4.5, 13.1 Hz, 1H), 2.09 - 1.97 (m, 1H). MS (ESI) m/z 270.2 [M+H]+ Step C. Preparation of Int DD
Figure imgf000213_0001
A solution of 2-(2,6-dioxopiperidin-3-yl)-3-oxoisoindoline-5-carbonitrile, Int Iz, (500 mg, 1.86 mmol, 1.00 eq) in methanol (100 mL) was added hydrochloric acid (28.3 g, 280 mmol, 10 mL, 36.0% purity, 54.3 eq) slowly and was degassed with nitrogen for 3 times. After that, platinum(IV) oxide (211 mg, 928 umol, 0 50 eq) was added under nitrogen atmosphere. The mixture was degassed with hydrogen for 3 times, and stirred at 25 °C for 12 h under hydrogen atmosphere (45 psi). The mixture was filtered to give a filter cake. The filter cake was dissolved by dimethyl formamide (10.0 mL). The solution was filtered to give a filtrate. The filtrate was concentrated in vacuum to afford 3-(6-(aminomethyl)-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int DD, (250 mg, crude) as a brown solid. H NMR (400 MHz, DMSO-d6) 3 = 11.01 (s, 1H), 7.90 (s, 1H), 7.75 (d, J = 7.8 Hz, 1H), 7.70 - 7.57 (m, 1H), 5.12 (dd, J = 5.1, 13.3 Hz, 1H), 4 55 - 4.44 (m, 1H), 4.40 - 4.29 (m, 1H), 4.15 (br s, 2H), 2.98 - 2.90 (m, 1H), 2.66 - 2.57 (m, 1H), 2.42 (dq, J = 4.4, 13.2 Hz, 1H), 2.09 - 1.97 (m, 1H).
Step D. Preparation of Compound IG-16
Figure imgf000213_0002
To a solution of 3-(6-(aminomethyl)-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int DD, (100 mg, 366 umol, 1.00 eq) in dimethyl formamide (3.00 mL) was added triethylamine (55.5 mg, 549 umol, 76.4 uL, 1.50 eq) and 2-chloro-4-isocyanato-l -methylbenzene (73.6 mg, 439 umol, 1.20 eq) . The mixture was stirred at 25°C for 2 h. The mixture was concentrated in vacuum to give a residue. The residue was purified by column chromatography (SiO2, Petroleum ether/Ethyl acetate = 5/1 to 0/1) to afford the crude product. The crude product was purified by T’re/2-HPLC (column Phenom enex luna C 18 150*25mm* 10um;mobile phase: [water(FA)-ACN];B%: 34%-54%,9min) and lyophilized to afford l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-3- oxoisoindolin-5-yl)methyl)urea, Compound IG-16, (31.4 mg, 71.2 umol, 10% yield, 99% purity) as a white solid. 1H NMR (400 MHz, DMSO-cfc) δ = 11.27 - 10.77 (m, 1H), 8.73 (s, 1H), 7.66 (s, 2H), 7.57 (s, 2H), 7.23 - 7.10 (m, 2H), 6 80 (t, J = 6.2 Hz, 1H), 5.12 (dd, J = 5.0, 13.0 Hz, 1H), 4.47 - 4.28 (m, 4H), 3.07 - 2.83 (m, 1H), 2.68 - 2.61 (m, 1H), 2.40 - 2.33 (m, 1H), 2.24 (s, 3H), 2.05 - 1.97 (m, 1H). MS (ESI) m/z 441.2 [M+H]+
The compounds in Table 9 were prepared in a manner similar to that described for Compound IG-16 using Int DD and the appropriately substituted aryl isocyanate, or phenyl carbamate (c.f. Example 2).
Table 9
Figure imgf000214_0001
EXAMPLE 8 Synthesis of 4-amino-2-(2,6-dioxopiperidin-3-yl)-l,3-dioxoisoindolin-5-yl 2- (trifluoromethoxy)benzenesulfonate (Compound IG-17) and 6-amino-2-(2,6-dioxopiperidin-3-yl)- l,3-dioxoisoindolin-5-yl 2-(trifluoromethoxy)benzenesulfonate (Compound IG-18)
Figure imgf000215_0001
Compound IG-17 Compound IG-18
Step A. Preparation of Int 2a and Int 2b
Figure imgf000215_0002
Int 2a Int 2b
4-hydroxyphthalic acid (10.0 g, 54.9 mmol, 1.00 eq) was suspension in sulfuric acid (200 mL, 85% purity) at 5 °C. Guanidine nitrate (6 57 g, 53.8 mmol, 0.980 eq) was added to the mixture slowly at 5 °C. Then the mixture was stirred at 25 °C for another 2 h. The reaction solution was poured into ice-water (500 mL) and extracted with ethyl acetate (500 mL). The organic layer was separated and concentrated under reduced pressure to afford a mixture of 4-hydroxy-5-nitrophthalic acid, lot 2a, and 4-hydroxy-3-nitrophthalic acid, Int 2b, (11.1 g, 29 3 mmol, 53 % yield) as a yellow solid. 1H NMR (400 MHz, DMSO-^) δ = 13.18 (s, 1H), 12.09 (br s, 2H), 8.28 (s, 1H), 7.91 (d, J= 8 8 Hz, 1H), 7.21 - 7.18 (m, 2H) Step B. Preparation of Int 2c and Int 2d
Figure imgf000215_0003
Int 2a Int 2b Int 2c Int 2d
A mixture of 4-hydroxy-5-nitrophthalic acid, Int 2a, and 4-hydroxy-3-nitrophthalic acid, Int 2b, (11.1 g, 29.3 mmol, 60% purity, 1.00 eq) in acetic anhydride (50.0 mL) was degassed and purged with nitrogen for 3 times, and then the mixture was stirred at 110 °C for 3 h under nitrogen atmosphere The reaction mixture was concentrated under reduced pressure to afford a mixture of 6-nitro-l,3-dioxo-l,3-dihydroisobenzofuran-5-yl acetate, Int 2c, and 4-nitro-l,3-dioxo-l,3- dihydroisobenzofuran-5-yl acetate, Int 2d, (6.00 g, 14.4 mmol, 49% yield) as black oil. 1H NMR (400 MHz, DMSO-d6) S = 8.79 (s, 1H), 8.42 (d, J= 8.4 Hz, 1H), 8.35 (s, 1H), 8.15 (d, J = 8.4 Hz, 1H), 2.38 (s, 3H), 2.22 (s, 3H).
Step C. Preparation of Int 2e and Int 2f
Figure imgf000216_0001
To a solution of a mixture of 6-nitro-l,3-dioxo-l,3-dihydroisobenzofuran-5-yl acetate, Int 2c, and 4-nitro-l,3-dioxo-l,3-dihydroisobenzofuran-5-yl acetate, Int 2d, (1.00 g, 2.39 mmol, 1 00 eq) in acetonitrile (20.0 mL) was added A,A-diisopropylethylamine (618 mg, 4.78 mmol, 833 uL, 2.00 eq) and 3-aminopiperidine-2, 6-dione (306 mg, 2.39 mmol, hydrochloric acid, 1.00 eq). The mixture was stirred at 80 °C for 3 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by reverse-phase HPLC ( 0.1% FA condition) The desired fraction was lyophilized to afford a mixture of 2-(2,6-dioxopiperidin-3-yl)-5-hydroxy-6- nitroisoindoline- 1,3 -dione, Int 2e, and 2-(2,6-dioxopiperidin-3-yl)-5-hydroxy-4-nitroisoindoline- 1, 3-dione, Int 2f, (400 mg, 1.25 mmol, 52% yield) as a white solid 1H NMR (400 MHz, DMSO- d6) δ = 11.14 (s, 1H), 8.36 (s, 1H), 7.96 (d, J = 8.4 Hz, 1H), 7.50 (s, 1H), 7.48 (s, 1H), 7.48 - 7.46 (m, 1H), 5.16 - 5.12 (m, 1H), 2.95 - 2.81 (m, 2H), 2.62 (br s, 1H), 2.06 (br s, 1H).
Step D, Preparation of Int 2g and Int 2h
Figure imgf000216_0002
To a solution of a mixture of 2-(2,6-dioxopiperidin-3-yl)-5-hydroxy-6-nitroisoindoline-l,3- dione, Int 2e, and 2-(2,6-dioxopiperidin-3-yl)-5-hydroxy-4-nitroisoindoline-l, 3-dione, Int 2f, (350 mg, 1.10 mmol, 1.00 eq) in dioxane (5.00 mL) was added palladium / carbon (100 mg, 10.0% purity) under nitrogen atmosphere The suspension was degassed and purged with hydrogen for 3 times. The mixture was stirred under hydrogen atmosphere (15 Psi) at 25 °C for 3 h. The filter cake was diluted with water (10.0 mL). The residue was purified by reversed-phase HPLC(column: Phenom enex luna C 18 150*25mm* 10um;mobile phase: [water(FA)-ACN];B%: 7%- 37%,10min),and the fraction was lyophilized to afford a mixture of 5-amino-2-(2,6-dioxopiperidin- 3-yl)-6-hydroxyisoindoline-l, 3-dione, Int 2g, and 4-amino-2-(2,6-dioxopiperidin-3-yl)-5- hydroxyisoindoline- 1,3 -dione, Int 2h, (200 mg, 318.07 umol,) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) 6 = 11.06 (s, 1H), 10.83 (br s, 1H), 6.97 (s, 1H), 6.93 - 6.90 (tn, 1H), 5.95 (s, 2H), 4.99 (br d, J= 5.4 Hz, 1H), 2.93 - 2.81 (m, 2H), 2.07 - 1.87 (m, 2H) MS (ESI) m/z 290.0 [M+H]+ Step E. Preparation of Compound IG-17 and Compound IG-18
Figure imgf000217_0001
Compound IG-17 Compound IG-18
A mixture of 5-amino-2-(2,6-dioxopiperidin-3-yl)-6-hydroxyisoindoline-l, 3-dione, Int 2g, and 4-amino-2-(2,6-dioxopiperidin-3-yl)-5-hydroxyisoindoline-l, 3-dione, Int 2h, (60.0 mg, 104 umol, 1.00 eq), 2-(trifluoromethoxy)benzenesulfonyl chloride (54 0 mg, 207 umol, 2.00 eq) and triethylamine (31.5 mg, 311 umol, 43.3 uL, 3 00 eq) in trichloromethane (5.00 mL) was degassed and purged with nitrogen atmosphere for 3 times, and then the mixture was stirred at 80 °C for 12 h under nitrogen atmosphere The mixture was filtered and the filtrate was concentrated to give a residue. The residue was purified by reverse-phase HPLC(column: Phenomenex luna C 18 150*25mm* 10um;mobile phase: [water(FA)-ACN];B%: 38%-58%, lOmin), and the fraction was lyophilized to afford 6-amino-2-(2,6-dioxopiperidin-3-yl)-l,3-dioxoisoindolin-5-yl 2- (trifluoromethoxy)benzenesulfonate, Compound IG-17, (8.08 mg, 15.4 umol, 14.9% yield, 98% purity) as a yellow solid and 4-amino-2-(2,6-dioxopiperidin-3-yl)-l,3-dioxoisoindolin-5-yl 2- (trifluoromethoxy)benzenesulfonate, Compound IG-18, (20.85 mg, 39.4 umol, 38% yield, 97% purity) as a yellow solid.
Compound IG-17 ’H NMR (400 MHz, DMSO-^) J = 11.08 (br s, 1H), 8.11 (dd, J= 1.7, 7.9 Hz, 1H), 8.06 - 7.99 (m, 1H), 7.79 (br d, J= 8.2 Hz, 1H), 7.69 (t, J= 7.7 Hz, 1H), 7.18 (s, 1H), 7.11 (s, 1H), 6.61 (br s, 2H), 5.03 (dd, J = 5.3, 12.9 Hz, 1H), 2.93 - 2.79 (m, 1H), 2.59 (br d, J= 2.8 Hz, 1H), 2.47 - 2.41 (m, 1H), 2.04 - 1.94 (m, 1H) MS (ESI) m/z 514.1 [M+H]+
Compound IG-18 1H NMR (400 MHz, DMSO-d6) 6 = 11.12 (br s, 1H), 8.09 (d, J= 7.6 Hz, 1H), 8.05 - 8.00 (m, 1H), 7.80 (br d, J= 8.4 Hz, 1H), 7.71 - 7.66 (m, 1H), 7.11 (d, .7 = 8.0 Hz, 1H), 7.01 (d, J= 8.0 Hz, 1H), 6.41 (s, 2H), 5.07 (dd, J= 5.6, 12.7 Hz, 1H), 2.90 - 2 82 (m, 1H), 2.61 (br s, 1H), 2.58 - 2.56 (m, 1H), 2.03 (br dd, J= 4.8, 11.6 Hz, 1H) MS (ESI) m/z 514.1 [M+H]+
EXAMPLE 9
Synthesis of 3-(4-((2-((2,3-dihydro-lH-inden-5-yl)methyl)pyrimidin-4-yl)amino)-l-oxoisoindolin- 2-yl)piperidine-2, 6-dione (Compound IG-19)
Figure imgf000218_0001
Int 2i
A solution of l-(2,3-dihydro-177-inden-5-yl)ethanone (24.0 g, 149 mmol, 1.00 eq) in sodium hypochlorite (500 mL, 5% purity) was stirred at 55 °C for 12 h. The reaction was adjusted to pH = 9 with sodium hydroxide and extracted with ethyl acetate (3 * 50 mL). The organic layer was discarded. The water phase was adjusted to pH = 4 with hydrochloric acid (36%) and extracted with ethyl acetate (3 * 50 mL). The organic layer was concentrated to give2,3-dihydro-177-indene- 5-carboxylic acid, Int 2i, (20.0 g, 123 mmol, 82% yield) as a yellow solid. 1H NMR (400 MHz, CDC13) δ = 7.97 (s, 1H), 7.92 (d, J= 7.8 Hz, 1H), 7.31 (d, J= 7.8 Hz, 1H), 2.97 (br t, J= 7.4 Hz, 4H), 2.17 - 2.10 (m, 2H). MS (ESI) m/z 163.2 [M+H]+
Step B. Preparation of Int 2j
Figure imgf000219_0001
To a solution of 2,3-dihydro-U7-indene-5-carboxylic acid, Int 2i, (10.0 g, 61.7 mmol, 1.00 eq) in tetrahydrofuran (100 mL) was added lithium aluminum hydride, LAH (7.02 g, 185 mmol, 3.00 eq) in four portions at 0 °C. Then the mixture was stirred at 25 °C for 12 h. The reaction mixture was treated with water (7 mL), sodium hydroxide (15%, 7 mL) and water (7 mL) again. Then the mixture was dried over anhydrous sodium sulfate and filtered. The filtrate was concentrated to give (2,3-dihydro-177-inden-5-yl)methanol, Int 2j, (8.80 g, crude) as a white solid. 1H), 7 17 - 7 11 (m, 1H), 4.66 (d,
Figure imgf000219_0002
Int 2j Int 2k
To a solution of (2,3-dihydro-l/7-inden-5-yl)methanol, Int 2j, (7.80 g, 52.6 mmol, 1.00 eq) in dimethyl formamide (80.0 mL) was added phosphorus tribromide, PBr3 (7.12 g, 26.3 mmol, 0.500 eq) at 0 °C. Then the mixture was stirred at 25 °C for 12 h. The reaction mixture was poured into sodium bicarbonate (Sat., 100 mL) at 0 °C and extracted with ethyl acetate (3 x 20 mL). The organic layer was dried over sodium sulfate and filtered. The filtrate was concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 120 g SepaFlash® Silica Flash Column, Eluent of 0-10% ethyl acetate/petroleum ether gradient @ 100 mL/min) to afford 5-(bromomethyl)-2,3-dihydro-177-indene, Int 2k, (8.00 g, 37.9 mmol, 72% yield) as yellow oil,. 1 H NMR (400 MHz, CDC13) δ = 7.27 (s, 1H), 7.23 - 7.12 (m, 2H), 4.52 (s, 2H), 2.90 (dt, J = 2.6, 7.4 Hz, 4H), 2.15 - 2.06 (m, 2H).
Step D. Preparation of Int 21
Figure imgf000220_0001
Int 2k Int 21
A mixture of 5-(bromomethyl)-2,3-dihydro-l/7-indene , Int 2k, (100 mg, 474 umol, 1.00 eq), iodine (24.0 mg, 94.7 umol, 19.1 uL, 0.200 eq) and zinc (92.9 mg, 1.42 mmol, 3 00 eq) in dimethyl formamide (2 mL) was stirred at 25 °C for 1 h. Then 2-chloro-4-methoxypyrimidine (68.5 mg, 474 umol, 1.00 eq), dicyclohexyl-(2-(2,6-dimethoxyphenyl)phenyl)phosphane (S-Phos) (38.9 mg, 94 7 umol, 0.20 eq) and tris(dibenzylidenethyl acetoacetate)dipalladium(O) (43.38 mg, 47.37 umol, 0.1 eq) were added and the mixture was stirred at 60 °C for 3 h. The mixture was diluted with ethyl acetate (5 mL) and washed with brine (3 >< 2 mL). The organic layer was concentrated to give a residue. The residue was purified by prep-TLC (Si O2, petroleum ether/ethyl acetate = 5/1) to afford 2-((2,3-dihydro-l/f-inden-5-yl)methyl)-4-m ethoxypyrimidine, Int 21, (60.0 mg, 249 umol, 52% yield) as yellow oil. 1H NMR (400 MHz, DMSO-uk) δ = 8.41 (d, J = 6 0 Hz, lH), 7 15 (s, 1H), 7.13 - 7.10 (m, 1H), 7.07 - 7.03 (m, 1H), 6.75 (d, J= 6.0 Hz, 1H), 4.02 (s, 2H), 3.89 (s, 3H), 2.85 - 2.72 (m, 4H), 1.97 (quin, J= 7 2 Hz, 2H). MS (ESI) m/z 241.2 [M+H]+
Step E. Preparation of Int 2m
Figure imgf000220_0002
2-((2,3-dihydro-l/7-inden-5-yl)methyl)-4-methoxypyrimidine, Int 21, (60.0 mg, 250 umol, 1.00 eq) in acetic acid (1 00 mL) and hydrogen bromide (0.200 mL, 48% purity) was stirred at 100 °C for 2 h. The reaction mixture was concentrated to give a residue. The residue was diluted with saturated sodium sulfate (2 mL) and extracted with ethyl acetate (3 * 1 mL). The organic layer was concentrated to give 2-((2,3-dihydro-177-inden-5-yl)methyl)pyrimidin-4(37/)-one, Int 2m, (20.0 mg, crude) as a yellow solid. 1H NMR (400 MHz, DMSO-<76) 3 = 7.81 (d, J - 6.8 Hz, 1H), 7.18 - 7.12 (m, 2H), 7.08 - 7.03 (m, 1H), 6.14 (d, J- 6.8 Hz, 1H), 3.78 (s, 2H), 2.80 (q, J= 7.2 Hz, 4H), 2.04 - 1.93 (m, 2H). MS (ESI) m/z 227.1 [M UI] Step F. Preparation of Int 2n
Figure imgf000221_0001
2-((2,3-dihydro-U7-inden-5-yl)methyl)pyrimidin-4(3ff)-one, Int 2m, (20.0 mg, 88.4 umol, 1 eq) in phosphorus oxychloride (1 00 mL) was stirred at 90 °C for 1 h. The mixture was cooled to 25 °C, poured into saturated sodium bicarbonate (5 mL) and extracted with ethyl acetate (3 x 1 mL). The organic layer was concentrated to give 4-chloro-2-((2,3-dihydro-177-inden-5-yl)methyl)pyrimidine, Int 2n, (20 mg, crude) as a yellow solid. MS (ESI) m/z 245.1 [M+H]+
Step G. Preparation of Compound IG-19
Figure imgf000221_0002
Int 2n Compound IG-19
To a solution of 4-chloro-2-((2,3-dihydro-l/7-inden-5-yl)methyl)pyrimidine, Int 2n, (20.0 mg, 81.7 umol, 1.00 eq) in isopropanol (1.0 mL) was added 3-(4-amino-l-oxoisoindolin-2- yl)piperidine-2, 6-dione (21.1 mg, 81.7 umol, 1 eq) and /?-toluenesulfonic acid (3.05 mg, 106 umol, 0.2 eq). Then the mixture was stirred at 90 °C for 2 h. The reaction mixture was concentrated to give a residue. The residue was triturated with sodium bicarbonate (2 mL) and filtered. The filter cake was purified by prep-HPLC (column: YMC-Actus Triart C1s 150*30mm*7um; mobile phase: [ water (FA) - ACN]; B%: 18%-38%, 10 min) to afford 3-(4-((2-((2,3-dihydro-l/7-inden-5- yl)methyl)pyrimidin-4-yl)amino)-l -ox oisoindolin-2-yl)piperidine-2, 6-dione, Compound IG-19, (31.36 mg, 62.3 umol, 76% yield, 93% purity, formate) as a white solid. rH NMR (400 MHz, DMSO-<&) δ = 11.00 (s, 1H), 9 31 (s, 1H), 8.23 (d, J= 6.0 Hz, 1H), 7.97 (dd, J= 1.6, 7.2 Hz, 1H), 7.51 - 7.41 (m, 2H), 7.15 - 7.08 (m, 2H), 7.01 (d, J= 8.4 Hz, 1H), 6.67 (d, J= 6.0 Hz, 1H), 5.13 (dd, J= 5.2, 13.2 Hz, 1H), 4.50 - 4.32 (m, 2H), 3.93 (s, 2H), 2.99 - 2.85 (m, 1H), 2.79 (dt, J= 3.2, 7.2 Hz, 4H), 2.61 - 2.56 (m, 1H), 2.29 (br dd, J= 4.4, 13 2 Hz, 1H), 2.04 - 1.92 (m, 3H). MS (ESI) m/z 245.1 [M+H]+
EXAMPLE 10
Synthesis of 3-(4-((2-((2,3-dihydro-lH-inden-5-yl)methyl)pyrimidin-4-yl)amino)-5-hydroxy-l- oxoisoindolin-2-yl)piperidine-2, 6-dione (Compound IG-21)
Figure imgf000222_0001
Int 2a
A solution of nitric acid (3.50 g, 36.1 mmol, 2.50 mL, 65% purity, 1.20 eq) and acetic acid (2 71 g, 45.1 mmol, 2.58 mL, 1.50 eq) was slowly added to a well-stirred solution of methyl 4- hydroxy-2-methylbenzoate (5.00 g, 30.1 mmol, 1 .00 eq) in acetic oxide (50.0 mL) over the course of 0.5 h at 0 °C. The reaction was stirred at 20 °C for 0.5 h. The reaction mixture are added to the ice water and filtered to give the filter cake. The filter cake was purified by flash silica gel chromatography (ISCO®; 80 g SepaFlash® Silica Flash Column, Eluent of 0-30% ethyl acetate/petroleum ether gradient @ 100 mL/min) to give methyl 4-hydroxy-2-methyl-3- nitrobenzoate, Int 2o, (1 .50 g, 7. 10 mmol, 24% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) δ = 11.78 (s, 1H), 7 89 (d, J= 8.8 Hz, 1H), 7.00 (d, J= 8.8 Hz, 1H), 3.80 (s, 3H), 2.37 (s, 3H).
Step B. Preparation of Int 2p
Figure imgf000223_0001
I nt 2o Int 2p
To a solution of methyl 4-hydroxy-2-methyl-3-nitrobenzoate, Int 2n, (1.35 g, 6.39 mmol, 1.00 eq) in dimethyl formamide (20.0 mL) was added potassium carbonate (3.53 g, 25.6 mmol, 4.00 eq) and chloro(methoxy)methane (1.03 g, 12.8 mmol, 971 uL, 2.00 eq). The mixture was stirred at 65 °C for 2 h. The reaction solution was poured into sodium bicarbonate solution (20.0 mL) and extracted with ethyl acetate (3 x 20.0 mL). After washed with an aqueous solution of sodium chloride, it was dried over anhydrous sodium sulfate and filtered. The filtrate was concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of 0 ~ 30% ethyl acetate/petroleum ether gradient @ 100 mL/min) to give methyl 4-(methoxymethoxy)-2-methyl-3-nitrobenzoate, Int 2p, (1.30 g, 5.09 mmol, 80% yield) as a white solid. 1H NMR (400 MHz, DMSO-Je) δ = 8.01 (d, J= 8.9 Hz, 1H), 7.34 (d, J= 8.9 Hz, 1H), 5 40 (s, 2H), 3 83 (s, 3H), 3.36 (s, 3H), 2.39 (s, 3H).
Step C. Preparation of Int 2q
Figure imgf000223_0002
Int 2p Int 2q
To a solution of methyl 4-(methoxymethoxy)-2-methyl-3-nitrobenzoate, Int 2p, (1.20 g, 4.70 mmol, 1.00 eq) in perchloromethane (20.0 mL) was added 7V-bromosuccinimide (1.00 g, 5.64 mmol, 1 20 eq) and 2,2-azobisisobutyronitrile (386 mg, 2.35 mmol, 0.50 eq). The mixture was stirred at 80 °C for 12 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiCL, petroleum ether/ethyl acetate = 30/1 to 20/1) to give methyl 2-(bromomethyl)-4-(methoxymethoxy)-3-nitrobenzoate, Int 2q, (500 mg, 1.50 mmol, 32% yield) as a yellow solid. ‘HNMR (400 MHz, DMSO-uf ) δ = 8.12 (d, J= 9.2 Hz, 1H), 7.52 (d, J= 9.2 Hz, 1H), 5.44 (s, 2H), 4.83 (s, 2H), 3.88 (s, 3H), 3.38 (s, 3H).
Step D. Preparation of Int 2r
Figure imgf000224_0001
Int 2q Int 2r
To a solution of methyl 2-(bromomethyl)-4-(methoxymethoxy)-3-nitrobenzoate, Int 2q, (500 mg, 1.50 mmol, 1.00 eq) in acetonitrile (10.0 mL) was added A(JV-diisopropylethylamine (387 mg, 2.99 mmol, 521 uL, 2.00 eq) and 3-aminopiperidine-2, 6-dione (211 mg, 1 65 mmol, 1.10 eq). The mixture was stirred at 80 °C for 3 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash® Silica Flash Column, eluent of 0-80% ethyl acetate/petroleum ether gradient @ 100 mL/min) to give 3 -(5-hydroxy-4-nitro-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 2r, (120 mg, 393 umol, 26% yield) as a blue solid. 1H NMR (400 MHz, DMSO-J,, ) 8 = 10.98 (s, 1H), 7.87 (d, J = 8.4 Hz, 1H), 7.28 (d, J= 8.4 Hz, 1H), 5.08 (dd, J= 5.0, 13.3 Hz, 1H), 4.73 - 4.67 (m, 1H), 4.62 - 4.55 (m, 1H), 2.95 - 2.83 (m, 1H), 2.58 (br d, J= 15.8 Hz, 1H), 2.46 - 2.42 (m, 1H), 1.99 - 1.97 (m, 1H).
Step E. Preparation of Int 2s
Figure imgf000224_0002
To a solution of 3-(5-hydroxy-4-nitro-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 2r, (120 mg, 393 umol, 1.00 eq) in dioxane (10.0 mL) was added palladium on carbon (10%, 0.05 g) under nitrogen atmosphere. The suspension was degassed and purged with hydrogen for 3 times. The mixture was stirred under hydrogen (15 Psi) at 25 °C for 2 h The reaction mixture was filtered The filtrate was concentrated to give a residue. The residue was triturated with acetonitrile (5 mL) at 25 °C for 10 min and filtered to give 3-(4-amino-5-hydroxy-l-oxoisoindolin-2-yl)piperidine-2,6- dione, Int 2s, (50.0 mg, 182 umol, 46% yield) as a blue solid. 1H NMR (400 MHz, DMSO-d6) J = 10.96 (br s, 1H), 9.99 - 9.53 (m, 1H), 6.89 - 6.83 (m, 1H), 6.82 - 6.77 (m, 1H), 5.05 (br dd, J= 5.2, 13.3 Hz, 1H),4.77 (br s, 2H), 4.22 - 4.03 (m, 2H), 2.95 - 2.84 (m, 1H), 2.60 (br d, J= 17.2 Hz, 1H), 2.32 - 2.19 (m, 1H), 2.03 - 1.96 (m, 1H).
Step F. Preparation of Compound IG-21
Figure imgf000225_0001
To a solution of 4-chloro-2-((2,3-dihydro-177-inden-5-yl)methyl)pyrimidine, Int 2n, (35.6 mg, 145 umol, 1.00 eq) in isopropanol (1.00 mL) was added para-toluenesulfonic acid (5.00 mg, 29.1 umol, 0.20 eq) and 3-(4-amino-5-hydroxy-l-oxoisoindolin-2-yl) piperidine-2, 6-dione, Int 2s, (40.0 mg, 145 umol, 1.00 eq). The mixture was stirred at 80 °C for 2 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was diluted with sodium bicarbonate (5.00m L) and filtered to give a residue. The residue was purified by prep- HPLC(column: Phenomenex luna C18 150 * 25 mm * 10 um, mobile phase: [water(FA)-ACN]; B%: 5%-35%, lOmin) and further purified by prcp-HPLC (column: Phenomenex luna C18 150*25 mm * 10 um; mobile phase: [water(FA)-ACN]; B%: 5%-35%, lOmin) to give 3-(4-((2-((2,3- dihydro-lZf-inden-5-yl)methyl)pyrimidin-4-yl)amino)-5-hydroxy-l-oxoisoindolin-2-yl)piperidine- 2,6-dione, Compound IG-21, (3.91 mg, 7.68 umol, 7.4% yield, 95% purity) as a yellow solid. ]H NMR (400 MHz, DMSO-d6) δ = 10.91 (s, 1H), 10.64 - 10.33 (m, 1H), 8.92 (s, 1H), 8.12 (d, J = 5.9 Hz, 1H), 7.48 (d, J = 8.1 Hz, 1H), 7.09 - 7.04 (m, 3H), 6.96 (br d, J = 7.4 Hz, 1H), 6.45 - 6.25 (m, 1H), 5.04 (dd, J = 5.2, 13.3 Hz, 1H), 4.23 (s, 2H), 3.84 (s, 2H), 2.92 - 2.82 (m, 1H), 2.80 - 2.74 (m, 4H), 2.59 (br d, Hz, 1H), 2.28 - 2.20 (m, 1H), 2.00 - 1.93 (m, 2H), 1.90 - 1.83 (m, 1H). MS (ESI) m/z 534.3
Figure imgf000225_0002
EXAMPLE 11
Synthesis of 3-(4-((2-((2,3-dihydro-lH-inden-5-yl)methyl)pyrimidin-4-yl)amino)-6-hydroxy-l- oxoisoindolin-2-yl)piperidine-2, 6-dione (Compound IG-22)
Figure imgf000226_0002
Int 2t
A mixture of methyl 5-bromo-2-methyl-3-nitrobenzoate (5.00 g, 18.2 mmol, 5.00 mL, 1 .00 eq) and potassium hydroxide (4.09 g, 73.0 mmol, 4.00 eq) in dioxane (30.0 mL) and water (30 0 mL) was stirred at 25 °C for 5 min. Then tris(dibenzylideneacetone)dipalladium(0) (1.67 g, 1.82 mmol, 0.100 eq) and ditert-butyl-(2-(2,4,6-triisopropylphenyl)phenyl)phosphane (775 mg, 1.82 mmol, 0. 100 eq) were added to the reaction mixture. The mixture was stirred at 100 °C for 12 h under nitrogen atmosphere. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO2, petroleum ether/ethyl acetate = 100/1 to 10/1) to afford 5-hydroxy-2-methyl-3-nitrobenzoic acid, Int 2t, (1.80 g, 9.13 mmol, 50 % yield) as a yellow solid. 1H NMR (400 MHz, DMSO-rA) 3 = 13 27 (br s, 1H), 10.48 (br s, 1H), 7.40 (d, J= 2.4 Hz, 1H), 7.34 (d, J = 2.4 Hz, 1H), 2 37 (s, 3H).
Step B. Preparation of Int 2u
Figure imgf000226_0001
Int 2t Int 2u
To a solution of 5-hydroxy-2-methyl-3-nitrobenzoic acid, Int 2t, (1.80 g, 9.13 mmol, 1.00 eq) in dimethylformamide (20 0 mL) was added iodomethane (5.18 g, 36.5 mmol, 2.27 mL, 4.00 eq) and potassium carbonate (5.05 g, 36.5 mmol, 4.00 eq). The mixture was stirred at 25 °C for 3 h. The reaction mixture was diluted with water (100 mL) and extracted with ethyl acetate (200 mL). The combined organic layers were washed with brine (50.0 mL) dried over anhydrous sodium sulfate, filtered and concentrated under reduced pressure to give a residue The residue was purified by column chromatography (SiO2, petroleum ether/ethyl acetate = 100/1 to 10/1) to afford 3-methyl 5- methoxy-2-methyl-3-nitrobenzoate, Int 2u, (1 .80 g, 7.59 mmol, 83 % yield, 95 % purity) as a white solid. 1H NMR (400 MHz, DMSO-Je) 5 = 7.66 (d, J= 2.8 Hz, 1H), 7.54 (d, J= 2.8 Hz, 1H), 3 88 (s, 3H), 3 86 (s, 3H), 2.37 (s, 3H).
Step C. Preparation of Int 2v
Figure imgf000227_0001
Int 2u Int 2v
To a solution of methyl 5-methoxy-2-methyl-3-nitro-benzoate, Int 2u, (1.00 g, 4.44 mmol, 1.00 eq) in carbon tetrachloride (15.0 mL) was added A-bromosuccinimide (948 mg, 5.33 mmol, 1.20 eq) and 2,2-azobisisobutyronitrile (72.9 mg, 444 umol, 0.100 eq). The mixture was stirred at 80 °C for 3 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiCL, petroleum ether/ethyl acetate = 100/1 to 5/1) to afford methyl 2-(bromomethyl)-5-methoxy-3-nitrobenzoate, Int 2v, (1.20 g, 3.95 mmol, 88% yield) as a white solid. 1H NMR (400 MHz, DMSO-cfc) δ = 7.76 (d, J= 2.8 Hz, 1H), 7.63 (d, J = 2.8 Hz, 1H), 4.95 (s, 2H), 3.92 (s, 3H), 3.91 (s, 3H).
Step D. Preparation of Int 2w
Figure imgf000227_0002
A mixture of methyl 2-(bromomethyl)-5-methoxy-3-nitrobenzoate, Int 2v, (1.20 g, 3.95 mmol, 1.00 eq), 3-aminopiperidine-2,6-dione;hydrochloride (714 mg, 4.34 mmol, 1.10 eq, hydrochloric acid), di isopropyl ethyl amine (1.02 g, 7.89 mmol, 1.37 mL, 2.00 eq) in acetonitrile (15.0 mL) was degassed and purged with nitrogen for 3 times, and then the mixture was stirred at 80 °C for 3 h under nitrogen atmosphere The reaction mixture was concentrated under reduced pressure to give a residue. The crude product was triturated with water (50.0 mL) and filtered to afford 3-(6- methoxy-4-nitro-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 2w, (1.20 g, 3.76 mmol, 95% yield) as a purple solid. 1H NMR (400 MHz, DMSO-d6) d = 11.03 (s, 1H), 7.94 (d, J= 2.4 Hz, 1H), 7.72 (d, J= 2 4 Hz, 1H), 5.18 (dd, J= 5.1, 13.2 Hz, 1H), 4.85 - 4.67 (m, 2H), 3.98 (s, 3H), 2.98 - 2.86 (m, 1H), 2.61 (br d, J= 18.8 Hz, 1H), 2.56 - 2.52 (m, 1H), 2.07 - 1.98 (m, 1H).
Step E. Preparation of Int 2x
Figure imgf000228_0001
Int 2w Int 2x
To a solution of 3-(6-methoxy-4-nitro-l-oxo-isoindolin-2-yl)piperidine-2, 6-dione, Int 2w, (1.60 g, 5.01 mmol, 1.00 eq) in dioxane (20.0 mL) was added palladium/carbon (200 mg, 10.0% purity) under nitrogen atmosphere The suspension was degassed and purged with hydrogen for 3 times The mixture was stirred under hydrogen atmosphere (15 Psi) at 25 °C for 12 h. The mixture was filtered and the filtrated was concentrated under reduced pressure to afford 3-(4-amino-6-methoxy- l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 2x, (1.30 g, 2 70 mmol, 53% yield, 60% purity) as a green solid. ’H NMR (400 MHz, DMSO-iL) δ = 10.98 (br s, 1H), 647 (d, J= 2.0 Hz, 1H), 6.37 (d, J= 2.4 Hz, 1H), 5.45 (s, 2H), 5.11 - 5.09 (m, 1H), 4.20 (d, J= 15.6 Hz, 2H), 3.78 (s, 3H), 2.91 (br d, J= 4.0 Hz, 1H), 2.62 (br s, 1H), 2.34 - 2.32 (m, 1H), 2.01 (br d, J= 7.2 Hz, 1H).
Step F. Preparation of Int 2y
Figure imgf000228_0002
To a solution of 3-(4-amino-6-methoxy-l-oxo-isoindolin-2-yl)piperidine-2, 6-dione, Int 2x, (700 mg, 2.42 mmol, 1.00 eq) in isopropyl alcohol (5.00 mL) was added p-toluene sulfonic acid (83.3 mg, 484 umol, 0.200 eq) and 4-chloro-2-(indan-5-ylmethyl)pyrimidine, Int 2n, (665 mg, 2.72 mmol, 1 12 eq). The mixture was stirred at 25 °C for 12 h. The reaction mixture was concentrated under reduced pressure to give a residue The residue was purified by reversed-phase HPLC(column: Waters Xbridge 150 * 25 mm * 5 um; mobile phase: [water( NHiHCChl-ACN]; B%: 32% - 62%, 9 min). The desired fraction was lyophilized to afford 3-(4-amino-6-methoxy-l- oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 2y, (100 mg, 200 umol, 8% yield) as a white solid. TH NMR (400 MHz, DMSO4) J = 11.01 (s, 1H), 9.27 (s, 1H), 8.26 (d, J = 6.0 Hz, 1H), 7 80 (d, J = 2.0 Hz, 1H), 7.15 - 7.09 (m, 2H), 7.04 - 6.99 (tn, 2H), 6.72 (d, J= 6.0 Hz, 1H), 5.18 - 5.10 (m, 1H), 4.40 - 4.28 (m, 2H), 3.95 (s, 2H), 3.82 (s, 3H), 2.79 (br t, J= 7.2 Hz, 4H), 2.39 (br s, 3H), 2.02 - 1.95 (m, 3H). MS (ESI) m/z 498.2 [M+H]+
Step G. Preparation of Compound IG-22
Figure imgf000229_0001
To a solution of 3-(4-amino-6-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 2y, (100 mg, 201 umol, 1.00 eq) in dichloromethane (3.00 mL) was added boron tribromide (504 mg, 2.01 mmol, 194 uL, 10.0 eq) at 0°C. The mixture was stirred at 25 °C for 1 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC(column: Waters Xbridge 150 * 25 mm * 5 urn; mobile phase: [water( NH4HCO3)-ACN]; B%: 20% - 50%, 5 min) to afford 3-(4-((2-((2,3-dihydro-17/-inden-5-yl)methyl)pyrimidin-4- yl)amino)-6-hydroxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Compound IG-22, (14.4 mg, 28.0 umol, 13% yield, 94% purity) as a white solid H NMR (400 MHz, DMSO-t/<) 6 = 10 99 (s, 1H), 9.86 (s, 1H), 9.21 (s, 1H), 8.23 (d, J = 6.0 Hz, 1H), 7.56 (d, 2.0 Hz, 1H), 7.14 (s, 1H), 7.12 -
7.08 (m, 1H), 7.06 - 7.01 (m, 1H), 6.85 (d, J= 2.0 Hz, 1H), 6.66 (d, J = 6.0 Hz, 1H), 5 09 (dd, J = 5.2, 13.2 Hz, 1H), 4.34 - 4.23 (m, 2H), 3.94 (s, 2H), 2.95 - 2.86 (m, 1H), 2.79 (dt, J= 3.2, 7.2 Hz, 4H), 2.59 (br d, J= 2.8 Hz, 1H), 2.26 (dq, J= 4.2, 13.2 Hz, 1H), 2.01 - 1.93 (m, 3H). MS (ESI) m/z 484.2 [M+-H]+
EXAMPLE 12
Synthesis of 3-(4-((2-((2,3-dihydro-lH-inden-5-yl)methyl)pyrimidin-4-yl)amino)-7-hydroxy-l- oxoisoindolin-2-yl)piperidine-2, 6-dione (Compound IG-23)
Figure imgf000230_0002
Int 2z
Methyl 6-fluoro-2-methyl-3-nitro-benzoate (1.00 g, 4.69 mmol, 1.00 eq) was added into a solution of sodium methoxide (507 mg, 9.38 mmol, 2.00 eq) in methanol (10.0 mL). The mixture was stirred at 25 °C for 12 h. The mixture was concentrated to give a residue. The mixture was concentrated to afford methyl 6-methoxy-2-methyl-3-nitro-benzoate, Int 2z, (980 mg, 4.35 mmol, 93% yield) as a yellow oily substance. 1 H NMR (400 MHz, DM SO-<7>) δ = 8.15 (d, J = 9 2 Hz, 1H), 7.19 (d, J= 9.2 Hz, 1H), 3.88 (d, J= 14.8 Hz, 6H), 2.36 (s, 3H). Step B. Preparation of Int 3a
Figure imgf000230_0001
Int 2z Int 3a
To a solution of methyl 6-methoxy-2-methyl-3-nitro-benzoate, Int 2z, (700 mg, 3.11 mmol, 1 .00 eq) in trichloromethane (10.0 mL) was added 2,2-azobisisobutyronitrile (153 mg, 933 umol, 0.300 eq) and A-bromosuccinimide (1.11 g, 6.22 mmol, 2.00 eq). The mixture was stirred at 80 °C for 12 h. The mixture was concentrated to give a residue. The residue was purified by column chromatography (SiO2, Petroleum ether/ethyl acetate=10/l). The desired fraction was collected and concentrated to afford methyl 2-(bromomethyl)-6-methoxy-3-nitro-benzoate, Int 3a, (600 mg, 1.97 mmol, 63% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-c/e) 6 = 8.26 (d, 7 = 9.2 Hz, 1H), 7.35 (d, J= 9.2 Hz, 1H), 4.70 (s, 2H), 3.93 (s, 3H), 3.89 (s, 3H).
Step C. Preparation of Int 3b
Figure imgf000231_0001
Int 3a Int 3b
To a solution of methyl 2-(bromomethyl)-6-methoxy-3-nitro-benzoate, Int 3a, (1.00 g, 3.29 mmol,
1.00 eq) in acetonitrile (10.0 mL) was added diisopropylethylamine (1.28 g, 9.87 mmol, 1.72 mL, 3.00 eq) and 3-aminopiperidine-2,6-dione;hydrochloride (541 mg, 3.29 mmol, 1.00 eq). The mixture was stirred at 80 °C for 12 h. The mixture was concentrated to give a residue. The residue was triturated with ethyl acetate (3.00 mL) and water (1.00 mL) at 25 °C for 1 h. The solid was collected by filtration and dried in vacuo to afford 3-(7-methoxy-4-nitro-l-oxo-isoindolin-2- yl)piperidine-2, 6-dione, Int 3b, (920 mg, crude) as a purple solid. 1H NMR (400 MHz, DMS0-7>) d = 10.99 (s, 1H), 8.46 (d, J= 9.2 Hz, 1H), 7.35 (d, 7= 9.2 Hz, 1H), 5.08 (dd, J= 5.2, 13.2 Hz, 1H), 4.88 - 4.61 (m, 2H), 4.03 (s, 3H), 2.96 - 2.85 (m, 1H), 2.58 (br d, 7= 18.0 Hz, 1H), 2.47 - 2.41 (m, 1H), 2.03 - 1.93 (m, 1H). MS (ESI) m/z 320.1 [M+H]+
Step D. Preparation of Int 3c
Figure imgf000231_0002
Int 3b Int 3c
To a solution of 3-(7-methoxy-4-nitro-l-oxo-isoindolin-2-yl)piperidine-2, 6-dione, Int 3b, (0.920 g, 2.88 mmol, 1.00 eq) in methanol (10.0 mL) and hydrochloric acid (2.00 mL) was added wet palladium on carbon (100 mg, 10% purity) under nitrogen. The mixture was stirred at 25 °C for 12 h under hydrogen (15 Psi). The mixture was filtered to give filtrate that was concentrated to afford 3-(4-amino-7-methoxy-l-oxo-isoindolin-2-yl)piperidine-2, 6-dione, Int 3c, (0.820 g, crude) as a black gum. XH NMR (400 MHz, DMSO-dg) δ = 11.01 (s, 1H), 9 26 - 9.08 (m, 1H), 7.62 (d, J= 8.8 Hz, 1H), 7.17 (d, J= 8.8 Hz, 1H), 5.07 (dd, 7= 5.2, 13.3 Hz, 1H), 4.55 - 4.48 (m, 1H), 4.43 - 4.36 (m, 1H), 3.88 (s, 3H), 2.96 - 2.87 (m, 1H), 2.62 - 2.57 (m, 1H), 2.48 - 2.40 (m, 1H), 2.03 - 1.96 (m, 1H). MS (ESI) m/z 290.2 [M+H]+
Step E. Preparation of Int 3d
Figure imgf000232_0001
To a solution of 3-(4-amino-7-methoxy-l-oxo-isoindolin-2-yl)piperidine-2, 6-dione, Int 3c, (380 mg, 1.31 mmol, 1.00 eq) and 4-chloro-2-(indan-5-ylmethyl)pyrimidine, Int 2n, (354 mg, 1.44 mmol, 1 10 eq) in isopropanol (10.0 mL) was added /?-toluenesulfonic acid (45.2 mg, 263 umol, 0.200 eq) The mixture was stirred at 100 °C for 2 h. The mixture was concentrated to give a residue. The residue was purified by prep-HPLC (0.1% FA). The desired fraction was collected and lyophilized to afford 3-(4-((2-((2,3-dihydro-lH-inden-5-yl)methyl) pyrimidin-4-yl)amino)-7- methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 3d, (266 mg, 535 umol, 41% yield) as a black solid. ^ NMR (400 MHz, DMSO-A) <3 = 10.97 (s, 1H), 8.31 (d, J= 7.2 Hz, 1H), 7.71 - 7.54 (m, 1H), 7.29 - 6.80 (m, 6H), 5.05 (dd, J= 5.0, 13.4 Hz, 1H), 4.38 - 4.18 (m, 2H), 4.09 (br s, 2H), 3.91 (s, 3H), 2.97 - 2.87 (m, 1H), 2.80 (q, J= 7.3 Hz, 4H), 2.57 (br s, 1H), 2.28 - 2.18 (m, 1H), 2 04 - 1.95 (m, 2H), 1.95 - 1.88 (m, 1H).
MS (ESI) m/z 498.2 [M UI]
Step F. Preparation of Compound IG-22
Figure imgf000232_0002
To a solution of 3-(4-((2-((2,3-dihydro-lH-inden-5-yl)methyl)pyrimidin-4-yl)amino)-7-methoxy-l- oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 3d, (80.0 mg, 161 umol, 1 00 eq) in dichloromethane (2 00 mL) was added boron tribromide (806 mg, 3.22 mmol, 310 uL, 20.0 eq) at 0 °C. The mixture was stirred at 0 °C for 2 h The mixture was diluted with water (20.0 ml) at 0 °C, and filtered to give filtered cake. The solid was purified by prep-HPLC (0.1% FA). The desired fraction was collected and lyophilized to afford 3-(4-((2-((2,3-dihydro-lH-inden-5-yl)methyl)pyrimidin-4- yl)amino)-7-hydroxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Compound IG-22, (8 22 mg, 16.7 umol, 10% yield, 98% purity) as a gray solid. H NMR (400 MHz, DMSO-c/s) 6 = 10.96 (s, 1H), 9.88 - 9.70 (m, 1H), 8.17 (d, J= 6.0 Hz, 1H), 7.53 - 7.42 (m, 1H), 7.14 - 7.09 (m, 2H), 6.99 (br d, J = 7.5 Hz, 1H), 6.85 (d, J= 8.4 Hz, 1H), 6.58 - 6.48 (m, 1H), 5.04 (dd, J= 5.2, 13.3 Hz, 1H), 4.24
(br d, J= 5.6 Hz, 2H), 3.92 (s, 2H), 2.97 - 2.85 (m, 1H), 2.82 - 2.77 (m, 4H), 2.56 (br d, J= 3.6 Hz, 1H), 2.30 - 2.24 (m, 1H), 2.01 - 1.96 (m, 2H), 1.94 - 1.88 (m, 1H) MS (ESI) m/z 484.2 [M+H]+
The compounds in Table 10 were prepared in a manner similar to that described for
Compound IG-22 using Int 3c and the appropriately substituted chloro-pyrimidine (c.f Example 2)
Table 10
Figure imgf000233_0002
EXAMPLE 13
Synthesis of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-7-hydroxy-l- oxoisoindolin-5-yl)methyl)urea (Compound IG-24)
Figure imgf000233_0001
Step A. Preparation of Int 3d
Figure imgf000234_0001
Int 3d
To a solution of methyl 4-bromo-2-fluoro-6-methylbenzoate (10.0 g, 40.5 mmol, 1.00 eq) in A',A'-dimethylformamide (100 mL) was added sodium methanolate (10.9 g, 202 mmol, 5 00 eq), the mixture was stirred at 25 °C for 12 h. The mixture was diluted with water (200 mL) and extracted with ethyl acetate (3 x 100 mL). The combined organic layers were washed with brine (2 * 500 mL), dried over sodium sulfate and fdtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 120 g SepaFlash® Silica Flash Column, Eluent of 0-10% ethyl acetate/petroleum ether @ 100 mL/min) to afford methyl 4-bromo-2-methoxy-6-methylbenzoate, Int 3d, (9.90 g, 38.2 mmol, 94% yield) as a white solid. ‘HNMR (400 MHz, CDC13) d = 6.98 (d, J= 1.2 Hz, 1H), 6.91 (d, J= 1.2 Hz, 1H), 3.91 (s, 3H), 3.82 (s, 3H), 2.26 (s, 3H).
Step B. Preparation of Int 3f
Figure imgf000234_0002
To a solution of methyl 4-bromo-2-methoxy-6-methylbenzoate, Int 3d, (9.90 g, 38.2 mmol, 1.00 eq) in perchloromethane (200 mL) was added 1 -bromopyrrolidine-2, 5-dione (8.16 g, 45.9 mmol, 1.20 eq) and (£)-3, 3 '-(diazene- l,2-diyl)bis(2-m ethylpropanenitrile) (627 mg, 3.82 mmol, 0.100 eq), the mixture was stirred at 90 °C for 12 h. The mixture was filtered and the filtrate was concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 120 g SepaFlash® Silica Flash Column, Eluent of 0-10% ethyl acetate/petroleum ether at 100 mL/min) to afford methyl 4-bromo-2-(bromomethyl)-6-methoxybenzoate, Int 3f, (13.0 g, crude) as colorless oil. 1HNMR (400 MHz, CDCI3) δ = 7.18 (d, J= 1.6 Hz, 1H), 7.04 (d, J= 1.6 Hz, 1H), 4.43 (s, 2H), 3.95 (s, 3H), 3.85 (s, 3H).
Step C. Preparation of Int 3g
Figure imgf000235_0001
To a solution of methyl 4-bromo-2-(bromomethyl)-6-methoxybenzoate, Int 3f, (17 0 g, 50.3 mmol, 1 00 eq) and 3 -aminopiperidine-2, 6-dione (12.4 g, 75 5 mmol, 1.50 eq, hydrochloride) in acetonitrile (150 mb) was added diisopropylethylamine (19.5 g, 151 mmol, 26.3 mL, 3.00 eq), the mixture was stirred at 90 °C for 12 h. The mixture was concentrated to give a residue. The residue was triturated with ethyl acetate/water = 2/1 (50.0 mL) and filtered to afford 3-(5-bromo-7- methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 3g, (15.0 g, 42.5 mmol, 84 % yield) as a brown solid. 1HNMR (400 MHz, DMSO4) 3 = 10.96 (s, 1H), 7.38 (s, 1H), 7.26 (s, 1H), 5.02 (dd, 7= 5.2, 13.2 Hz, 1H), 4.45 - 4.31 (m, 1H), 4.29 - 4.18 (m, 1H), 3.89 (s, 3H), 2.96 - 2.82 (m, 1H), 2.61 - 2.54 (m, 1H), 2.39 - 2.26 (m, 1H), 2.02 - 1.88 (m, 1H).
Step D. Preparation of Int 3h
Figure imgf000235_0002
Pd(OAc)2, CS2CO3 di(adamantan-1-yl)(butyl)phosphine
Figure imgf000235_0003
dioxane, H2O, 100 °C, 12 h
To a solution of 3-(5-bromo-7-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 3g, (1 00 g, 2.83 mmol, 1.00 eq) and potassium;(((ferLbutoxycarbonyl)amino)methyl)trifluoroborate (872 mg, 3.68 mmol, 1.30 eq) in dioxane (20.0 mL) and water (2.00 mL) was added cesium carbonate (1.85 g, 5.66 mmol, 2.00 eq), bis(l-adamantyl)-butyl-phosphane (406 mg, 1.13 mmol, 0.400 eq) and palladium!//) acetate (127 mg, 566 umol, 0.200 eq) The mixture was stirred at 100 °C for 12 h under nitrogen atmosphere. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash® Silica Flash Column, Eluent of 0-100% ethyl acetate/petroleum ether @ 100 mL/min) to afford fc/Z-butyl ((2-(2,6-dioxopiperidin-3-yl)-7-methoxy-l-oxoisoindolin-5- yl)methyl)carbamate, Int 3h, (650 mg, 1.27 mmol, 15% yield, 79% purity) as a yellow solid. 1H NMR (400 MHz, DMSO-cfc) b = 10.94 (br s, 1H), 7.47 (brt, J= 5.6 Hz, 1H), 6.94 (d, J= 15.2 Hz, 2H), 5.01 (dd, J= 5.2, 13.3 Hz, 1H), 4.37 - 4.17 (m, 4H), 3.84 (s, 3H), 2.90 (ddd, J= 5.2, 13.8, 17.4
Hz, 1H), 2.62 - 2.54 (m, 2H), 2 45 - 2.34 (m, 1H), 1.40 (s, 9H). MS (ESI) m/z 404.1 [M+H]
Step E. Preparation of Int 3i
Figure imgf000236_0001
To a solution of 3 -(5-(aminomethyl)-7-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 3h, (600 mg, 1.29 mmol, 87% purity, 1.00 eq) in ethyl acetate (5.00 mL) was added hydrochloric acid / ethyl acetate (4.00 M, 323 uL, 1.00 eq). The mixture was stirred at 25 °C for 2 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by triturated with ethyl acetate (10 0 mL) and lyophilized to afford 3-(5-(aminomethyl)-7-methoxy-l-oxoisoindolin-2- yl)piperidine-2, 6-dione, Int 3i, (370 mg, 1.22 mmol, 94% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) δ = 10.93 (s, 1H), 8.48 (br s, 2H), 7.27 (s, 1H), 7.19 (s, 1H), 5.01 (dd, J= 5.2, 13.3 Hz, 1H), 4.38 - 4.19 (m, 2H), 4.12 - 4.06 (m, 2H), 3.87 (s, 3H), 2.97 - 2.80 (m, 1H), 2 56 (br d, J= 17 2 Hz, 1H), 2.37 - 229 (m, 1H), 1.97 - 1.92 (m, 1H). MS (ESI) m/z 304.3 [M+H]+
Figure imgf000236_0002
To a solution of 3 -(5-(aminomethyl)-7-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 3i, (370 mg, 1.22 mmol, 1.00 eq) in A/ZV-dimethylformamide (4.00 mL) was added phenyl (3-chloro-4- methylphenyl)carbamate (245 mg, 1.46 mmol, 201 uL, 1.20 eq) and diisopropylethylamine (472 mg, 3.66 mmol, 637 uL, 3.00 eq). The mixture was stirred at 25 °C for 12 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC (C18, 80 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1% formic acid) and lyophilized to afford l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-7-methoxy-l-oxoisoindolin-5- yl)methyl)urea, Int 3j, (110 mg, 203 umol, 16% yield, 87%> purity) as a white solid. 'l l NMR (400 MHz, DMSO-rfg) d = 10.95 (s, 1H), 8.79 - 8.72 (m, 1H), 7.66 (d, J= 1.6 Hz, 1H), 7.20 - 7. 10 (m, 2H), 7.00 (d, J= 18.8 Hz, 2H), 6.82 - 6.75 (m, 1H), 5.01 (dd, J= 5.2, 13.3 Hz, 1H), 4.42 - 4.29 (m, 3H), 4.25 - 4.16 (m, 1H), 3.85 (s, 3H), 2 96 - 2.84 (m, 1H), 2.59 - 2.54 (m, 1H), 2.35 - 2.30 (m, 1H),
2.22 (s, 3H), 1.95 (br dd, J= 5.2, 10.9 Hz, 1H). MS (ESI) m/z 471.3 [M+Hf
Step G. Preparation of Compound IG-24
Figure imgf000237_0001
To a solution of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-7-methoxy-l- oxoisoindolin-5-yl)methyl)urea, Int 3j, (50.0 mg, 106 umol, 1.00 eq) in dichloromethane (5.00 mL) was added Boron tribromide (266 mg, 1.06 mmol, 102 uL, 10.0 eq) at 0 °C. The mixture was stirred at 25 °C for 1 h. The mixture was quenched with water (5.00 mL) and concentrated under reduced pressure to removed dichloromethane (5 00 mL) to give a residue The residue was purified by reversed-phase HPLC (C18, 40 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1% formic acid) and lyophilized to afford l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-7- hydroxy-l-oxoisoindolin-5-yl)methyl)urea, Compound IG-24, (5 86 mg, 12 5 umol, 12% yield, 98% purity) as a white solid. ' l l NMR (400 MHz, DMSO-J<) 3 = 10.95 (s, 1H), 9 82 - 9.67 (m, 1H), 8.79 (s, 1H), 7.66 (d, 7= 2.0 Hz, 1H), 7.19 - 7.11 (m, 2H), 6.88 (br s, 1H), 6.84 - 6.71 (m, 2H), 5.01 (dd, 7= 5.2, 13.0 Hz, 1H), 4.36 - 4.17 (m, 4H), 2.96 - 2 83 (m, 1H), 2.60 (br s, 1H), 2.44 - 2.34 (m, 1H), 2.23 (s, 3H), 1.99 - 1.92 (m, 1H). MS (ESI) m/z 457.3 [M+H]+
EXAMPLE 14
Synthesis of 5-amino-2-(2,6-dioxopiperidin-3-yl)-l,3-dioxoisoindolin-4-yl 2- (trifluoromethoxy)benzenesulfonate (Compound IG-29) and 7-amino-2-(2,6-dioxopiperidin-3-yl)- l,3-dioxoisoindolin-4-yl 2-(trifluoromethoxy)benzenesulfonate (Compound IG-30)
Figure imgf000237_0002
Compound IG-29 Compound IG-30
Step A. Preparation of Int 3k and 31
Figure imgf000238_0001
To a solution of 2-(2,6-dioxopiperidin-3-yl)-4-hydroxyisoindoline-l, 3-dione (1.00 g, 3.65 mmol, 1 00 eq) in sulfuric acid (10.0 mL) was added a mixture of sulfuric acid (10.0 mL) and nitric acid (389 mg, 4.01 mmol, 278 uL, 65% purity, 1.10 eq). The mixture was stirred at 0 °C for 2 h. The reaction are added to the ice water (1000 mL) and filtered to give residue. The residue was purified by flash silica gel chromatography (ISCO ®; 20 g SepaFlash® Silica Flash Column, Eluent of 0-80% ethyl acetate/petroleum ether gradient @ 100 tnL/min) to give the mixture of 2-(2,6- dioxopiperidin-3-yl)-4-hydroxy-5-nitroisoindoline-l, 3-dione, Int 3k, and 2-(2,6-dioxopiperidin-3- yl)-4-hydroxy-7-nitroisoindoline-l, 3-dione, Int 31, (1 .20 g, crude) as a yellow solid. MS (ESI) m/z 320 0 [M+H]+
Step B. Preparation of Int 3m and 3n
Figure imgf000238_0002
To a solution of the mixture of 2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-5-nitroisoindoline- 1, 3-dione, Int 3k, and 2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-7-nitroisoindoline-l, 3-dione, Int 31, (1 10 g, 3 45 mmol, 1 00 eq) in dioxane (20 0 mL) was added palladium on carbon (10%, 10 mg) under nitrogen atmosphere The suspension was degassed and purged with hydrogen for 3 times The mixture was stirred under hydrogen (15 Psi) at 25 °C for 1 h. The reaction mixture was filtered to give filtrate The filtrate was concentrated to give a mixture of 5-amino-2-(2,6-dioxopiperidin-3- yl)-4-hydroxyisoindoline-l, 3-dione, Int 3m, and 4-amino-2-(2,6-dioxopiperidin-3-yl)-7- hydroxyisoindoline- 1,3 -dione, Int 3n, (1 00 g, crude) as blue oil. (LCMS and 1H NMR were from pilot run) 1H NMR (400 MHz, DMSO4) 3 = 10.97 (br s, 1H), 7.05 (br d, J= 8..0 Hz, 1H), 6.72 (d, J - 7.6 Hz, 1H), 5.98 (br s, 2H), 4.91 (dd, J = 5 6, 12.8 Hz, 2H), 2.85 - 2.73 (m, 2H), 2.52 (br d, J =
2.4 Hz, 1H), 1.96 - 1.87 (tn, 2H). MS (ESI) m/z 290.1 [M+H]+
Step C. Preparation of Compound IG-29 and Compound IG-30
Figure imgf000239_0001
To a solution of the mixture of 5-amino-2-(2,6-dioxopiperidin-3-yl)-4-hydroxyisoindoline- 1, 3-dione, Int 3m, and -4-amino-2-(2,6-dioxopiperidin-3-yl)-7-hydroxyisoindoline- 1,3 -dione, Int 3n, (200 mg, 691 μmol, 1 00 eq) in tetrahydrofuran (5.00 mL) was added pyridine (140 mg, 1.38 mmol, 192 iiL, 2.00 eq) and 2-(trifluoromethoxy)benzenesulfonyl chloride (180 mg, 691 μmol, 1.00 eq). The mixture was stirred at 25 °C for 2 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by /vep-HPLC (column: Phenomenex luna C1s 150 * 25 mm * 10 um; mobile phase: [ water ( FA ) -ACN]; B%: 35% - 65%, 10 min) to give 5-amino-2-(2,6-dioxopiperi din-3 -yl)- 1 ,3 -dioxoisoindolin-4-yl 2- (trifhioromethoxy)benzenesulfonate, Compound IG-29, (69.9 mg, 133 umol, 19% yield, 98% purity) as a yellow solid and 7-amino-2-(2,6-dioxopiperidin-3-yl)-l,3-dioxoisoindolin-4-yl 2- (trifluoromethoxy)benzenesulfonate, Compound IG-30, (15. 1 mg, 28.4 μmol, 4% yield, 97% purity) as a yellow solid.
Compound IG-29 ]H NMR (400 MHz, DMSO-tfc) h = 11.03 (s, 1H), 8.02 (dd, J= 1.2, 7 9 Hz, 1H), 7.97 - 7.90 (m, 1H), 7.69 (br d, J= 8.0 Hz, 1H), 7.62 (t, J= 7.7 Hz, 1H), 7.55 (d, J= 8.0 Hz, 1H), 7.10 (d, J= 8.4 Hz, 1H), 6.30 (s, 2H), 4.90 (dd, J= 5.6, 12.9 Hz, 1H), 2.89 - 2.76 (m, 1H), 2.61 - 2.53 (m, 1H), 2.36 - 2.27 (m, 1H), 2.07 (s, 1H), 1.93 - 1.81 (m, 1H). MS (ESI) m/z 514.0 [M+H]\ Compound IG-30 ’H NMR (400 MHz, DMSO-c/e) δ = 11.08 (s, 1H), 7.94 (br dd, J= 3.6, 7.8 Hz, 2H), 7.72 (br d, J= 8.4 Hz, 1H), 7.65 - 7.57 (m, 1H), 7.01 (q, J= 9.2 Hz, 2H), 6.72 (br s, 2H), 4.96 (br dd, 7= 5.6, 12.6 Hz, 1H), 2.95 - 2.78 (m, 1H), 2.58 (br s, 1H), 2.41 - 2.36 (m, 1H), 1.93 (br dd, J = 4.4, 10.4 Hz, 1H). MS (ESI) m/z 514.0 [M+H]+.
EXAMPLE 15
Synthesis of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-4-(methylamino)-l- oxoisoindolin-5-yl)methyl)urea (Compound IG-31)
Figure imgf000240_0001
To a solution of diisopropylamine (6.07 g, 60.00 mmol, 8.48 ml, 1.20 eq) in tetrahydrofuran (50.0 mL) was added n -butyllithium (2.5 M, 22.00 mL, 1.10 eq) dropwise at -78 °C ,the mixture was stirred at -78 °C for 0.5 h. Then a solution of 4 4-bromo-2-fluorobenzonitrile (10.0 g, 50.0 mmol, 1 00 eq) in tetrahydrofuran (50.0 mL) was added at -78 °C, then iodomethane (7.81 g, 55.0 mmol, 3 42 mL, 1.10 eq) was added to, the mixture was stirred at -78 °C for 2 h under nitrogen atmosphere. The mixture was quenched with saturated ammonium chloride (100 mL) and extracted with ethyl acetate (3 * 100 mL). The combined organic layers were washed with brine (20.0 mL), dried over sodium sulfate and filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO2, petroleum ether/ethyl acetate=10 / 1) to give 4-bromo-2-fluoro-3-methylbenzonitrile, Int 3o, (3.50 g, 14.7 mmol, 29% yield, 90% purity) as a yellow solid. 1H NMR (400 MHz, DMSO-dg) δ = 7.40 (d, 1H), 7.25 (, m, 1H), 2.31 (t, 3H).
Step B. Preparation of Int 3p
Figure imgf000241_0001
To a solution of 4-bromo-2-fluoro-3-methylbenzonitrile, Int 3o, (1.00 g, 4.67 mmol, 1.00 eq) in methanol (10.0 mL) were added triethylamine (473 mg, 4.67 mmol, 650 uL, 1.00 eq) and [l, l-bis(diphenylphosphino)ferrocene] dichloropalladium(II) (342 mg, 467 umol, 0.100 eq). The mixture was stirred at 80 °C for 12 h under carbon monoxide atmosphere (50 Psi). The mixture was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 4 / 1) to give methyl 4-cyano-3- fluoro-2-methylbenzoate, Int 3p, (810 mg, 4.19 mmol, 89% yield) as a white solid.
Figure imgf000241_0002
(400 MHz, DMSO-i/r.) J = 7.89 (t, J= 7.2 Hz, 1H), 7.74 (d, J= 8.0 Hz, 1H), 3.88 (s, 3H), 2.42 (s, 3H) Step C. Preparation of Int 3q
Figure imgf000241_0003
Int 3p Int 3q
To a solution of methyl 4-cyano-3-fluoro-2-methyl-benzoate, Int 3p, (760 mg, 3.93 mmol, 1.00 eq) in chloroform (15.0 mL) was added JV-bromosuccinimide (770 mg, 4.33 mmol, 1.10 eq) and benzoyl peroxide (95.3 mg, 393 umol, 0. 100 eq). The mixture was stirred at 80 °C for 12 h under nitrogen atmosphere The mixture was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 5 / 1) to give methyl 2-(bromomethyl)-4-cyano-3-fluorobenzoate, Int 3q, (500 mg, 1 .84 mmol, 46% yield) as a white solid. II NMR (400 MHz, DMSO-J,,) 3 = 8.08 (dd, J= 6.4, 8.1 Hz, 1H), 7.85 (d, J= 8.4 Hz, 1H), 4.92 (d, J= 2.0 Hz, 2H), 3.93 (s, 3H).
Step D. Preparation of Int 3r
Figure imgf000241_0004
Int 3q Int 3r To a solution of methyl 2-(bromomethyl)-4-cyano-3-fluorobenzoate, Int 3q, (650 mg, 2.39 mmol, 1 00 eq) in acetonitrile (10.0 mL) was added /V,.V-diisopropylcthylaminc (926 mg, 7.17 mmol, 1 25 mL, 3.00 eq) and 3-aminopiperidine-2, 6-dione (393 mg, 2.39 mmol, 1.00 eq, hydrogen chloride). The mixture was stirred at 85 °C for 12 h. The mixture was concentrated under reduced pressure to give a residue. The residue was triturated with water (25.0 mL) at 25 °C for 15 min and collected by fdtration to give 2-(2,6-dioxopiperidin-3-yl)-4-fluoro-l-oxoisoindoline-5-carbonitrile, Int 3r, (650 mg, 2.26 mmol, 94% yield) as a white solid. 1H NMR (400 MHz, DMSO-<7s) δ = 11.05 (s, 1H), 8.10 (dd, J = 5.6, 7.6 Hz, 1H), 7 78 (d, <7= 8.0 Hz, 1H), 5.16 (dd, J = 52, 13.2 Hz, 1H), 4.72 - 4.62 (m, 1H), 4.58 - 4.43 (m, 1H), 2.99 - 2.84 (m, 1H), 2.61 (br d, J= 17.2 Hz, 1H), 2.44 - 2.41 (m, 1H), 2.05 - 1.98 (m, 1H).
Step E. Preparation of Int 3s
Figure imgf000242_0001
Int 3r Int 3s
To a solution of 2-(2,6-dioxopiperidin-3-yl)-4-fluoro-l-oxoisoindoline-5-carbonitrile, Int 3r, (500 mg, 1 .74 mmol, 1 .00 eq) in acetonitrile (10.0 mL) was added methylamine (2 M, 8.70 mL, 10 eq) The mixture was stirred at 60 °C for 12 h. Ethyl acetate (40.0 mL) and water (40.0 mL) were added and layers were separated. The aqueous phase was extracted with ethyl acetate (2 x 30.0 mL) Combined extracts were washed with brine (40.0 mL), dried over sodium sulfate and filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (0.1% FA conditions) to give crude product. The crude product was triturated with ethyl acetate (5.00 mL) at 25 °C for 15 min and collected by filtration to give 2-(2,6- dioxopiperidin-3-yl)-4-(methylamino)-l-oxoisoindoline-5-carbonitrile, Int 3s, (100 mg, 335 μmol, 19% yield) as a white solid. 1H NMR (400 MHz, DMSO-c/e) δ = 11.02 (br s, 1H), 7.56 (d, J= 8.0 Hz, 1H), 6.94 (d, <7= 7.9 Hz, 1H), 6.42 (br d, J= 5 2 Hz, 1H), 5.10 (dd, J= 5.2, 13.3 Hz, 1H), 4.58 - 4.37 (m, 2H), 3.15 - 3.09 (m, 3H), 2.96 - 2.86 (m, 1H), 2 63 - 2.58 (m, 1H), 2.39 - 2.32 (m, 1H), 2.06 - 1.98 (m, 1H).
Step F. Preparation of Int 3t
Figure imgf000243_0001
Int 3s Int 3t
To a solution of 2-(2,6-dioxopiperidin-3-yl)-4-(methylamino)-l-oxoisoindoline-5- carbonitrile, Int 3s, (100 mg, 335 μmol, 1.00 eq) in tetrahydrofuran (3.00 mL) was added triethylamine (204 mg, 2.01 mmol, 280 μL, 6.00 eq), di-tert-butyl dicarbonate (219 mg, 1.01 mmol, 231 μL, 3.00 eq) and Raney -Ni (50.0 mg) under nitrogen atmosphere. The mixture was stirred at 25 °C for 4 h under hydrogen atmosphere (15Psi). The resulting mixture was filtered over C6lite and the filtrate was concentrated under reduced pressure to give crude product. The crude product was triturated with ethyl acetate (3.00 mL) at 25 °C for 10 minutes and collected by filtration to give tert-butyl ((2-(2,6-dioxopiperidin-3-yl)-4-(methylamino)-l-oxoisoindolin-5-yl)methyl)carbamate, Int 3t, (56 mg, 139 μmol, 41% yield) as a white solid.
Figure imgf000243_0002
(400 MHz, DMSO-tfc) 3 = 10.97 (s, 1H), 7 36 (br t, J= 6.0 Hz, 1H), 7.13 (d, J= 7.6 Hz, 1H), 6.95 (d, J= 7.6 Hz, 1H), 5.22 (br d, J = 4.8 Hz, 1H), 5.08 (dd, J= 5.2, 13.2 Hz, 1H), 4 72 - 4.49 (m, 2H), 4.04 (br d, J= 6.0 Hz, 2H), 2.97 (d, J= 52 Hz, 3H), 2.94 - 2 84 (m, 1H), 2 64 - 2 53 (m, 1H), 2.46 - 2.38 (m, 1H), 2.01 - 1.94 (m, 1H), 1.40 (s, 9H).
Step G. Preparation of Int 3u
Figure imgf000243_0003
A solution of tert-butyl ((2-(2,6-dioxopiperidin-3-yl)-4-(methylamino)-l-oxoisoindolin-5- yl)methyl) carbamate, Int 3t, (56.0 mg, 139 μmol, 1.00 eq) in hydrochloric acid / dioxane (4M, 1.00 mL) was stirred at 25 °C for 2 h. The mixture was concentrated under reduced pressure to give 3- (5-(aminomethyl)-4-(methylamino)-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 3u, (45 mg, crude) as a white solid. MS (ESI) m/z 286.2 [M+H]+
Step H. Preparation of Compound IG-31
Figure imgf000244_0001
To a solution of 3-(5-(aminomethyl)-4-(methylamino)-l-oxoisoindolin-2-yl)piperidine-2,6- dione, Int 3u, (45.0 mg, 149 μmol, 1.00 eq) in dimethyl formamide (2.00 mL) was added triethylamine (60.3 mg, 595 μmol, 82.9 μL, 4.00 eq) and phenyl (3-chloro-4- methylphenyl)carbamate (42.9 mg, 164 μmol, 1.10 eq). The mixture was stirred at 50 °C for 1 h. The mixture was concentrated under reduced pressure to give a residue The residue was purified by reversed-phase HPLC (column: Phenomenex luna C18 150*25mm* 10um;mobile phase: [water(FA)-ACN];B%: 25%-55%,10min ) and lyophilized to afford l-(3-chloro-4-methylphenyl)-3- ((2-(2,6-dioxopiperidin-3-yl)-4-(methylamino)-l-oxoisoindolin-5-yl)methyl)urea, Compound IG- 31, (39.83 mg, 83.9 μmol, 56% yield, 99% purity) as a white solid. XH NMR (400 MHz, DMSO-c4>) 3 = 10.95 (br s, 1H), 8.81 - 8.75 (m, 1H), 7.63 (d, .7= 2 0 Hz, 1H), 7.22 (d, J= 7.6 Hz, 1H), 7.20 - 7.16 (m, 1H), 7.15 - 7.10 (m, 1H), 6.96 (d, J= 7.6 Hz, 1H), 6.67 (br d, J= 5.6 Hz, 1H), 5.44 (q, J = 5.2 Hz, 1H), 5.08 (dd, J = 5.2, 13.3 Hz, 1H), 4.74 - 4.50 (m, 2H), 4 23 (d, .7= 6.0 Hz, 2H), 2.99 (d, J = 5.1 Hz, 3H), 2.96 - 2.86 (m, 1H), 2.63 - 2.55 (m, 1H), 2.48 - 2.39 (m, 1H), 2.23 (s, 3H), 2.04 - 1.92 (m, 1H). MS (ESI) m/z 470.1 [M+H]+
EXAMPLE 16
Synthesis of (2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5-yl)methyl (3-chloro-4- methylphenyl)carbamate (Compound IG-33)
Figure imgf000244_0002
Compound IG-33
Step A. Preparation of Int 3v
Figure imgf000244_0003
Int lo Int 3v To a solution of 3 -(5-bromo-4-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int lo, (600 mg, 1.70 mmol, 1.00 eq) in dioxane (20.0 mL) was added tetrakis[triphenylphosphine]palladium(0) (255 mg, 220 μmol, 0 130 eq) and tributylstannylmethanol (2.73 g, 8.49 mmol, 5.00 eq). The mixture was stirred at 100 °C for 12 h under nitrogen atmosphere. The reaction mixture was concentrated under reduced pressure to give a residue The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 0/1) to give 3-(5-(hydroxymethyl)-4-methoxy-l- oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 3v, (250 mg, 821 umol, 48% yield) as a green solid.
I I NMR (400 MHz, DMSO-t/e) 3 = 10.99 (s, 1H), 7.56 (d, J= 7.6 Hz, 1H), 7.42 (d, J = 7.6 Hz, 1H), 5.24 (t, J = 5.6 Hz, 1H), 5.10 (dd, J= 5.1, 13.2 Hz, 1H), 4.71 - 4.64 (m, 1H), 4.58 (d, J= 5.4 Hz, 2H), 4.53 - 4.46 (m, 1H), 3 92 (s, 3H), 3.00 - 2.86 (m, 1H), 2.60 (br d, J= 17.8 Hz, 1H), 2.47 - 2.38 (tn, 1H), 2.05 - 1.99 (m, 1H).
Step B. Preparation of Int 3w
Figure imgf000245_0001
To a solution of 3-(5-(hydroxymethyl)-4-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 3v, (250 mg, 821 μmol, 1.00 eq) in dimethylformamide (6.00 mL) was added phenyl (3-chloro-4- methylphenyl)carbamate (236 mg, 903 μmol, 1.10 eq) and sodium hydride (65.7 mg, 1.64 mmol, 60% purity, 2.00 eq). The mixture was stirred at 0-25 °C for 1 h. The reaction mixture was quenched by addition water (20.0 mL) at 25 °C, collect the crystalline solid by suction filtration, washed with 2 mL portions of cold water. The solid was dry in vacuo to give crude product. The crude product was triturated with ethyl acetate (10.0 ml) at 25 °C for 5 min and collected by filtration to give (2-(2,6-dioxopiperidin-3-yl)-4-methoxy-l-oxoisoindolin-5-yl)methyl (3-chloro-4- methylphenyl)carbamate, Int 3w, (140 mg, 272 μmol, 33% yield, 92% purity) as a white solid 1H NMR (400 MHz, DMSCM,) 3 = 11.00 (s, 1H), 9.90 (s, 1H), 7.59 (d, J= 1.2 Hz, 1H), 7 55 (d, J= 7.2 Hz, 1H), 7.45 (d, J= 7.6 Hz, 1H), 7.30 - 7.23 (m, 2H), 5.23 (s, 2H), 5. 12 (dd, J= 4.6, 13.2 Hz, 1H), 4.75 (d, J= 17.2 Hz, 1H), 4.57 (d, J= 17.2 Hz, 1H), 4.00 (s, 3H), 2.94 - 2.87 (m, 1H), 2.58 (br d, J = 1.2 Hz, 1H), 2.45 - 2.43 (m, 1H), 2.25 (s, 3H), 2.03 - 1.98 (m, 1H).
Step C. Preparation of Compound IG-33
Figure imgf000246_0001
Int 3w Compound IG-33
To a solution of (2-(2,6-dioxopiperidin-3-yl)-4-methoxy-l-oxoisoindolin-5-yl)methyl (3- chloro-4-methylphenyl)carbamate, Int 3w, (140 mg, 296 μmol, 1.00 eq) in dichloromethane (5 00 mL) was added boron tribromide (743 mg, 2.97 mmol, 286 uL. 10.0 eq). The mixture was stirred at 0 °C for 0.5 h. The reaction mixture was quenched by addition of ice water (20.0 ml) and then concentrated under reduced pressure to give a residue. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 0/1) to give crude product. The crude product was triturated with ethyl acetate (10.0 ml) at 25 °C for 5 min and collected by filtration to afford (2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5-yl)methyl (3-chloro-4- methylphenyl)carbamate, Compound IG-33, (41.32 mg, 88.4 μmol, 29% yield, 98% purity) as a white solid. ‘HNMR (400 MHz, DMSO-t/6) δ = 11.00 (s, 1H), 10.00 (br s, 1H), 9.88 (br s, 1H), 7.60 (s, 1H), 7.49 (d, J= 7.6 Hz, 1H), 7.32 - 7.27 (m, 1H), 7.27 - 7.24 (m, 2H), 5.24 (s, 2H), 5.11 (dd, J= 5 2, 13 2 Hz, 1H), 4 42 - 4 36 (m, 1H), 4 30 - 4 24 (m, 1H), 2 96 - 2 87 (m, 1H), 2 64 - 2 59 (m, 1H), 2.39 - 2.33 (m, 1H), 2.26 (s, 3H), 2.07 - 2.01 (m, 1H). MS (ESI) m/z 458. 1 [M+H] EXAMPLE 17 Synthesis of N-(2-(2,6-dioxopiperidin-3-yl)-7-hydroxy-l,3-dioxoisoindolin-
5-yl)-2-(trifluoromethoxy)benzenesulfonamide (Compound IG-34)
Figure imgf000246_0002
Int 3x To a solution of 2-methyl-5-nitrobenzoic acid (5.00 g, 27.6 mmol, 1.00 eq) in sulfuric acid (40.0 mL) was slowly added /V-bromosuccinimide (5.90 g, 33.1 mmol, 1.20 eq). The mixture was stirred at 60 °C for 12 h. After being cooled to 25 °C, the mixture was added into ice-water (100 mL). The mixture was filtered to give filtered cake that was concentrated to give 3 -bromo-2- methyl-5-nitrobenzoic acid, Int 3x, (4.70 g, 18.1 mmol, 65% yield) as a yellow solid. 'HNMR (400 MHz, DMSO-d6 ) δ = 13.88 (br s, 1H), 8 52 (d, J= 1.6 Hz, 1H), 8.43 (d, J= 1.6 Hz, 1H), 2.64 (s, 3H).
Step B. Preparation of Int 3y
Figure imgf000247_0001
Int 3x Int 3y
To a solution of 3-bromo-2-methyl-5-nitrobenzoic acid, Int 3x, (4.70 g, 18. 1 mmol, 1.00 eq) in water (100 mL) was added sodium hydroxide (2.17 g, 54.2 mmol, 3.00 eq), then was slowly added potassium permanganate (12.2 g, 77.3 mmol, 4.27 eq). The mixture was stirred at 80 °C for 12 h. The mixture was filtered to give filtrate. The filtrate was adjusted pH=l with hydrochloric acid and extracted with water/ethyl acetate (100 mL/200 mL). The organic layer was collected and concentrated to give 3-bromo-5-nitrophthalic acid, Int 3y, (3.60 g, 11.8 mmol, 65% yield, 95% purity) as a yellow solid. ‘H NMR (400 MHz, DMSO-cA) ri = 14.71 - 13.32 (m, 2H), 8.69 (d, J = 2.4 Hz, 1H), 8.58 (d, J= 2.0 Hz, 1H).
Step C. Preparation of Int 3z
Figure imgf000247_0002
y
To a solution of 3-bromo-5-nitrophthalic acid, Int 3y, (1.00 g, 3.45 mmol, 1.00 eq) in dimethyl sulfoxide (10.0 mL) was added potassium carbonate (953 mg, 6.90 mmol, 2.00 eq) and methyl iodide (4 89 g, 34.5 mmol, 2.15 mL, 10.0 eq). The mixture was stirred at 50 °C for 4 h. The mixture was extracted with water/ethyl acetate (40.0 mL/100 mL) The organic layer was collected and concentrated to give dimethyl 3-bromo-5-nitrophthalate, Int 3z, (1.00 g, 2.67 mmol, 77% yield, 85% purity) as a yellow solid. ‘H NMR (400 MHz, DMSO-A) 3 = 8.80 (d, J= 2.0 Hz, 1H), 8.62 (d, J= 2.0 Hz, 1H), 3.92 (d, J= 1.6 Hz, 6H).
Figure imgf000248_0001
To a solution of dimethyl 3 -bromo- 5 -nitrophthal ate, Int 3z, (1.00 g, 3.14 mmol, 1.00 eq) in methanol (20.0 mL) and water (5.00 mL) was added iron power (527 mg, 9.43 mmol, 3.00 eq) and ammonium chloride (841 mg, 15 7 mmol, 5.00 eq). The mixture was stirred at 80 °C for 2 h. The mixture was filtered to give a filtrate that was concentrated to give a residue. The residue was extracted with water/ethyl acetate (50.0 mL/100 mL). The organic layer was collected and concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash® Silica Flash Column, Eluent of 0-60% Ethyl acetate/Petroleum ether gradient @ 100 mL/min) to give dimethyl 5-amino-3-bromophthalate, Int 4a, (450 mg, 1.48 mmol, 47% yield, 95% purity) as a yellow solid. 1H NMR (400 MHz, DMSO-<4) δ = 7.08 (d, J= 2.0 Hz, 1H), 6.99 (d, J= 2.4 Hz, 1H), 6.03 (s, 2H), 3.78 (s, 3H), 3.74 (s, 3H).
Figure imgf000248_0002
To a solution of dimethyl 5-amino-3 -bromophthalate, Int 4a, (410 mg, 1.42 mmol, 1.00 eq) in pyridine (5.00 mL) was added 2-(trifluoromethoxy)benzenesulfonyl chloride (408 mg, 1.57 mmol, 1.10 eq). The mixture was stirred at 80 °C for 4 h. The mixture was concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 4 g SepaFlash® Silica Flash Column, Eluent of 40-50% Ethyl acetate/Petroleum ether gradient @ 80 mL/min) to give dimethyl 3-bromo-5-((2-(trifluoromethoxy)phenyl) sulfonamido)phthalate, Int 4b, (0.400 g, 702 μmol, 49% yield, 90% purity) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) δ = 11.33 (s, 1H), 8.05 (dd, J = 1.4, 8.0 Hz, 1H), 7.82 (dt, J= 1.6, 8.0 Hz, 1H), 7.71 (d,J = 2.0 Hz, 1H), 7.65 - 7.57 (m, 3H), 3.81 (s, 3H), 3.80 (s, 3H).
Step F. Preparation of Int 4c
Figure imgf000249_0001
To a solution of dimethyl 3-bromo-5-((2-(trifluoromethoxy)phenyl)sulfonamido)phthalate, Int 4b, (0400 g, 781 μmol, 1.00 eq) in methanol (1.00 mL) and water (0.300 mL) was added lithium hydroxide (65.5 mg, 1.56 mmol, 2.00 eq). The mixture was stirred at 25 °C for 12 h. The mixture was adjusted pH=3 with hydrochloric acid and concentrated to give a residue. The residue was extracted with water/ethyl acetate (20.0 mL/80.0 mL). The organic layer was collected and concentrated to give 3-bromo-2-(methoxycarbonyl)-5-((2-(trifluoromethoxy) phenyl)sulfonamido)benzoic acid, Int 4c, (360 mg, 722 μmol, 92% yield) as a yellow solid. ’H
NMR (400 MHz, DMSO-Jr,) J =13.5 (s, 1H), 11 28 (s, 1H), 8.04 (dd, J= 1.6, 8.0 Hz, 1H), 7.81 (dt, J= 1.6, 8.0 Hz, 1H), 7.69 (d, J= 2.0 Hz, 1H), 7.65 - 7.53 (m, 3H), 3.76 (s, 3H).
Step G. Preparation of Int 4d
Figure imgf000249_0002
To a solution of 3-bromo-2-(methoxycarbonyl)-5-((2- (trifluoromethoxy)phenyl)sulfonamido)benzoic acid, Int 4c, (0.250 g, 502 μmol, 1.00 eq) in dimethyl formamide (10.0 mL) was added O-(7-azabenzotriazol-l-yl)-N,N,NN’- tetramethyluronium hexafluorophosphate (382 mg, 1.00 mmol, 2.00 eq), diisopropylethylamine (64.8 mg, 502 μmol, 87.4 μL, 1.00 eq) and 3-aminopiperidine-2,6-dione;hydrochloride (99.1 mg, 602 μmol, 1.20 eq). The mixture was stirred at 25 °C for 12 h. The mixture was filtered to give filtrate. The filtrate was purified by prep-HPLC (0.1% FA). The desired fraction was concentrated and extracted with water/ethyl acetate (20.0 mL/50.0 mL). The organic layer was collected and concentrated to give A-(7-bromo-2-(2,6-dioxopiperidin-3-yl)-l,3-dioxoisoindolin-5-yl)-2- (trifhioromethoxy)benzenesulfonamide, Int 4d, (230 mg, 379 μmol, 75% yield, 95% purity) as a yellow solid. ]HNMR (400 MHz, DMSO-cfe) δ = 11.93 (s, 1H), 11.11 (s, 1H), 8.15 - 8 09 (m, 1H), 7.84 (dt, J= 1.6, 8.0 Hz, 1H), 7.68 - 7.58 (m, 3H), 7.49 (d, J= 1.6 Hz, 1H), 5.09 (dd, J= 5 6, 12.8 Hz, 1H), 2.89 - 2.80 (m, 1H), 2 59 (br d, J= 2.4 Hz, 1H), 2.49 - 2.42 (m, 1H), 2.02 (dt, J= 2.4, 5.2
Hz, 1H). MS (ESI) m/z 576.0 [M+H]+
Step H. Preparation of Int 4e
Figure imgf000250_0001
To a solution of jV-(7-bromo-2-(2,6-dioxopiperidin-3-yl)-l,3-dioxoisoindolin-5-yl)-2- (trifluoromethoxy) benzenesulfonamide, Int 4d, (200 mg, 347 μmol, 1.00 eq) in dioxane (10.0 mL) was added bis(pinacolato)diboron (132 mg, 521 μmol, 1.50 eq), potassium acetate (68.1 mg, 694 μmol, 2.00 eq) and [l,l'-bis(diphenylphosphino) ferrocene]dichloropalladium(II) (25.4 mg, 34.7 μmol, 0.100 eq) under nitrogen The mixture was stirred at 110 °C for 4 h under nitrogen The mixture was concentrated to give a residue. The residue was purified by p/e/i-HPLC (0.1% FA). The desired fraction was collected and concentrated, extracted with water /ethyl acetate (20.0 mL/40.0 mL). The organic layer was collected and concentrated to give (2-(2,6-dioxopiperidin-3- yl)-l,3-dioxo-6-((2-(trifluoromethoxy)phenyl)sulfonamido)isoindolin-4-yl)boronic acid, Int 4e, (100 mg, 166 μmol, 48% yield, 90% purity) as a yellow solid. 1 H NMR (400 MHz, DMSO-ufc) d = 11.54 (s, 1H), 11.12 (s, 1H), 8.75 (br d, J= 2.4 Hz, 1H), 8.21 - 7.99 (m, 2H), 7.86 - 7.75 (m, 2H), 7.63 - 7.56 (m, 3H), 5.12 (dd, J= 5.6, 12 8 Hz, 1H), 2.91 - 2.82 (m, 1H), 2.61 - 2.55 (m, 1H), 2.48 - 2.41 (m, 1H), 2.08 - 1.99 (m, 1H). MS (ESI) m/z 542.3 [M+H]+
Step I. Preparation of Compound IG-34
Figure imgf000250_0002
To a solution of (2-(2,6-dioxopiperidin-3-yl)-l,3-dioxo-6-((2- (trifluoromethoxy)phenyl)sulfonamido) isoindolin-4-yl)boronic acid, Int 4e, (80.0 mg, 148 μmol, 1.00 eq) in ethanol (1.00 mL) was added hydrogen peroxide (1.74 g, 15.5 mmol, 1.47 mL, 30% purity, 104 eq) at 0 °C. The mixture was stirred at 0 °C for 0.5 h. Then the mixture was stirred at 25 °C for 11 .5 h. The mixture was concentrated and extracted with water / ethyl acetate (10.0 mL / 20.0 mL) The organic layer was collected and concentrated to give a residue The residue was purified by prep-HPLC (column: Phenomenex luna C18 150*25mm* lOum; mobile phase: [water (FA)-ACN]; B%: 32%-62%, 7 min ). The desired fraction was collected and lyophilized to give N- (2-(2,6-dioxopiperidin-3-yl)-7-hydroxy-l,3-dioxoisoindolin-5-yl)-2-
(trifluoromethoxy)benzenesulfonamide, Compound IG-34, (29.05 mg, 54.3 μmol, 37% yield, 96% purity) as an off-white solid 1 H NMR (400 MHz, DMSO-uC) δ = 11.44 (br s, 1H), 11 .30 (br s, 1H), 11.05 (s, 1H), 8.05 (dd, J= 1.4, 7.9 Hz, 1H), 7.90 - 7.74 (m, 1H), 7.66 - 7.55 (m, 2H), 6.99 (br d, J - 4.4 Hz, 2H), 4.99 (dd, J= 5.6, 12.8 Hz, 1H), 2.84 (ddd, .7 - 4,8, 13.6, 17.6 Hz, 1H), 2.57 (br d, J = 2.4 Hz, 1H), 2.43 (br d, J = 4.0 Hz, 1H), 2.02 - 1.90 (m, 1H) MS (ESI) m/z 514.1 [M U I]
EXAMPLE 17
Synthesis of 1 -((3-(2,6-di oxopiperi din-3 -yl)-4-oxo-3,4-dihydrobenzo[d] [1,2, 3]triazin-6-yl)m ethyl)- 3-(3-hydroxy-4-methylphenyl)urea (Compound IG-35)
Figure imgf000251_0001
To a solution of methyl 5-bromo-2-nitrobenzoate (0.500 g, 1.92 mmol, 1 00 eq) in the mixture of dioxane (20.0 mL) and water (2.00 mL) was added potassium(I);(((tert- butoxycarbonyl)amino)methyl)trifluoroborate (456 mg, 1.92 mmol, 1.00 eq), cesium carbonate (1 25 g, 3.85 mmol, 2.00 eq), bis(l-adamantyl)-butyl-phosphane (276 mg, 769 umol, 0.400 eq) and palladium(II) acetate (86.3 mg, 385 umol, 0.200 eq). The mixture was stirred at 100 °C for 12 h under nitrogen. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (Si Ch, Petroleum ether/Ethyl acetate=l/O to 3/1) to give methyl 5-(((Z<?rLbutoxycarbonyl)amino)methyl)-2-nitrobenzoate, Int 4f, (1.60 g, 5.16 mmol, 67% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-rfe) δ = 8.05 (d, J= 8.4 Hz, 1H), 7.68 (s, 1H), 7.64 (br d, J= 8.4 Hz, 1H), 7.61 - 7.56 (m, 1H), 4.25 (br d, J= 6.0 Hz, 2H), 3.85 (s, 3H), 1.39 (s, 9H). Step B. Preparation of Int 4g
Figure imgf000252_0001
Int 4f Int 4g
To a solution of methyl 5-[(/ert-butoxycarbonylamino)methyl]-2-nitro-benzoate, Int 4f, (1.50 g, 4.83 mmol, 1.00 eq) in methanol (7.50 mb) was added a solution of lithium hydroxide (174 mg, 7.25 mmol, 1.50 eq) in tetrahydrofuran (30 0 ml) and water (7.50 mL). The mixture was stirred at 25 °C for 4 h. The reaction mixture was concentrated under reduced pressure to give a residue. The reaction mixture was concentrated and diluted with water. The aqueous solution was acidified with hydrochloric acid (1.00 M, 10.0 ml) to pH = 6 and extracted with ethyl acetate (50 mL). The organic layer was dried over anhydrous sodium sulfate and concentrated under reduced pressure to give 5-(((A?rt-butoxycarbonyl)amino)methyl)-2-nitrobenzoic acid, Int 4g, (1.40 g, 4.73 mmol, 97% yield) as a yellow oil. 1H NMR (400 MHz, DMSO-^) d = 7 96 (d, J= 8.4 Hz, 1H), 7.66 (s, 1H), 7.62 - 7.53 (m, 2H), 4.24 (br d, J = 6.0 Hz, 2H), 1.39 (s, 9H). MS (ESI) m/z 197.1 [M+H-100]+
Step C. Preparation of Int 4h
Figure imgf000252_0002
3 4
To a solution of 5-(((tert-butoxycarbonyl)amino)methyl)-2-nitrobenzoic acid, Int 4g, (0.700 g, 2.36 mmol, 1.00 eq) in dimethyl formamide (30.0 mL) was added M,M-diisopropylethylamine (1 22 g, 9.45 mmol, 1.65 mL, 4.00 eq), <J-(7- Azabenzotri azol -I -yl)-A',A/A'’,A'7-tetramethyluronium Hexafluorophosphate (1.35 g, 3.54 mmol, 1.50 eq) and 3-aminopiperidine-2, 6-dione (467 mg, 2.84 mmol, 1 20 eq, hydrochloric acid). The mixture was stirred at 25 °C for 12 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was diluted with water (300 mL) and extracted with ethyl acetate (2 x 300mL). The organic phase was dried over sodium sulfate, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiC>2, Petroleum ether/Ethyl acetate=5/l to 0/1) to give ze/7-butyl (3- ((2,6-dioxopiperidin-3-yl)carbamoyl)-4-nitrobenzyl)carbamate, Int 4h, (2.56 g, crude) as green oil. H NMR (400 MHz, DMSO-J<) § = 10.87 (s, 1H), 9.02 (br d, J= 8.4 Hz, 1H), 8.06 (d, J= 8.4 Hz,
1H), 7.60 (br t, 7= 6.0 Hz, 1H), 7.53 (dd, 7= 2.0, 8.4 Hz, 1H), 7.45 (s, 1H), 4.73 (ddd, 7= 6.0, 8.0,
11.6 Hz, 1H), 4.25 (br d, 7= 6.0 Hz, 2H), 3.62 (qd, 7= 6.4, 10.4 Hz, 1H), 3.20 - 3.08 (m, 1H), 2.84 - 2.75 (m, 1H), 2.57 (br t, 7= 3 6 Hz, 1H), 1.40 (s, 9H). MS (ESI) m/z 351.1 [M+H-56]+
Step D. Preparation of Int 4i
Figure imgf000253_0001
Int 4h Int 41
To a solution of tert-butyl (3-((2,6-dioxopiperidin-3-yl)carbamoyl)-4-nitrobenzyl)carbamate, Int 4h, (2.20 g, 5.41 mmol, 1.00 eq) in dioxane (30.0 mL) was added palladium on carbon (200 mg, 10% purity). The mixture was stirred at 25 °C for 12 h under hydrogen (50 Psi). The mixture was filtered to give a filter liquor, then was concentrated under reduced pressure to give ter/-butyl (4- amino-3-((2,6-dioxopiperidin-3-yl)carbamoyl) benzyl)carbamate, Int 4i, (1.00 g, crude) as a yellow solid. MS (ESI) m/z 321.1 [M+H-56]+
Step E. Preparation of Int 4j
Figure imgf000253_0002
To a solution of tert-butyl (4-amino-3-((2,6-dioxopiperidin-3- yl)carbamoyl)benzyl)carbamate, Int 4i, (350 mg, 930 μmol, 1.00 eq) in acetic acid (10.0 mL) was added sodium nitrite (128 mg, 1 .86 mmol, 2.00 eq). The mixture was stirred at 50 °C 12 h. The mixture was filtered to give a filter cake, then was concentrated under reduced pressure to give tertbutyl ((3-(2,6-dioxopiperidin-3-yl)-4-oxo-3,4-dihydrobenzo[7][l,2,3]triazin-6-yl)methyl)carbamate, Int 4j, (290 mg, 749 μmol, 80% yield) as a yellow solid. 1 H NMR (400 MHz, DMSO-Ts) δ = 11.20 (br s, 1H), 8.22 (d, 7= 8.4 Hz, 1H), 8.11 (s, 1H), 7.98 (dd, 7= 1.6, 8.4 Hz, 1H), 7.67 (br t, 7= 6.0 Hz, 1H), 5.99 (br dd, 7= 5.6, 12.4 Hz, 1H), 4.37 (br d, J= 6.0 Hz, 2H), 2.98 - 2.92 (m, 1H), 2.71 - 2.66 (m, 2H), 2.31 - 2.25 (m, 1H), 1.40 (s, 9H). MS (ESI) m/z 388.3 [M+H]
Step F. Preparation of Int 4k
Figure imgf000254_0001
A solution of tert-butyl ((3-(2,6-dioxopiperidin-3-yl)-4-oxo-3,4-dihydrobenzo[t/][l,2,3]triazin-6- yl)methyl) carbamate, Int 4j, (290 mg, 749 μmol, 1.00 eq) in hydrochloric acid/ethyl acetate (4.00 M, 10 mL, 53 4 eq) was stirred at 25 °C for 12 h The reaction mixture was concentrated under reduced pressure to give 3-(6-(aminomethyl)-4-oxobenzo|7/][l,2,3]triazin-3(47/)-yl)piperidine-2,6- dione, Int 4k, (250 mg, crude) as a white solid. ’H NMR (400 MHz, DMSO-tfc) δ = 11.22 - 11.17 (m, 1H), 8.44 (d, J= 1.6 Hz, 1H), 8.34 - 8 30 (m, 1H), 8.26 (s, 1H), 6.05 - 5.98 (m, 1H), 4.31 (s, 2H), 3.01 - 2.94 (m, 1H), 2.76 (br s, 2H), 2.30 - 2.24 (m, 1H).
Step G. Preparation of Compound IG-35
Figure imgf000254_0002
Compound IG-35
To a solution of 3-(6-(aminomethyl)-4-oxobenzo|X][l, 2, 3]triazin-3(47/)-yl)piperidine-2, 6-dione, Int 4k, (60 0 mg, 209 μmol, 1.00 eq) in dimethyl formamide (1.00 mL) was added triethylamine (63 4 mg, 627 μmol, 87.2 μL, 3 00 eq) and phenyl (3-hydroxy-4-methylphenyl)carbamate (50.8 mg, 209 μmol, 1.00 eq). The mixture was stirred at 25 °C for 2 h. The reaction mixture was concentrated under reduced pressure to give a residue The residue was purified by TVep-HPLC (column: YMC- Actus Triart C18 150*30mm*7um;mobile phase: [water(FA)-ACN];B%: 23%-53%, 10 min). Further purified by reversed-phase HPLC (column: spherical Cl 8, 20-45 um, lOOA, SW 40, mobile phase: [water(0.1%Formic Acid)-ACN]) to give l-((3-(2,6-dioxopiperidin-3-yl)-4-oxo-3,4- dihydrobenzo[r/][l,2,3]triazin-6-yl)methyl)-3-(3-hydroxy-4-methylphenyl) urea, Compound IG-35, (23.0 mg, 52.6 μmol, 25% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6) δ = 11.19 (br s, 1H), 9.13 (s, 1H), 8.53 (s, 1H), 8.23 (d, J= 8.4 Hz, 1H), 8.17 (s, 1H), 8.08 - 8.02 (m, 1H), 7.04 (d, J = 2.0 Hz, 1H), 6.86 (d, J= 8.0 Hz, 1H), 6.80 - 6.75 (m, 1H), 6.64 (dd, J= 2.0, 8.0 Hz, 1H), 6.03 - 5.94 (m, 1H), 4.51 (d, J= 5.6 Hz, 2H), 2.99 - 2.90 (m, 1H), 2.70 (br d, J= 5.2 Hz, 1H), 2.44 (br dd, J= 3.6, 8.0 Hz, 1H), 2.29 - 2 24 (m, 1H), 2 01 (s, 3H). MS (ESI) m/z 437 2 [M+H]+ EXAMPLE 18
Synthesis of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-6-hydroxy-l- oxoisoindolin-5-yl)methyl)urea (Compound IG-36)
Figure imgf000255_0002
Int 41
To a solution of 2-(hydroxymethyl)isoindoline-l, 3-dione (4.60 g, 26.0 mmol, 1.20 eq) and 4-bromo-3-methoxybenzoic acid (5.00 g, 21.6 mmol, 1.00 eq) in sulfuric acid (20.0 mL) was heated to 80 °C and stirred for 3 h. The mixture was cooled to 25°C and poured into ice water. The suspension was stirred for 15 min and filtered, the yellow solid was washed by water (20.0 mL x 3). Then the solid was dissolved in ammonium hydroxide (30.0 mL, 28%) and ethyl alcohol (30.0 mL) and heated to 80 °C for 3h. The mixture was concentrated under reduced pressure to give a residue. The residue was triturated with water (50.0 mL) at 25 °C for 15 min and collected by filtration to give crude product. Then further triturated with acetonitrile (50.0 mL) at 25 °C for 15 min. The solid was collected by filtration and dried in vacuo to give 5-bromo-6-methoxyisoindolin-l-one, Int 41, (4.00 g, 11.6 mmol, 53% yield, 70% purity) as a white solid. MS (ESI) m/z 244.0 [M+H]+ Step B. Preparation of Int 4m
Figure imgf000255_0001
To a solution of 5-bromo-6-methoxyisoindolin-l-one, Int 41, (1.00 g, 4.13 mmol, 1.00 eq) in dimethyl formamide (5.00 mL) was added 3 -bromopiperidine-2, 6-dione (3.97 g, 20.66 mmol, 5.00 eq) and sodium hydride (1.65 g, 41.3 mmol, 60% purity, 10.0 eq) under nitrogen atmosphere at 0 °C. The mixture was stirred at 25 °C for l2 h. The reaction was quenched with formic acid (10% in water 100 mL). The mixture was extracted with ethyl acetate (3 * 100 mL). The combined organic extracts were washed with brine (200 mL), dried over sodium sulfate and fdtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (0.1% formic acid conditions). The desired fraction was collected and lyophilized to afford 3 -(5-bromo-6-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 4m, (1.50 g, 4.16 mmol, 33% yield, 98% purity) as a white solid. ‘I I NMR (400 MHz, DMSO-c/r,) δ = 10.99 (s, 1H), 7.95 (s, 1H), 7.89 (s, 1H), 7.36 (s, 1H), 5.11 (dd, J= 5.2, 13.4 Hz, 1H), 4.42 - 4.35 (m, 1H), 4.29 - 4.24 (tn, 1H), 3.94 (s, 3H), 2.96 - 2.89 (m, 1H), 2.62 - 2.56 (m, 1H), 2.45 - 2.35 (m, 1H), 2.05 - 1.99 (m, 1H).
Step C. Preparation of Int 4n
Figure imgf000256_0001
di(adamantan-1-yl)(butyl)phosphine
Figure imgf000256_0002
dioxane/H2O, 100 °C, 12 h
To a solution of 3 -(5-bromo-6-m ethoxy- l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 4m, (400 mg, 1.13 mmol, 1.00 eq) in dioxane (10 0 mL) and water (2 00 mL) was added cesium carbonate (738 mg, 2.27 mmol, 2.00 eq), bis(l-adamantyl)-butyl-phosphane (162 mg, 453 μmol, 0.400 eq), potassium;(tert-butoxycarbonylamino)methyl-trifluoro-boranide (269 mg, 1 13 mmol, 1 00 eq) and palladium(II) acetate (51 mg, 227 μmol, 0 200 eq) under nitrogen atmosphere The mixture was stirred at 100 °C for 12 h under nitrogen atmosphere. The reaction mixture was cooled to 25 °C. Ethyl acetate (40.0 mL) and water (40.0 mL) were added and layers were separated. The aqueous phase was extracted with ethyl acetate (2 x 30.0 mL). Combined extracts were washed with brine (40.0 mL), dried over sodium sulfate and filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by /w/i-HPI.C (formic acid 0.1% conditions) The desired fraction was concentrated under reduced pressure to give tert-butyl ((2-(2,6- dioxopiperidin-3-yl)-6-methoxy-l-oxoisoindolin-5-yl)methyl)carbamate, Int 4n, (70.0 mg, 174μmol, 7% yield) as a white solid H NMR (400 MHz, DMSO-Jf)) d = 10.97 (s, 1H), 7 33 (s, 1H), 7.23 (s, 1H), 5.10 (dd, J= 5 6, 13.4 Hz, 1H), 4.42 - 4.33 (m, 1H), 4.26 - 4.20 (m, 1H), 4.17 (br d, J = 6.0 Hz, 2H), 3.88 (s, 3H), 2.98 - 2 85 (tn, 1H), 2.59 (br dd, J= 3.2, 16.9 Hz, 1H), 2.40 - 2.35 (m, 1H), 2.03 - 1.97 (m, 1H), 1.71 (br s, 1H), 1.40 (s, 9H).
Step D. Preparation of Int 4o
Figure imgf000257_0001
To a solution of tert-butyl ((2-(2,6-dioxopiperidin-3-yl)-6-methoxy-l-oxoisoindolin-5- yl)methyl)carbamate, Int 4n, (70.0 mg, 174 μmol, 1.00 eq) in hydrochloric acid / dioxane (4M, 2.00 mL)) The mixture was stirred at 25 °C for 1 h. The mixture was concentrated under reduced pressure to give 3-(5-(aminomethyl)-6-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 4o, (50.0 mg, 165 μmol, 95% yield) as a white solid. MS (ESI) m/z 287.2 [M+H]+
Step E. Preparation of Int 4p
Figure imgf000257_0002
To a solution of 3-(5-(aminomethyl)-6-methoxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 4o, (45.0 mg, 148 μmol, 1 .00 eq) in dimethyl formamide (2.00 mL) was added triethylamine (60.1 mg, 593 μmol, 82.6 μL, 4.00 eq) and phenyl (3-chloro-4-methylphenyl)carbamate (42.7 mg, 163 μmol, 1.10 eq). The mixture was stirred at 50 °C for 1 h The mixture was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (0.1% formic acid conditions). The desired fraction was collected and lyophilized to afford l-(3-chloro-4- methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-6-methoxy-l-oxoisoindolin-5-yl)methyl) urea, Int 4p, (25 mg, 53.1 μmol, 35% yield) as a white solid. MS (ESI) m/z 471 3 [M+H]+
Step F. Preparation of Compound IG-36
Figure imgf000257_0003
Int 4p Compound IG-36
To a solution of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-6-methoxy-l- oxoisoindolin-5-yl)methyl)urea, Int 4p, (22.0 mg, 46.7 μmol, 1.00 eq) in dichloromethane (1.00 mL) was added tribromoborane (117 mg, 467 μmol, 45.0 μL, 10.0 eq) The mixture was stirred at 0 °C for 1 h. The reaction was quenched with water (5.00 mL) and the reaction mixture was filtered to give filter cake. The filter cake was purified by prep-HPLC (column: Phenomenex luna C18 150*25mm* 10um;mobile phase: [water(FA)-ACN];gradient:25%-55% B over 10 min). The desired fraction was collected and lyophilized to afford l-(3-chloro-4-methylphenyl)-3-((2-(2,6- dioxopiperidin-3-yl)-6-hydroxy-l-oxoisoindolin-5-yl)methyl)urea, Compound IG-36, (2 18 mg, 4.77 μmol, 10% yield) as a white solid. 1H NMR (400 MHz, DM SOM) δ = 10.96 (s, 1H), 10. 11 (s, 1H), 8.77 (s, 1H), 7.65 (d, ./- 2.0 Hz, 1H), 7.35 (s, 1H), 7.19 - 7.15 (m, 1H), 7.13 - 7.06 (m, 2H), 6.67 - 6.56 (m, 1H), 5.05 (dd, J = 5.2, 13.7 Hz, 1H), 4.37 - 4 25 (m, 3H), 4.22 - 4.14 (m, 1H), 2.94 - 2.84 (m, 1H), 2.60 (br d, J= 2.8 Hz, 1H), 2.37 - 2.32 (m, 1H), 2.22 (s, 3H), 2.01 - 1.95 (m, 1H). MS (ESI) m/z 457.3 [M+H]
The compounds in Table 11 were prepared in a manner similar to that described for Compound IG-36 using Int 4o and the appropriately substituted aryl isocyanate, or phenyl carbamate (c.f. Example 2).
Table 11
Figure imgf000258_0002
EXAMPLE 19
Synthesis of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-6-(methylamino)-l- oxoisoindolin-5-yl)methyl)urea (Compound IG-45)
Figure imgf000258_0001
Step A. Preparation of Int 5a
Figure imgf000259_0001
Int 5a
To a solution of 3-(5-bromo-l-oxo-isoindolin-2-yl)piperidine-2, 6-dione (3.00 g, 9 28 mmol, 1.00 eq) in sulfuric acid (25.0 mL) was added a solution of nitric acid (12.5 g, 129 mmol, 8.93 mL, 65.0% purity, 13.9 eq) in sulfuric acid (16.0 mL) dropwise at 0 °C under nitrogen atmosphere. The mixture was stirred at 25 °C for 2 h. The mixture was added to ice water (50.0 mL) dropwise then filtered, the filter cake was washed with water (5.00 mL x 3) and dried in vacuo. The solid was triturated with ethyl acetate (10.0 mL) at 25 °C to afford 3-((5-bromo-2- methoxyphenyl)amino)propanoic acid, Int 5a, (3.20 g, 8 69 mmol, 93% yield) as a brown solid. JH NMR (400 MHz, DMSO-d6) δ = 11.05 (s, 1H), 8.35 (s, 1H), 8.25 (s, 1H), 5.15 (dd, J= 5.2, 13.2 Hz, 1H), 4.62 - 4.43 (m, 2H), 2.96 - 2.87 (m, 1H), 2.61 (br d, J= 18.0 Hz, 1H), 2.47 - 2.38 (m, 1H), 2.08 - 2.01 (m, 1H).
Step B. Preparation of Int 5b
Figure imgf000259_0002
Int 5a di(adamantan-1-yl)(butyl)phosphine Int 5b dioxane, H2O, 100 °C, 3 h
To a solution of 3-(5-bromo-6-nitro-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 5a, (1.90 g, 5.16 mmol, 1.00 eq) in dioxane (100 mL) was added water (10.0 mL), potassium(I)(((tert- butoxycarbonyl) amino) methyl) trifluoroborate (1 35 g, 5.68 mmol, 1.10 eq), bis(l-adamantyl)- butyl-phosphane (740 mg, 2.06 mmol, 0.400 eq), cesium carbonate (3.36 g, 10.3 mmol, 2 00 eq) and palladium(II) acetate (463 mg, 2.06 mmol, 0.400 eq) under nitrogen atmosphere. The mixture was stirred at 100 °C for 3 h. The reaction mixture was concentrated under reduced pressure to remove solvent. The residue was diluted with water (500 mL) and extracted with ethyl acetate (500 mL x 3). The combined organic layers were concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®, 40 g SepaFlash® Silica Flash Column, Eluent of 0- 80% Ethyl acetate/Petroleum ether gradient @ 100 mL/min) to give /c77-butyl ((2-(2,6-dioxopiperidin-3-yl)-6-nitro-l-oxoisoindolin-5-yl)methyl)carbamate, Int 5b, (600 mg, 1.43 mmol, 28% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-c/,,) 5 = 11.04 (s, 1H), 8.26 (s, 1H), 7.76 (s, 1H), 7.57 (br t, J= 6.0 Hz, 1H), 5.16 (dd, J= 5.2, 13.2 Hz, 1H), 4.67 - 4.59 (m, 1H), 4.53 . 4.44 (m> 3H), 2.95 - 2.88 (m, 1H), 2.64 (br s, 1H), 2.41 (br dd, J= 4.0, 13.2 Hz, 1H), 2.07 - 2.03 (m, 1H), 1.40 (s, 9H).
Step C. Preparation of Int 5c
Figure imgf000260_0001
Int 5b Int 5c
To a solution of tert-butyl ((2-(2,6-dioxopiperidin-3-yl)-6-nitro-l-oxoisoindolin-5- yl)methyl)carbamate, Int 5b, (600 mg, 1.43 mmol, 1.00 eq) in dioxane (20.0 mb) were added methanol (20.0 mL) and wet palladium on carbon (100 mg, 10% purity) under nitrogen atmosphere. The suspension was degassed under vacuum and purged with hydrogen several times. The mixture was stirred under hydrogen (15 psi) at 25 °C for 3 h. The reaction mixture was filtered. The filtrate was concentrated to give tert-butyl ((6-amino-2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)methyl)carbamate, Int 5c, (300 mg, crude) as a yellow solid. MS (ESI) m/z 333.1 [M+H-56] Step D. Preparation of Int 5d
Figure imgf000260_0002
To a solution of tert-butyl ((6-amino-2-(2, 6-dioxopiperi din-3 -yl)-l -oxoisoindolin-5- yl)methyl)carbamate, Int 5c, (150 mg, 386 μmol, 1.00 eq) in tetrahydrofuran (5.00 mL) were added formaldehyde solution (313 mg, 3.86 mmol, 287 μL, 37% purity, 10.0 eq) and sodium cyanoborohydride (72.8 mg, 1.16 mmol, 3.00 eq) The mixture was stirred at 25 °C for 2 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (column: Phenomenex Luna C18 150*25mm*10um;mobile phase:[water(FA)-ACN]; gradient:20%-50% B over 10 min) to give tert-butyl ((2-(2,6- dioxopiperidin-3-yl)-6-(methylamino)-l-oxoisoindolin-5-yl)methyl)carbamate, Int 5d, (100 mg, 156 μmol, 41% yield, 63% purity) as a white solid. MS (ESI) m/z 403.2 [M+H]+ Step E. Preparation of Int 5e
Figure imgf000261_0001
Int 5d Int 5e
To a solution of tert-butyl ((2-(2,6-dioxopiperidin-3-yl)-6-(methylamino)-l-oxoisoindolin-5- yl)methyl) carbamate, Int 5d, (20.0 mg, 49.7 μmol, 1.00 eq) in ethyl acetate (2.00 mL) was added hydrochloric acid/ethyl acetate (4 M, 5.00 mL). The mixture was stirred at 20 °C for 0.5 h The reaction mixture was concentrated under reduced pressure to give 3-(5-(aminomethyl)-6- (methylamino)-l-oxoisoindolin-2-yl)piperidine-2, 6-dione, Int 5e, (10.0 mg, crude) as a white solid. MS (ESI) m/z 286. 1 [M+H-17]+
Step F. Preparation of Compound IG-45
Figure imgf000261_0002
To a solution of 3-(5-(aminomethyl)-6-(methylamino)-l-oxoisoindolin-2-yl)piperidine-2,6- dione, Int 5e, (10.0 mg, 33.1 μmol, 1.00 eq) in dimethyl formamide (1.00 mL) were added triethylamine (10.0 mg, 99.2 μmol, 13.8 μL, 3.00 eq), phenyl (3-chloro-4-methylphenyl)carbamate (10.4 mg, 39.7 μmol, 1.20 eq). The mixture was stirred at 20 °C for 6 h. The reaction mixture was concentrated under reduced pressure to give residue. The residue was purified by prep-HPLC (column: Phenomenex Luna C18 150*25mm*10um;mobile phase: [water(FA)- ACN];gradient:32%-62% B over 10 min ). The desired fraction was collected and lyophilized to afford l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-6-(methylamino)-l- oxoisoindolin-5-yl)methyl)urea, Compound IG-45, (4.40 mg, 9.27 μmol, 28% yield, 99% purity) as a white solid ’H NMR (400 MHz, DMSO-d6) J = 10.96 (s, 1H), 8 87 (s, 1H), 7 65 (d, J = 2.0 Hz, 1H), 7.28 (s, 1H), 7.20 - 7.17 (m, 1H), 7.15 - 7.12 (m, 1H), 6.76 (s, 1H), 6.73 (br t, J= 6.0 Hz, 1H), 5.68 (q, .7= 4.4 Hz, 1H), 5.08 (dd, J= 4.8, 13 4 Hz, 1H), 4.32 - 4 27 (m, 1H), 4.24 (br d, J = 5.6 Hz, 2H), 4.19 - 4.13 (m, 1H), 2.80 (d, J= 4.8 Hz, 3H), 2.61 - 2.56 (m, 1H), 2.36 (br dd, J= 4.4, 13.2 Hz, 1H), 2.23 (s, 4H), 2.01 - 1.98 (m, 1H). MS (ESI) m/z 470.3 [M+H] 1
EXAMPLE 20 Synthesis of 7V-(2-(2,6-dioxopiperidin-3-yl)-6-hydroxy-l,3-dioxoisoindolin-5-yl)-2-
(trifluoromethoxy)benzenesulfonamide (Compound IG-46)
Figure imgf000262_0001
Int 4q
To a suspension of 4-hydroxyphthalic acid (10.0 g, 54.9 mmol, 1.00 eq) in sulfuric acid (200 mL, 85% purity) was slowly added guanidine nitrate (6.57 g, 53.8 mmol, 0.980 eq) at 5 °C. Then the mixture was stirred at 25 °C for another 2 h. Then the reaction solution was poured into ice- cold water (500 mL) and extracted with ethyl acetate (500 mL). The organic layer was separated and concentrated under reduced pressure to afford 4-hydroxy-5-nitro-phthalic acid, Int 4q, (11.1 g, 29.3 mmol, 53% yield, 60% purity) as a yellow solid.
Figure imgf000262_0002
5 = 12.09 (br s, 2H), 8.28 (s, 1H), 7.20 (s, 1H).
Step B. Preparation of Int 4r
Figure imgf000262_0003
Int 4q Int 4r
To a solution of 4-hydroxy-5-nitro-phthalic acid, Int 4q, (2 00 g, 8.81 mmol, 1.00 eq) in dimethyl formamide (20.0 mL) was added methyl iodide (7.50 g, 52.8 mmol, 3.29 mL, 6.00 eq) and potassium carbonate (3.65 g, 26.4 mmol, 3.00 eq). Then the mixture was stirred at 25 °C for 12 h. The reaction mixture was diluted with water (100 mL) and extracted with ethyl acetate (30 0 mL). The combined organic layers were washed with brine (20 mL), dried over anhydrous sodium sulfate, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash® Silica Flash Column, Eluent of 0-40% ethyl acetate/petroleum ether gradient @ 60 mL/min) to give dimethyl 4-methoxy-5-nitro- benzene- 1,2-dicarboxylate, Int 4r, (900 mg, 3.34 mmol, 37% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6) δ = 8.36 (s, 1H), 7.63 (s, 1H), 4 04 (s, 3H), 3.87 (s, 3H), 3.84 (s, 3H).
Step C. Preparation of Int 4s
Figure imgf000263_0001
To a solution of dimethyl 4-methoxy-5-nitro-benzene-l,2-di carboxylate, Int 4r, (900 mg, 3.34 mmol, 1.00 eq) in methyl alcohol (10.0 mb) and water (5.00 mL) was added iron (933 mg, 16.7 mmol, 5.00 eq) and ammonium chloride (894 mg, 16.7 mmol, 5 00 eq). The mixture was stirred at 80 °C for 2 h. After the reaction mixture was partitioned between saturated sodium bicarbonate aqueous solution (15.0 mL) and ethyl acetate (10.0 mL x 3). The combined organic phase was separated, dried over anhydrous sodium sulfate filtered and concentrated under reduced pressure to afford dimethyl 4-amino-5-methoxy-benzene-l,2-dicarboxylate, Int 4s, (420 mg, 1.76 mmol, 52% yield) as a gray solid. II NMR (400 MHz, DMSO-<4) δ = 7.14 (s, 1H), 6.77 (s, 1H), 5.72 (s, 2H), 3.84 (s, 3H), 3.73 (d, J= 3.2 Hz, 6H).
Step D. Preparation of Int 4t
Figure imgf000263_0002
To a solution of dimethyl 4-amino-5 -methoxy -benzene- 1,2-dicarboxylate, Int 4s, (400 mg, 1.67 mmol, 1.00 eq) in pyridine (5.00 mL) was added dimethylaminopyridine (20.4 mg, 167 μmol, 0.10 eq) and 2-(trifluoromethoxy)benzenesulfonyl chloride (523 mg, 2.01 mmol, 1.20 eq). The mixture was stirred at 80 °C for 12 h. The reaction mixture was partitioned between water (15.0 mL) and ethyl acetate (10 0 mL * 3). The organic phase was separated, dried over anhydrous sodium sulfate filtered and concentrated under reduced pressure to afford dimethyl 4-methoxy-5- ((2-(trifluoromethoxy)phenyl)sulfonamido)phthalate, Int 4t, (590 mg, 1.27 mmol, 76% yield) as a white solid. ‘HNMR (400 MHz, DMSO-d6) δ = 10.14 (s, 1H), 7.86 (dd, J= 1.6, 7.9 Hz, 1H), 7.79 - 7.74 (m, 1H), 7.67 (s, 1H), 7.57 - 7.48 (m, 2H), 7.18 (s, 1H), 3.78 (d, J= 2.0 Hz, 6H), 3.62 (s, 3H). Step E. Preparation of Int 4u
Figure imgf000264_0001
To a solution of dimethyl 4-methoxy-5-((2- (trifluoromethoxy)phenyl)sulfonamido)phthalate, Int 4t, (590 mg, 1.27 mmol, 1 00 eq) in methyl alcohol (5.00 mL) and water (5 00 mL) was added lithium hydroxide (244 mg, 10.2 mmol, 8.00 eq). The mixture was stirred at 50 °C for 5 h. After the reaction mixture was partitioned between water (15.0 mL) and ethyl acetate (10.0 mL><3). The combined organic phase was separated, dried over anhydrous sodium sulfate filtered and concentrated under reduced pressure to afford 4-methoxy-5- ((2-(trifluoromethoxy)phenyl)sulfonamido)phthalic acid, Int 4u, (320 mg, 735 μmol, 57% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-t/, 1 d = 13.12 (br s, 2H), 10.02 (s, 1H), 7.83 (dd, J= 1.2, 8.0 Hz, 1H), 7.79 - 7.73 (m, 1H), 7.62 (s, 1H), 7.57 (br d, J= 8.0 Hz, 1H), 7.49 (t, J = 7.6 Hz, 1H), 7.10 (s, 1H), 3.59 (s, 3H).
Step F. Preparation of Int 4v
Figure imgf000264_0002
To a solution of 4-methoxy-5-((2 -(trifluoromethoxy )phenyl)sulfonamido)phthalic acid (320 mg, 735 μmol, 1 .00 eq) in acetic anhydride, Int 4u, (5.00 mL) was degassed and purged with nitrogen for 3 times and then the mixture was stirred at 100 °C for 12 h under nitrogen atmosphere. After the reaction mixture was concentrated under reduced pressure to give A-(6-methoxy-l,3- dioxo-l,3-dihydroisobenzofuran-5-yl)-2-(trifluoromethoxy) benzenesulfonamide, Int 4v, (460 mg, crude) as a white solid. MS (ESI) m/z 418.1 [Al I II]
Figure imgf000264_0003
To a solution of A-(6-methoxy-l,3-dioxo-isobenzofuran-5-yl)-2-
(trifluoromethoxy)benzenesulfonamide, Int 4v, (306 mg, 733 μmol, 1.00 eq) in acetic acid (5.00 mL) was added sodium acetate (120 mg, 1.47 mmol, 2.00 eq), 3-aminopiperidine-2,6- dione;hydrochloride (121 mg, 733 umol. 1.00 eq). The mixture was stirred at 100 °C for 12 h under nitrogen atmosphere. After the reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC (0.1% FA) and lyophilized to afford N- (2-(2,6-dioxopiperidin-3-yl)-6-methoxy-l,3-dioxoisoindolin-5-yl)-2- (trifluoromethoxy)benzenesulfonamide, Int 4w, (150 mg, 284 μmol. 38% yield) as a white solid.
H NMR (400 MHz, DMSO-cZ6) 8 = 10.94 (br s, 1H), 8.21 (d, J= 8.0 Hz, 1H), 8.01 (s, 1H), 7.90 (t, J = 8.0 Hz, 1H), 7.73 (s, 1H), 7.64 (d, J= 7.6 Hz, 1H), 7.53 - 7.44 (m, 1H), 5.15 (dd, J = 5.6, 12.8 Hz, 1H), 3.98 (s, 3H), 2.93 - 2.84 (m, 1H), 2.67 - 2.57 (m, 2H), 2.15 - 2.09 (m, 1H).
Step H. Preparation of Compound IG-46
Figure imgf000265_0001
To a solution of A-(2-(2,6-dioxopiperidin-3-yl)-6-methoxy-l,3-dioxoisoindolin-5-yl)-2- (tri fluoromethoxy) benzenesulfonamide, Int 4w, (130 mg, 246 μmol, 1.00 eq) in dichloromethane (2 00 mL) was added boron tribromide (617 mg, 2.46 mmol, 236 pF, 10.0 eq) at 0 °C. Then the mixture was stirred at 0 °C for 2 h. The reaction mixture was poured into ice water and filtered. The filter cake was purified by prep-HPLC (column: Waters Abridge 150*25mm* 5um; mobile phase: [water (NH4HCO3) - ACN]; gradient: 18%-48% B over 9 min) and prep-HPLC (column: Phenomenex Luna Cl 8 150 * 25 mm * 10 um; mobile phase: [water (FA)-ACN]; gradient:28%- 58% B over 10 min) to afford A-(2-(2,6-dioxopiperidin-3-yl)-6-hydroxy-l,3-dioxoisoindolin-5-yl)- 2-(trifluoromethoxy)benzenesulfonamide, Compound IG-46, (6.65 mg, 12.4 μmol, 5% yield, 96%> purity) as a yellow solid. 1H NMR (400 MHz, DMSO4) 3 = 11.08 (s, 1H), 7.94 (dd, J= 1.6, 7.9 Hz, 1H), 7.79 - 7.73 (m, 1H), 7.61 (s, 1H), 7.58 - 7.48 (m, 2H), 7.15 (s, 1H), 5.04 (dd, J= 5.6, 12.8 Hz, 1H), 2.91 - 2.80 (m, 1H), 2 59 (br d, ,J= 2.8 Hz, 1H), 2.46 (br d, J= 4.4 Hz, 1H), 2.04 - 1.96 (m, 1H). MS (ESI) m/z 514.2 [M+H]+
EXAMPLE L-3: Synthesis of 4-((5)-2-((S)-2-(3-(2,5-dioxo-2,5-dihydro-l/7-pyrrol-l- yl)propanamido)propanamido)propanamido)benzyl (2-(2-chloro-4-(3-(2-(2,6-dioxopiperidin-3-yl)- l-oxoisoindolin-5-yl)propanamido)phenethoxy)ethyl) (m ethylcarbamate (IG-L-3)
Figure imgf000266_0001
To a solution of A^-(3-chloro-4-(2-(2-(methylamino)ethoxy)ethyl)phenyl)-3-(2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)propenamide, Compound IG-2, (100 mg, 190 umol, 1.00 eq) and 4-((.S’)-2-(0S')-2-(3-(2,5-dioxo-2,5-dihydro- lj¥-pyrrol- l- yl)propanamido)propanamido)propanamido)benzyl (4-nitrophenyl) carbonate (1 10 mg, 190 umol, 1.00 eq) in .'V,A'-dimcthylformamidc (0.5 mL) was added 1 -hydroxybenzotriazole (25.6 mg, 190 umol, 1.00 eq) and diisopropylethylamine (73.6 mg, 569 umol, 99.2 uL, 3.00 eq), the mixture was stirred at 0 °C for 1 h. The mixture was filtered. The filtrate was purified by /‘/ep-HPLC (column: Unisil 3-100 C18 Ultra 150*50mm*3 um;mobile phase: [water(FA)-ACN];B%: 35%-65%,7min) and lyophilized to afford 4-((.SJ-2-(U')-2-(3-(2,5-dioxo-2,5-dihydro- 1 //-pyrrol- 1- yl)propanamido)propanamido)propanamido)benzyl (2-(2-chloro-4-(3-(2-(2,6-dioxopiperidin-3-yl)- l-oxoisoindolin-5-yl)propanamido)phenethoxy)ethyl) (methyl)carbamate, Compound IG-L-3, (52.96 mg, 54. 1 umol, 29% yield, 99% purity) as a white solid.
Figure imgf000267_0001
DMSO-uk) δ = 10.97 (br s, 1H), 10.05 (s, 1H), 9.85 (s, 1H), 8.20 (d, J= 7.2 Hz, 1H), 8 11 (d, J= 7.1 Hz, 1H), 7.78 (d, J= 1.8 Hz, 1H), 7.62 (dd, J= 8.0, 16.2 Hz, 3H), 7.48 (s, 1H), 7.40 (d, J = 8.0 Hz, 1H), 7.37 -
7.17 (tn, 4H), 6.99 (s, 2H), 5.10 (dd, J= 5.1, 13.2 Hz, 1H), 4.98 (s, 2H), 4.50 - 4 11 (m, 4H), 3.60 (t, J= 7.3 Hz, 2H), 3.56 - 3.47 (m, 3H), 3.37 - 3.34 (m, 2H), 3.02 (br t, J= 7.4 Hz, 2H), 2.96 - 2.86 (m, 2H), 2.82 (br d, J= 8.4 Hz, 4H), 2.67 (br t, J= 7.6 Hz, 3H), 2.62 - 2.60 (m, 1H), 2.45 - 2.35 (m, 3H), 2.03 - 1.93 (m, 1H), 1.30 (d, J= 7.2 Hz, 3H), 1.17 (d, J= 7.2 Hz, 3H)
The compounds in Table 12 were prepared in a manner similar to that described for Compound IG-L-3 using the appropriate compound as starting material.
Table 12
Figure imgf000268_0001
Figure imgf000269_0001
Figure imgf000270_0001
Figure imgf000271_0001
Figure imgf000272_0001
Figure imgf000273_0001
Figure imgf000274_0001
Figure imgf000275_0001
Figure imgf000276_0001
EXAMPLE L-20: Synthesis of 34-(2-(3-(((2S)-l-(((2S)-l-((4-((((2-(2-chloro-4-(3-((2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl) (methyl)carbamoyl)oxy)methyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl) amino)-3-oxopropyl)-5 -(2, 5-dioxo-2, 5 -dihydro- I //-pyrrol - I -yl)phenoxy)-
3.6.9.12.15.18.21.24.27.30-decamethyl-4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,
24.27.30-decaazatetratriacontanoic acid (IG-L-20)
Figure imgf000277_0002
Int 10a
To a solution of tert-butyl methylglycinate (100 g, 550 mmol, 1.00 eq, hydrochloride) and Ar-(((9/7-fluoren-9-yl)methoxy)carbonyl)-Ar-methylglycine (171 g, 550 mmol, 1.00 eq) in dimethyl formamide (400 mL) was added diisopropylethylamine (142 g, 1.10 mol, 192 mL, 2.00 eq) and O-(7-azabenzotriazol- l-yl)-A'A',.'V ',.V -tetrainethyluronium hexafluorophosphate (251 g, 661 mmol, 1 .20 eq). Then the mixture was stirred at 25 °C for 1 h. The reaction mixture was poured into water (3 L) and extracted with ethyl acetate (3 x 200 mL). The organic layer was washed with brine (3 x 200 mL) and concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 330 g SepaFlash ® Silica Flash Column, Eluent of 30-90% ethyl acetate/petroleum ether gradient @ 120 mL/min) to afford tertebutyl
Figure imgf000277_0001
fluoren-9-yl)methoxy)carbonyl)-A-methylglycyl)-rV-methylglycinate, Int 10a, (230 g, 524 mmol, 95% yield) as yellow oil. 1H NMR (400 MHz, DMSO-d6 ) δ = 7.89 (t, J = 8.4 Hz, 2H), 7.69 - 7 56 (m, 2H), 7.41 (q, J= 7.4 Hz, 2H), 7.37 - 7.25 (m, 2H), 4.33 - 4.08 (m, 4H), 4.04 -
3.93 (m, 3H), 2.97 - 2.79 (m, 6H), 1.45 - 1.35 (m, 9H).
Step B. Preparation of Int 10b
Figure imgf000278_0001
A solution of tert-butyl A-(A-(((9//-fluoren-9-yl)methoxy)carbonyl)-A-methylglycyl)-A- methylglycinate, Int 10a, (230 g, 524 mmol, 1.00 eq) in trifluoroacetic acid (500 mL) and dichloromethane (500 mL) was stirred at 25 °C for 3 h. The reaction mixture was concentrated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 330 g SepaFlash® Silica Flash Column, Eluent of 50-100% ethyl acetate/petroleum ether gradient @ 120 mL/min) to afford A-(Ar-(((9/Z-fluoren-9-yl)methoxy)carbonyl)-A-methylglycyl)-Ar- methylglycine, Int 10b, (200 g, 523 mmol, 99% yield) as yellow oil. 'l l NMR (400 MHz, DMSO-tfc) δ = 7.89 (br t, J= 8.8 Hz, 2H), 7.72 - 7.56 (m, 2H), 7 41 (q, J= 7.2 Hz, 2H), 7.37 - 7.25 (m, 2H), 4.35 - 4.23 (m, 2H), 4.23 - 4.08 (m, 2H), 4.07 - 3.97 (m, 3H), 3.01 - 2.77 (m, 6H). Step C. Preparation of Int lOd
Figure imgf000278_0002
Int lOd
To a solution of 2V-(A-(((9//-fluoren-9-yl)methoxy)carbonyl)-A-methylglycyl)-JV- methylglycine, Int 10b, (35.0 g, 91.5 mmol, 1.00 eq) in di chloromethane (600 mL) was added to 2-chlorotrityl chloride resin (175 g). Then diisopropylethylamine (29.6 g, 228 mmol, 39.9 mL, 2.50 eq) was added. The mixture was stirred at 25°C for 2 h. The mixture was filtered and washed with dimethyl formamide (600 mL) and dichloromethane/methanol/diisopropylethylamine (600 mL, 80:15:5). The mixture was filtered and washed with dimethyl formamide (3 x 600 mL) and dichloromethane (3 x 600 mL). This reaction was in parallel twice. The resin, Int 10c, was stored at 0 °C for next step.
Elongation of the poly sarcosine oligomer was performed until the desired length was obtained, by alternating remove Fmoc and amide coupling steps. In the first step, the resin, Int 10c, was treated with piperidine (50%) in dimethyl formamide at 25°C for 1 min and washed with dimethyl formamide (4 times) For the amide coupling step, to the resin was added a solution of JV-(7V-(((9//-fluoren-9-yl)methoxy)carbonyl)-JV-methylglycyl)-JV-methylglycine (1.30 eq), O-(7-azabenzotriazol-l-yl)-N,N,N,N ’,N’-tetramethyluronium hexafluorophosphate (1.50 eq) and diisopropylethylamine (2 eq) in dimethylformamide The reaction vessel was stirred at 25 °C for 2 h and the resin was extensively washed with dimethyl formamide (4 times) and dichloromethane (3 times). The resin, Int lOd, was dried under vacuum and stored at 0 °C.
Step D. Preparation of Int lOe
Figure imgf000279_0001
Int 10e
The resin, Int lOd, in piperidine (500 mL) and dimethyl formamide (500 mL) was agitated with nitrogen atmosphere at 15 °C for 1 min. The mixture was filtered and washed with dimethyl formamide (3 x 500 mL) and di chloromethane (500 mL), then the filter cake was concentrated in vacuum. The resin, Int lOe, (the equivalent of 50 g of Int lOf loaded on resin) was dried under vacuum and stored at 0 °C.
Step E. Preparation of Int lOf
Figure imgf000280_0001
Int 10f
The resin, Int lOd, (42 g) in piperidine (40.0 mL) and dimethyl formamide (160 mL) was agitated with nitrogen atmosphere for 1 h at 25°C. Then the solution was drained and the resin was washed with dimethyl formamide (3 * 120 mL) and dichloromethane (3 * 120 mL). Then it was agitated in 1, l,l,3,3,3-Hexafluro-2-propanol (40 mL) and DCM (160 mL) with nitrogen atmosphere for 1 h at 25 °C and filtered. The filtrate was concentrated to give a residue, which was purified by prep-HPLC (column: Waters Atlantis T3 150*30mm*5um;mobile phase: [water(FA)-ACN] gradient: l%-20% B over 10 min) to give 5,8,l l,14,17,20,23,26,29-nonamethyl-4,7,10, 13,16,19,22,25,28-nonaoxo- 2,5,8,l l,14,17,20,23,26,29-decaazahentriacontan-31-oic acid, Int lOf, (550 mg, 754 μmol) as a white solid. H \MR (400 MHz, DMSO-d6) 3 = 4.50 - 3.50 (m, 24H), 2.95 - 270 (m, 23H), 2.49 - 2.37 (m, 3H).
Step F. Preparation of Int 10g
Figure imgf000280_0002
Int 10g To a mixture of 2-bromo-5-nitrophenol (125 g, 573 mmol, 1.00 eq) and cesium carbonate (374 g, 1.15 mol, 2.00 eq), potassium iodide (9.52 g, 57.3 mmol, 0.100 eq) in N,N- dimethyl formamide (500 mL) was added tert-butyl 4-bromobutanoate (141 g, 631 mmol, 1.10 eq). The mixture was stirred at 85 °C for 12 h. The reaction mixture was poured into ice water (5 L). After a large quantity of brown precipitate was formed. The precipitate was washed with water (300 mL). After filtration, the solid was concentrated under reduced pressure to afford tert-butyl 4-(2-bromo-5-nitrophenoxy)butanoate, Int 10g, (372 g, crude) as a yellow solid which was used in next step without purification. 1 H NMR (400 MHz, DMSO-dc) 3 = 7.88 (d, J= 8 4 Hz, 1H), 7.81 (d, J= 2.0 Hz, 1H), 7.74 (dd, J= 2.4, 8.8 Hz, 1H), 4.21 (t, J= 6.4 Hz, 2H), 2.42 (t, J= 7.2 Hz, 2H), 1.99 (quin, J= 6.8 Hz, 2H), 1.39 (s, 9H)
Step G. Preparation of Int lOh
Figure imgf000281_0001
g
A mixture of tert-butyl 4-(2-bromo-5-nitrophenoxy)butanoate, Int 10g, (50.0 g, 139 mmol, 1.00 eq), ethyl (£)-3-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)acrylate (78 5 g, 347 mmol, 2.50 eq), tris(dibenzylideneacetone) dipalladium(O) (6.36 g, 6.94 mmol, 0.0500 eq), dicyclohexyl(2',6'-dimethoxy-[l,r-biphenyl]-2-yl)phosphane (5.70 g, 13.9 mmol, 0.100 eq), potassium phosphate (30.0 g, 141 mmol, 1.02 eq) in water (100 mL) and dioxane (400 mL) was stirred at 90°C for 12 h under nitrogen atmosphere. After being cooled to room temperature, the mixture was concentrated under reduced pressure to give a residue, which was purified by flash silica gel chromatography (ISCO®;330 g SepaFlash® Silica Flash Column, Eluent of 0-30% ethyl acetate / petroleum ether gradient @ 120 mL/min). The desired fraction collected and concentrated under reduced pressure to afford te/7-butyl (E)-4-(2-(3 -ethoxy-3 -oxoprop- 1-en-l- yl)-5-nitrophenoxy)butanoate, Int lOh, (50.0 g, 132 mmol, 94% yield) as a yellow solid. 1 H NMR (400 MHz, DMSO-d6 ) 3 = 8.05 - 7.99 (m, 1H), 7.87 (d, J= 16.4 Hz, 1H), 7.83 (br s, 2H), 6.82 (d, J= 16.0 Hz, 1H), 4.28 - 4.16 (m, 4H), 2.41 (br t, J= 7.2 Hz, 2H), 2.02 (quin, J = 6.4 Hz, 2H), 1.27 (t, J = 7.2 Hz, 3H).
Step H. Preparation of Int lOi
Figure imgf000281_0002
To a solution of tert-butyl (E)-4-(2-(3-ethoxy-3-oxoprop-l-en-l-yl)-5- nitrophenoxy)butanoate, Int lOh, (50.0 g, 132 mmol, 1.00 eq) in methanol (500 mL) was added palladium on activated carbon (20.0 g, 10% purity) under hydrogen (50 Psi). The mixture was stirred at 25 °C for 12 h. The mixture was filtered by celite with diatomite to give the filtrate, and concentrated to afford tert-butyl 4-(5-amino-2-(3-ethoxy-3-oxopropyl)phenoxy) butanoate, Int lOi, (39.5 g, crude) as yellow oil which was used in next step without purification. ]H NMR (400 MHz, DMSO-d6) 6 = 6.74 (d, J= 8.0 Hz, 1H), 6. 17 (d, J= 1 .6 Hz, 1H), 6.05 (dd, J= 1.6, 8.0 Hz, 1H), 4.89 (s, 2H), 4.04 - 4.00 (m, 2H), 3.86 (t, J= 6.0 Hz, 2H), 2.69 - 2.59 (m, 2H), 2.43 (t, J= 7.6 Hz, 2H), 2 39 (t, J= 7 6 Hz, 2H), 1 93 (quin, J= 6 8 Hz, 2H), 1 16 (t, J= 7 2 Hz, 3H)
Figure imgf000282_0001
To a solution of tert-butyl 4-(5-amino-2-(3 -ethoxy-3 -oxopropyl)phenoxy)butanoate, Int lOi, (34.0 g, 96.8 mmol, 1.00 eq) in tetrahydrofuran (30.0 mL), methanol (30.0 mL) and water (30.0 mL) was added lithium hydroxide monohydrate (13.3 g, 318 mmol, 3.28 eq). The mixture was stirred at 25 °C for 1 h. The mixture was quenched with hydrochloric acid (IM) until pH= 7. The mixture was concentrated to remove tetrahydrofuran and methanol. The mixture was diluted with water (300 mL) and extracted with ethyl acetate (3 * 150 mL). The organic layer was dried over anhydrous sodium sulfate, concentrated to afford 3-(4-amino-2-(4-(tert-butoxy)- 4-oxobutoxy)phenyl)propanoic acid, Int lOj, (20.0 g, crude) as yellow oil which was used in next step without purification. 1H NMR (400 MHz, DMSO-cfc) J = 6.73 (d, J= 8.0 Hz, 1H), 6.15 (d, J= 1.6 Hz, 1H), 6.03 (dd, J= 1.6, 8.0 Hz, 1H), 5.13 - 4.51 (m, 2H), 3.85 (t, J= 6.0 Hz, 2H), 2.59 (br t, J= 7.6 Hz, 2H), 2.37 (t, J= 7.6 Hz, 2H), 2.34 - 2.27 (m, 2H), 1.91 (quin, J= 6.8 Hz, 2H), 1.39 (s, 9H). MS (ESI) m/z 324.0 | M 1 111 Step J. Preparation of Int 10k
Figure imgf000283_0001
To a solution of 3-(4-amino-2-(4-(tert-butoxy)-4-oxobutoxy)phenyl)propanoic acid, Int 10j, (19.5 g, 60.3 mmol, 1.00 eq) in di chloromethane (100 ml) was added tri ethylamine (18.3 g, 181 mmol, 25.2 mL, 3.00 eq) and methyl 2,5-dioxo-2,5-dihydro-127-pyrrole-l-carboxylate (10.3 g, 66.3 mmol, 10.3 mL, 1.10 eq) at 0 °C. The mixture was stirred at 15 °C for 2 h. The mixture was quenched with trifluoroacetic acid until pH= 6, and then diluted with water (500 mL). The aqueous layer was extracted with ethyl acetate (3 * 300 mL). The combined organic layers were dried over anhydrous sodium sulfate, concentrated to afford 3-(2-(4-(terLbutoxy)-4-oxobutoxy)- 4-(2,5-dioxo-2,5-dihydro-127-pyrrol-l-yl)phenyl)propanoic acid, Int 10k, (33.0 g, crude) as yellow oil. MS (ESI) m/z 402.2 [M-H]+
Step K. Preparation of Int 101
Figure imgf000283_0002
To a mixture of 3-(2-(4-(terLbutoxy)-4-oxobutoxy)-4-(2,5-dioxo-2,5-dihydro-l//-pyrrol- l-yl)phenyl) propanoic acid, Int 10k, (32.0 g, 79.3 mmol, 1.00 eq) and 2,3,5,6-tetrafluorophenol (26.4 g, 159 mmol, 2.00 eq) in M/V-dimethylacetamide (30.0 mL) and di chloromethane (300 mL) was added 3 -(((ethylimino) rnethylene)amino)-.¥,A'-dimethylpropan- l -arniniurn chloride, EDCI (30.4 g, 159 mmol, 2.00 eq) at 0 °C, and then stirred at 15 °C for 1 h. The mixture was concentrated to give a residue, which was purified by flash silica gel chromatography (ISCO®;330 g SepaFlash® Silica Flash Column, Eluent of 0-16% ethylacetate/petroleum ether gradient @ 150 mL/min). The desired fraction was collected and concentrated under reduced pressure to afford ferZ-butyl 4-(5-(2,5-dioxo-2,5-dihydro-17T-pyrrol-l-yl)-2-(3-oxo-3-(2,3,5,6- tetrafluorophenoxy )propyl)phenoxy) butanoate, Int 101, (29.0 g, 52.3 mmol, 66% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-<4) δ = 7.99 - 7.87 (m, 1H), 7.32 (d, J = 8.0 Hz, 1H), 7.16 (s, 2H), 6.96 (d, J= 1 2 Hz, 1H), 6.85 (dd, J= 1.6, 8.0 Hz, 1H), 4.00 - 3.94 (m, 2H), 3.11 - 3.04 (m, 2H), 3.04 - 2.97 (m, 2H), 2.41 (t, J= 7.6 Hz, 2H), 1.98 - 1.92 (m, 2H), 1.37 (s, 9H). Step L. Preparation of Int 10m
Figure imgf000284_0001
To a solution of tert-butyl 4-(5-(2,5-dioxo-2,5-dihydro-l//-pyrrol-l-yl)-2-(3-oxo-3- (2,3,5,6-tetrafluorophenoxy)propyl)phenoxy)butanoate, Int 101, (14.5 g, 26.3mmol, 1.00 eq) in dichloromethane (80.0 mL) was added trifluoroacetic acid (30.7 g, 269 mmol, 20.0 mL, 10.2 eq). The mixture was stirred at 15 °C for 1 h. The mixture was concentrated under reduced pressure to give a residue, which was diluted with water (300 mL) and the aqueous phase was extracted with ethyl acetate (3 x 200 mL). The combined organic layer was washed with brine (200 mL), dried with anhydrous sodium sulfate, filtered and concentrated in vacuum. The crude product was diluted with water (100 mL) and lyophilized, then the crude product was triturated with 2-methoxy-2-methylpropane (3 x 50 mL) to afford 4-(5-l'2,5-dioxo-2,5-dihydro- I H-pyrrol- l-yl)-2-(3-oxo-3-(2,3,5,6-tetrafluorophenoxy)propyl)phenoxy)butanoic acid, Int 10m, (23.0 g, 46.4 mmol, 88% yield) as a white solid. 1 H NMR (400 MHz, DMSCW<) d = 12.11 (br s, 1H), 7.98 - 7 86 (m, 1H), 7.31 (d, J= 8.0 Hz, 1H), 7. 16 (s, 2H), 6.97 (d, J= 2.0 Hz, 1H), 6.84 (dd, J = 1.6, 7 6 Hz, 1H), 4.00 (t, J= 6.0 Hz, 2H), 3.14 - 3.05 (m, 2H), 3.04 - 2.96 (m, 2H), 2.42 (t, J = 7.6 Hz, 2H), 1.99 (quin, J= 6.4 Hz, 2H)
Step M. Preparation of Int lOn
Figure imgf000284_0002
To a solution of 4-(5-(2,5-dioxo-2,5-dihydro-17/-pyrrol-l-yl)-2-(3-oxo-3-(2, 3,5,6- tetrafluorophenoxy)propyl) phenoxy )butanoic acid, Int 10m, (2.00 g, 4.04 mmol, 1.00 eq) in dichloromethane (10.0 mL) was added l-chloro-A,A,2-trimethylprop-l-en-l-amine (1.08 g, 8.07 mmol, 1.07 mL, 2.00 eq). The mixture was stirred at 15 °C for 1 h. The mixture was concentrated under reduced pressure to afford 2,3,5,6-tetrafluorophenyl 3-(2-(4-chloro-4- oxobutoxy)-4-(2,5-dioxo-2,5-dihydro-177-pyrrol-l-yl)phenyl)propanoate, Int lOn, (2.00 g, crude) as yellow oil which was used in next step without purification.
Step N. Preparation of Int lOo
Figure imgf000285_0001
Int lOo
To a solution of 2,3,5,6-tetrafluorophenyl 3-(2-(4-chloro-4-oxobutoxy)-4-(2,5-dioxo-2,5- dihydro-l/f-pyrrol-l-yl)phenyl)propanoate, Int lOn, (2.00 g, 3.89 mmol, 1.00 eq) in dichloromethane (20.0 mL) was added diisopropylethylamine (1.51 g, 11.7 mmol, 2.03 mL, 3.00 eq) and 5,8,l l,14,17,20,23,26,29-nonamethyl-4,7,10,13,16,19,22,25,28-nonaoxo-
2.5.8.11.14.17.20.23.26.29-decaazahentriacontan-31-oic acid, Int lOf, (2.84 g, 3.89 mmol, 1.00 eq) at 0 °C. The mixture was stirred at 15 °C for 1 h. The mixture was concentrated under reduced pressure to give a residue, which was purified by reversed-phase HPLC (column: spherical C1 8, 20-45 um, 100A, SW 80, mobile phase: [ water (0. l%Formic Acid)-ACN];B%: 10%-60%, 30 min). The desired fraction was collected and lyophilized to afford 34-(5-(2,5- di oxo-2, 5 -dihydro- 1 H-py rrol-1 -yl)-2-(3 -oxo-3 -(2,3 ,5, 6-tetrafluorophenoxy)propyl)phenoxy)- 3 ,6,9, 12, 15, 18,21 ,24,27,30-decamethyl-4,7, 10, 13 , 16, 19,22,25,28,31-decaoxo-
3.6.9.12.15.18.21.24.27.30-decaazatetratriacontanoic acid, Int lOo, (1.30 g, 1.08 mmol, 27% yield) as a white solid. 1H NMR (400 MHz, DMSO-tfc) δ = 8.01 - 7.87 (m, 1H), 7.34 - 7 26 (m, 1H), 7.17 (s, 2H), 6.96 (br d, J= 8.8 Hz, 1H), 6.86 - 6.79 (m, 1H), 4.35 - 3.94 (m, 22H), 2.98 - 2.71 (m, 34H), 2.53 - 2.52 (m, 1H), 2.34 - 2.23 (m, 1H), 2.01 - 1.90 (m, 2H)
Step O. Preparation of Int lOp
Figure imgf000286_0001
Int 10p
To a solution of tert-butyl ((5)-l-(((6)-l-((4-(hydroxymethyl)phenyl)amino)-l- oxopropan-2-yl)amino)- 1 -oxopropan-2-yl)carbamate (3.00 g, 8.21 mmol, 1.00 eq) infVyV- dimethylformamide (30.0 mL) was added bis(4-nitrophenyl) carbonate (2.50 g, 8.21 mmol, 1.00 eq) and diisopropyl ethyl amine (1.59 g, 12.3 mmol, 2.14 mL, 1.50 eq). The mixture was stirred at 25 °C for 2 h. The mixture was diluted with water (200 mL) and extracted with ethyl acetate (3 x 400 mL). The combined organic layers were washed with brine (2 x 200 mL), dried over sodium sulfate and filtered The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 80 g SepaFlash® Silica Flash Column, Eluent of 0-60% ethyl acetate/petroleum ether @ 100 mL/min) to afford terLbutyl ((<$)- 1 -(((5)- 1 -((4-((((4-nitrophenoxy)carbonyl)oxy)methyl)phenyl)amino)- 1 - oxopropan-2-yl)amino)- 1 -oxopropan-2-yl) carbamate, Int lOp, (2.70 g, 5.04 mmol, 61% yield, 99% purity) as a yellow solid. MS (ESI) m/z 531 . 1 [M+H]+
Step P. Preparation of Int lOq
Figure imgf000287_0001
To a solution of tert-butyl ((S)-l-(((5)-l-((4-((((4- nitrophenoxy)carbonyl)oxy)methyl)phenyl)amino)- 1 -oxopropan-2-yl)amino)- 1 -oxopropan-2- yl)carbamate, Int lOp, (100 mg, 188 μmol, 1 00 eq) in N,N-dimethylformamide (3.00 mL) was added l-(3-chloro-4-(2-(2-(methylamino)ethoxy)ethyl)phenyl)-3-((2-(2,6-dioxopiperidin-3-yl)- l-oxoisoindolin-5-yl)methyl)urea, Compound IG-3, (99.5 mg, 188 μmol, 1.00 eq) and triethylamine (38.2 mg, 377 μmol, 52.5 μL, 2.00 eq). The mixture was stirred at 25 °C for 1 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC (C18, 40 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1% formic acid) and lyophilized to afford 4-((5)-2-((S)-2-((tert- butoxycarbonyl)amino)propanamido)propanamido)benzyl (2-(2-chloro-4-(3-((2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int lOq, (120 mg, 129 μmol, 69% yield, 99% purity) as a white solid. rH NMR (400 MHz, DMSO-d6) d = 10.97 (s, 1H), 9.79 (br s, 1H), 8.79 (s, 1H), 8.21 - 7 96 (m, 1H), 7.71 - 7.65 (m, 2H), 7.63 - 7.56 (m, 2H), 7.51 (s, 1H), 7.44 (d, J= 8.0 Hz, 1H), 7.29 (br d, J= 7.2 Hz, 2H), 7.21 - 7.10 (m, 2H), 7.07 - 6.94 (m, 1H), 6.82 (t, J = 6.0 Hz, 1H), 5.10 (dd, J= 5.2, 13.2 Hz, 1H), 4.99 (s, 2H), 4.49 - 4.26 (m, 5H), 3.99 (quin,
Figure imgf000287_0002
6.8 Hz, 1H), 3.56 - 3.46 (m, 4H), 3.37 - 3.34 (m, 2H), 2.97 - 2.86 (m, 1H), 2.83 (br d, J= 8.4 Hz, 5H), 2.60 (br dd, J= 1.6, 17.2 Hz, 1H), 2.46 - 2.34 (m, 1H), 2.04 - 1.94 (m, 1H), 1.40 - 1.32 (m, 9H), 1.29 (dd, J= 2.4, 7.2 Hz, 3H), 1.17 (br d, J= 7.2 Hz, 3H). MS (ESI) m/z 919.2 [M+H]+ Step Q. Preparation of Int lOr
Figure imgf000288_0001
To a solution of 4-((S)-2-((5)-2-((tert- butoxycarbonyl)amino)propanamido)propanamido)benzyl (2-(2-chloro-4-(3-((2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int 10q, (100 mg, 109 μmol, 1.00 eq) in dichloromethane (4.00 mL) was added trifluoroacetic acid (1.54 g, 13.5 mmol, 1.00 mL, 124 eq) The mixture was stirred at 25 °C for 0.5 h. The mixture was concentrated under reduced pressure to afford 4-((5)-2-((5)-2- aminopropanamido)propanamido)benzyl (2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int lOr, (80.0 mg, 68.4 μmol, 63% yield, 70% purity) as a white solid. MS (ESI) m/z 819.4 [M+H]+
Step R. Preparation of Compound IG-L-20
Figure imgf000289_0001
To a solution of 4-((S)-2-((1S)-2-aminopropanamido)propanamido)benzyl (2-(2-chloro-4- (3 -((2-(2,6-dioxopiperi din-3 -yl)- 1 -oxoi soindolin-5 - yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int 10r, (40.0 mg, 34.2 prnol, 1.00 eq) in 7V,2V-dimethylformamide (1.00 mL) was added triethylamine (6.92 mg, 68.4 μmol, 9 51 μL, 2.00 eq) and 34-(5-(2,5-dioxo-2,5-dihydro-lJT-pyrrol-l-yl)-2-(3-oxo-3-(2, 3,5,6- tetrafluorophenoxy) propyl)phenoxy)-3,6,9,12,15,18,21,24,27,30-decamethyl- 4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15, 18,21,24,27,30-decaazatetratriacontanoic acid, Int 10o, (53.6 mg, 44.4 μmol, 1.30 eq). The mixture was stirred at 15 °C for 1 h. The residue was purified by Prep-HPLC (column: Phenomenex luna C1 8 150*25mm* 10um;mobile phase: [water(FA)-ACN];gradient:20%-50% B over 10 min), /Vc/?-HPLC (column: Phenomenex luna Cl 8 150*25mm* 10um;mobile phase: [water(FA)-ACN];gradient:20%-50% B over 10 min) and lyophilized to afford 34-(2-(3-(((25)-l-(((2S)-l-((4-((((2-(2-chloro-4-(3-((2- (2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl) (methyl)carbamoyl)oxy)methyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl) amino)-3-oxopropyl)-5 -(2, 5-dioxo-2, 5 -dihydro- I //-pyrrol - I -yl)phenoxy)-
3.6.9.12.15.18.21.24.27.30-decamethyl-4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,
24.27.30-decaazatetratriacontanoic acid, Compound IG-L-20, (19.3 mg, 9.87 μmol, 29% yield, 95% purity) as a white solid 1H NMR (400 MHz, DMSO-d6) δ = 10.96 (s, 1H), 9 92 - 9.71 (m, 1H), 8.81 (s, 1H), 8.45 - 8.27 (m, 1H), 8.22 - 8 02 (m, 1H), 7.72 - 7.58 (m, 4H), 7.51 (s, 1H),
7.43 (d, J = 7.6 Hz, 1H), 7.29 (br d, ./ ~ 8.4 Hz, 2H), 7.22 - 7. 11 (m, 5H), 6.90 (br d. ./ ~ 9.2 Hz, 1H), 6.79 - 6.73 (m, 1H), 5. 10 (dd, J= 4.8, 13.4 Hz, 1H), 4.98 (s, 2H), 4.47 - 4. 18 (m, 15H), 4.09 - 3 88 (m, 12H), 3.55 - 3.45 (m, 4H), 3.36 - 3.33 (m, 2H), 3.00 - 2.70 (m, 42H), 2.62 - 2.57 (m, 1H), 2.40 - 2.36 (m, 1H), 2.01 - 1.89 (m, 3H), 1.30 (br d, J= 7.2 Hz, 3H), 1.19 (br d, ./ ~ 7,2 Hz, 3H). MS (ESI) m/z 930.8 [1/2M+H]+
Table 13 The following compounds were prepared in a manner similar to that described for Compound IG-L-20 using the appropriate compound as starting material.
Figure imgf000291_0001
Figure imgf000292_0001
Figure imgf000293_0001
EXAMPLE L-15: Synthesis of (2,S')-A'-(4-(i (5-((3-( 3-chloro-4-mctliylphcnyl )urcido)mcthyl)-2- (2,6-dioxopiperidin-3 -yl )- 1 -oxoisoindolin-4-y l)oxy )methy l)phenyl)-2-((S)-2-(3 -(2, 5 -dioxo-2, 5 - dihydro-17/-pyrrol-l-yl)propanamido)propanamido)propenamide (IG-L-15)
Figure imgf000294_0001
Int 10s
To a solution of 3-(2,5-dioxo-2,5-dihydro-177-pyrrol-l-yl)-A-((*SY)-l-(((5’)-l-((4- (hydroxymethyl)phenyl) amino)- 1 -oxopropan -2 -yl)amino)-l-oxopropan-2-yl)propanamide (3.00 g, 7.20 mmol, 1.00 eq) in dichloromethane (40.0 mL) was added thionyl chloride (1.71 g, 14.4 mmol, 1.05 mL, 2.00 eq). The mixture was stirred at 25 °C for 12 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by triturated with ethyl acetate (30.0 mL) and filtered to afford (5)-A-(4-(chloromethyl)phenyl)-2-((S)-2-(3-(2,5-dioxo-2,5-dihydro-177- pyrrol-l-yl) propanamido)propanamido) propenamide, Int 10s, (2.00 g, 3.22 mmol, 22% yield, 70% purity) as a yellow solid. ‘HNMR (400 MHz, DMSO-fik) 7 = 9.93 (s, 1H), 8.22 (d, J= 7.0 Hz, 1H), 8. 13 (d, J= 7.2 Hz, 1H), 7.63 (d, J = 8.4 Hz, 2H), 7.36 (d, J= 8.8 Hz, 2H), 7.00 (s, 2H), 4.74 - 4.68
(m, 3H), 4.37 (br t, J= 7.2 Hz, 1H), 3.61 (t, 7= 7.2 Hz, 2H), 2.41 (t, 7'= 7.2 Hz, 2H), 1.31 (d, J = 7.2 Hz, 3H), 1.18 (d, 7 = 7.2 Hz, 3H).
Step B. Preparation of Compound IG-L-15
Figure imgf000295_0001
To a solution of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l- oxoisoindolin-5-yl)methyl)urea, Compound IG-15, (20.0 mg, 43.8 μmol, 1.00 eq) and (S)-A-(4- (chk)romethy I (phenyl )-2-((S)-2-(3 -(2, 5-di oxo-2, 5-dihydro- l //-pyrrol- 1 - yl)propanamido)propanamido)propanamide, Int 10s, (79.3 mg, 109 nmol, 2.50 eq) inN^- dimethylformamide (1.00 mL) was added potassium carbonate (12.1 mg, 87.5 μmol, 2.00 eq). The mixture was stirred at 60 °C for 4 h under nitrogen atmosphere. The mixture was adjusted pH=4 with formic acid and filtered, the filtrate was purified by Prep-HPLC (column: Phenomenex Luna C18 150*25mm*10um;mobile phase: [water(TFA)-ACN]; gradient:35%-65% B over 10 min), Prep-HPLC (column: Waters Xbridge 150*25mm* 5um;mobile phase: [water( NH4HCO3)- ACN];gradient:26%-56% B over 9 min), /'rep-HPLC (column: Phenomenex Luna C 18 150*25mm*10um;mobile phase: [water(TFA)-ACN];gradient:35%-65% B over 10 min) and lyophilized to afford (26’)-2V-(4-(((5-((3-(3-chloro-4-methylphenyl)ureido)methyl)-2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-4-yl)oxy)methyl)phenyl)-2-((6’)-2-(3-(2,5-dioxo-2,5-dihydro- 177-pyrrol-l-yl)propanamido)propanamido)propenamide, Compound IG-L-15, (3.58 mg, 4.14 μmol, 2% yield, 99% purity) as a white solid. ‘HNMR (400 MHz, DMSO-d6 ) δ = 10.99 (s, 1H), 9.88 (s, 1H), 8.73 (s, 1H), 8.20 (d, J= 6.8 Hz, 1H), 8. 11 (d, J= 6.8 Hz, 1H), 7.68 - 7.62 (m, 3H), 7.47 - 7.40 (m, 4H), 7.18 - 7.15 (m, 1H), 7.12 - 7.09 (m, 1H), 6.99 (s, 2H), 6.62 (br t, J= 5.6 Hz, 1H), 5.20 - 5.06 (m, 3H), 4.64 - 4.55 (m, 1H), 4.54 - 4.46 (m, 1H), 4.42 - 4.35 (m, 3H), 4.23 (t, J = 7.2 Hz, 1H), 3.61 (s, 2H), 2.92 (br s, 1H), 2.65 - 2.57 (m, 1H), 2.40 (br t, J= 7.2 Hz, 2H), 2.33 (s, 1H), 2.22 (s, 3H), 1.98 (br s, 1H), 1.31 (d, J = 7.2 Hz, 3H), 1.18 (d, J= 7.2 Hz, 3H). The following compounds were prepared in a manner similar to that described for
Isoindolinone-glutarimide linker compound IG-L-15 of Table 2 using the appropriate compound as starting material.
Table 14
Figure imgf000297_0001
Figure imgf000298_0001
Figure imgf000299_0001
Figure imgf000300_0001
EXAMPLE L-26: Synthesis of (2<S)-N-(4-(((5-((3-(3-chloro-4-methylphenyl)ureido)methyl)-2- (2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-4-yl)oxy)methyl)phenyl)-2-((S)-2-(3-(2,5-dioxo-2,5- dihydro-lZ/-pyrrol-l-yl)propanamido)propanamido)propenamide (IG-L-26)
Figure imgf000301_0001
To a solution of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl)urea, Compound IG-1, (200 mg, 454 μmol, 1.00 eq) in dimethyl formamide (4.00 ml) was added cesium carbonate (222 mg, 681 μmol, 1.50 eq) and chloromethyl (4-nitrophenyl) carbonate (315 mg, 1.36 mmol, 3.00 eq). The mixture was stirred at 25 °C for 2 h. The mixture was filtered to give filtrate. The filtrate was purified by reversed-phase HPLC (0. 1% FA condition). The desired fraction was collected and lyophilized to give was residue. The residue was purified by column chromatography (SiO2, Petroleum ether/Ethyl acetate- 1/1 to 0/1) The desired fraction was collected and concentrated to give (3-(5-((3-(3-chl oro-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l-yl)methyl (4-nitrophenyl) carbonate, Int Ila, (250 mg, 334 μmol, 74 % yield, 85% purity) as a white solid. 1H NMR (400 MHz, DMSO-c/fi) 6 = 8.75 (s, 1H), 8.34 - 8.30 (m, 1H), 7.72 (d, J= 8 0 Hz, 1H), 7.66 (d, J= 2.0 Hz, 1H), 7.59 - 7.53 (m, 2H), 7.45 (br d, J= 8.0 Hz, 1H), 7.24 - 7.02 (m, 2H), 6.86 - 6.71 (m, 1H), 5.90 - 5.80 (m, 1H), 5.52 - 5.17 (m, 2H), 4.56 - 4.19 (m, 4H), 3.21 - 3.05 (m, 1H), 2.94 - 2.79 (m, 1H),
2.48 - 2.34 (m, 1H), 2.23 (s, 3H), 2.15 - 2.03 (m, 1H). LC-MS (ESI) m/z 636.1 [M+H] Step B. Preparation of Int lib
Figure imgf000302_0001
To a solution of (3-(5-((3-(3-chloro-4-methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)- 2,6-dioxopiperidin-l-yl)methyl (4-nitrophenyl) carbonate, Int Ila, (190 mg, 299 μmol, 1.00 eq) in dimethyl formamide (2.00 mL) was added tri ethylamine (90.7 mg, 896 prnol, 125 μL, 3.00 eq) and 4-((6')-2-((<5)-2-((tert-butoxycarbonyl)amino)propanamido)propanamido)benzyl methyl(2- (methylamino)ethyl)carbamate (143 mg, 299 μmol, 1.00 eq) The mixture was stirred at 25 °C for 1 h. The mixture was filtered to give filtrate. The filtrate was purified by reversed-phase HPLC (0 1 % formic acid condition). The desired fraction was collected and lyophilized to give 4-((S)-2-
((5)-2-((tert-butoxycarbonyl)amino)propanamido)propanamido) benzyl((3-(5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l-yl) methyl) ethane- 1,2- diylbis(methylcarbamate), Int 11b, (130 mg, 113μmol, 38% yield, 85% purity) as a white solid. 1H NMR (400 MHz, DMSO-d6) J = 9.98 (br s, 1H), 8.84 (s, 1H), 8.25 - 8.17 (m, 1H), 8.01 (br d, J = 1.2 Hz, 1H), 7.70 (d, J= 8.0 Hz, 1H), 7.57 (br d, J= 8.8 Hz, 2H), 7.44 (br d, J= 8.0 Hz, 1H), 7.31 - 7.24 (tn, 3H), 7.19 - 7.15 (m, 1H), 7.08 - 6.96 (m, 1H), 6 93 - 6.84 (m, 1H), 5.89 - 5.48 (m, 2H), 5.36 - 5. 14 (m, 1H), 5.03 - 4.87 (m, 2H), 4.52 - 4.24 (m, 4H), 4.04 - 3.95 (m, 1H), 3.52 - 3.34 (m, 3H), 3.31 - 3.24 (m, 2H), 3.14 - 3.00 (m, 1H), 2.92 - 2.66 (m, 8H), 2.45 - 2.34 (m, 1H), 2.22 (s, 2H), 2.07 - 1.99 (m, 2H), 1.38 - 1.34 (m, 9H), 1.29 (br dd, J= 2.4, 6.8 Hz, 3H), 1.17 (br d, 6.8 Hz, 3H). LC-MS (ESI) m/z 976.1 [M+H]+
Step C. Preparation of Int 11c
Figure imgf000303_0001
To a solution of 4-((S)-2-((S)-2-((tert- butoxycarbonyl)amino)propanamido)propanamido)benzyl ((3-(5-((3-(3-chloro-4- methylphenyl)ureido)methyl)- 1 -oxoisoindolin-2-yl)-2, 6-dioxopiperidin-l -yl)methyl) ethane- 1,2- diylbis(methyl carbamate), Int lib, (80.0 mg, 82.0 Limol. 1.00 eq) in dichloromethane (1.00 mL) was added trifluoroacetic acid (9.34 mg, 82.0 μmol, 6.09 μL, 1.00 eq). The mixture was stirred at
25 °C for 0.5 h. The mixture was concentrated to give a residue. The residue was purified by prep- HPLC (column: Phenomenex luna C18 150*25mm* lOum; mobile phase: [water (FA)-ACN]; gradient: 22%-52% B over 9 min). The desired fraction was collected and lyophilized to give 4- ((5’)-2-((S)-2-aminopropanamido)propanamido)benzyl ((3-(5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l-yl)methyl) ethane-1,2- diylbis(methylcarbamate), Int 11c, (30.0 mg, 32.5 umol, 40% yield, 95% purity) as a white solid. LC-MS (ESI) m/z 876.7 [M+H]+
Step D. Preparation of Compound IG-L-26
Figure imgf000305_0001
Compound IG-L-26
To a solution of 4-((S)-2-(((S)-2-aminopropanamido)propanamido)benzyl ((3-(5-((3-(3- chloro-4-methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l-yl)m ethyl) ethane-l,2-diylbis (methylcarbamate), Int 11c, (20.0 mg, 22,8 μmol, 1.00 eq) in dimethyl formamide (1.00 mL) was added triethylamine (6 93 mg, 68.5 μmol, 9.53 μL. 3.00 eq) and 34-(5- (2,5-dioxo-2,5-dihydro-17/-pyrrol-l-yl)-2-(3-oxo-3-(2,3,5,6-tetrafluorophenoxy)propyl)phenoxy)- 1.6.9.12.15.18.21.24.27.30-decamethyl-4,7,10,13,16,19,22,25,28,31-decaoxo-
3.6.9.12.15.18.21.24.27.30-decaazatetratriacontanoic acid, Int 10o, (33.0 mg, 27.4 μmol, 1.20 eq). The mixture was stirred at 25 °C for 1 h. The mixture was filtered to give filtrate. The filtrate was purified by p/vp-I IPLC (column: Phenomenex luna C18 150*25mm* lOum; mobile phase: [water (FA)-ACN]; gradient: 35%-65% B over 9 min). The desired fraction was collected and lyophilized to give (2S)-A-(4-(((5-((3-(3-chloro-4-methylphenyl)ureido)methyl)-2-(2,6-dioxopiperi din-3 -yl)-l- oxoisoindolin-4-yl)oxy)methyl)phenyl)-2-((S)-2-(3-(2,5-dioxo-2,5-dihydro-17/-pyrrol-l- yl)propanamido)propanamido)propenamide , Compound IG-L-26, (21.78 mg, 11.3 μmol, 49% yield, 99% purity) as a white solid. ]H NMR (400 MHz, DMSO-d6) δ = 9.90 - 9.69 (m, 1H), 8.70 (brt, J= 6.0 Hz, 1H), 8.39 - 7 92 (m, 2H), 7.65 - 7.50 (m, 4H), 7.46 - 7.34 (m, 2H), 7.21 (br d, J =
6.8 Hz, 2H), 7.14 - 7.04 (m, 5H), 6.93 - 6.64 (m, 3H), 5.63 - 5.41 (m, 2H), 5.27 - 5.10 (m, 1H), 5.00 - 4.78 (m, 2H), 4.39 - 4.11 (m, 17H), 4.06 - 3.82 (m, 14H), 2.91 - 2.62 (m, 44H), 2.37 - 2.33 (m, 2H), 2.16 (s, 3H), 2.00 - 1.85 (m, 3H), 1.23 (br d, J = 6.4 Hz, 3H), 1. 12 (br d, J= 6.8 Hz, 3H). LC- MS (ESI) m/z 1916.6[M+H]+ The compound in Table 15 was prepared in a manner similar to that described for Compound IG- L-26 using the appropriate compound as starting material.
Table 15
Figure imgf000307_0001
EXAMPLE L-16: Synthesis of l-(3-chloro-4-(2-(2-(2,5-dioxo-2,5-dihydro-177-pyrrol-l- yl)ethoxy)ethyl)phenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl) urea (IG-
L-16)
Figure imgf000308_0001
Step A. Preparation of Compound IG-L-16
Figure imgf000308_0002
Compound IG-L-16
To a solution of phenyl (3-chloro-4-(2-(2-(2,5-dioxo-2,5-dihydro-l//-pyrrol-l- yl)ethoxy)ethyl)phenyl) carbamate (10 0 mg, 24.1 μmol, LOO eq) and 3-(5-(aminomethyl)-l- oxoisoindolin-2-yl)piperidine-2, 6-dione, Int AA, (7.91 mg, 28.9 μmol, 1.20 eq) in dimethyl formamide (1.00 mL) was added N, A'-di isopropyl ethylamine (6.23 mg, 48.2 μmol, 8.40 μL, 2.00 eq), the mixture was stirred at 25 °C for 2 h. The reaction mixture was purified by Prep-t fPLC (column: Phenom enex Luna C18 150*25mm* 10um;mobile phase: [water(formic acid)- acetonitrile];gradient:23%-53% B over 10 min) and lyophilized to afford l-(3-chloro-4-(2-(2- (2,5-dioxo-2,5-dihydro-117-pyrrol-l-yl)ethoxy)ethyl)phenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl) urea IG-L-16 (2.38 mg, 3.81 μmol, 15% yield) as a white solid. rH NMR (400 MHz, DVISO-tA) r) = 11.13 - 10.78 (m, 1H), 8.82 (s, 1H), 7.69 (d, J= 8.0 Hz, 1H), 7.64 (s, 1H), 7.51 (s, 1H), 7.44 (d, J= 9.0 Hz, 1H), 7.12 (d, J= 1.0 Hz, 2H), 6.99 (s, 2H), 6.89 - 6.83 (m, 1H), 5.15 - 5.05 (m, 1H), 4.48 - 4.39 (m, 3H), 4.34 - 4.28 (m, 1H), 3.55 - 3.49 (m, 6H), 2.93 - 2 87 (m, 1H), 2.76 (br t, ~ 7.0 Hz. 2H). 2.61 (br d, J = 1.8 Hz, 1H), 2.47 - 2.35 (m, 1H), 2.05 - 1 95 (m, 1H). MS (ESI) m/z 594.3 [M+H]+
EXAMPLE L-18: Synthesis of 4-((377?,40S,43A)-37-(2-(2-(2-(3-(2,5-dioxo-2,5-dihydro-U7- pyrrol-l-yl)propanamido)ethoxy) ethoxy)acetamido)-40,43-dimethyl-38,41-dioxo- 2 ,8,l l,14,17,20,23,26,29,32-undecaoxa-35-thia-39,42-diazatetratetracontan-44-amido)benzyl
(2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl) methyl)ureido)phenethoxy)ethyl)(methyl) carbamate (IG-L-18)
Figure imgf000309_0001
Int 12a
To a solution of2,5,8, l l,14,17,20,23,26,29,32-undecaoxatetratriacontan-34-ol (900 mg, 1.74 mmol, 1.00 eq) and triethylamine (353 mg, 3.48 mmol, 485 μL, 2.00 eq) in dichloromethane (10.0 mL) was added para-toluenesulfonyl chloride (664 mg, 3.48 mmol, 2.00 eq). Then the mixture was stirred at 25 °C for 12 h. The reaction mixture was concentrated to give a residue. The residue was purified by column chromatography (SiO2, Petroleum ether/Ethyl acetate=l/l to 0/1) to afford 2,5,8,l l,14,17,20,23,26-nonaoxaoctacosan-28-yl 4- methylbenzenesulfonate, Int 12a, (1.10 g, 1.64 mmol, 94% yield) as colorless oil. 1H NMR (400 MHz, CDCh) δ = 7.85 - 7.76 (m, 2H), 7.35 (d, J= 8.0 Hz, 2H), 4.20 - 4.14 (m, 2H), 3.69 - 3.61 (m, 33H), 3.58 (s, 3H), 3.57 - 3.53 (m, 2H), 3.38 (s, 3H), 3.15 - 3.10 (m, 4H), 2.45 (s, 3H). Step B. Preparation of Int 12b
Figure imgf000309_0002
Int 12a Int 12b
To a solution of 2,5,8, l l,14,17,20,23,26-nonaoxaoctacosan-28-yl 4- methylbenzenesulfonate, Int 12a, (600 mg, 894 μmol, 1.00 eq) in tetrahydrofuran (5.00 mL) was added sodium hydride (143 mg, 3 58 mmol, 60% purity, 4 00 eq) and (tert- butoxycarbonyl)-L. -cysteine (297 mg, 1.34 mmol, 1.50 eq). The mixture was stirred at 0 °C for 3 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC (C18, 80 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1%formic acid) and lyophilized to afford (J?)-37-((terZ-butoxycarbonyl)amino)- 2,5,8,l l,14,17,20,23,26,29,32-undecaoxa-35-thiaoctatriacontan-38-oic acid, Int 12b, (500 mg, 695 μmol, 77% yield) as colorless oil. 1H NMR (400 MHz, CDCh) 3 = 5.60 (br d, J= 7.2 Hz, 1H), 4.53 (br d, J= 6.4 Hz, 1H), 3.69 - 3.64 (tn, 40H), 3.57 - 3.54 (m, 2H), 3.39 (s, 3H), 3.10 (br d, J= 4.4 Hz, 2H), 2.84 - 2.68 (m, 2H), 1.45 (s, 9H).
Step C. Preparation of Int 12c
Figure imgf000310_0001
Int 12c
To a solution of (Z?)-37-((fert-butoxycarbonyl)amino)-2,5,8,l 1, 14,17,20,23,26,29,32- undecaoxa-35-thiaoctatriacontan-38-oic acid, Int 12b, (500 mg, 695 μmol, 1.00 eq) and (5)-2- amino-N-((S')- 1 -((4-(hy droxymethyl)phenyl)amino)- 1 -oxopropan-2-yl)propanamide (184 mg, 695 μmol, 1.00 eq) in dimethyl formamide (5.00 mL) was added /V,yV-di isopropyl ethyl amine (179 54 mg, 1.39 mmol, 242 μL, 2.00 eq) and O-(7-Azabenzotriazol-l-yl)-/V,A,JV’,Ar’- tetramethyluronium Hexafluorophosphate (343 mg, 902 μmol, 1.30 eq). Then the mixture was stirred at 25 °C for 2 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC (Cl 8, 80 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1%formic acid) and lyophilized to afford /e/V-butyl ((377?,405,435)-44-((4- (hydroxymethyl)phenyl) amino)-40,43-dimethyl-38,41,44-trioxo-2,5,8,l 1,14,17,20,23,26,29,32- undecaoxa-35-thia-39,42-diazatetratetracontan-37-yl)carbamate, Int 12c, (670 mg, 693 μmol, 99% yield) as colorless oil. 1H NMR (400 MHz, CDCh) 3 = 8.62 (s, 1H), 7.76 (d, J= 8.4 Hz, 2H), 7 61 - 7 46 (m, 2H), 7 31 (d, J= 8 4 Hz, 2H), 5 71 (br d, 6 8 Hz, 1H), 4.65 - 4.61 (m, 3H), 4.45 (q, J= 6.8 Hz, 1H), 4.31 (br dd, J= 4.8, 7.2 Hz, 1H), 3.67 - 3.60 (m, 40H), 3.56 - 3.54 (m, 2H), 3.38 (s, 3H), 2 92 - 2.87 (m, 2H), 2.84 (br d, J= 4.8 Hz, 1H), 2.86 - 2.74 (m, 1H), 1.50 (dd, J= 2.4, 7.3 Hz, 6H), 1.45 (s, 9H)
Step D. Preparation of Int 12d
Figure imgf000311_0001
To a solution of tert-butyl ((37J?,405,435)-44-((4-(hydroxymethyl)phenyl)amino)-40,43- dimethyl-38,41,44-trioxo-2,5,8,l l,14,17,20,23,26,29,32-undecaoxa-35-thia-39,42- diazatetratetracontan-37-yl)carbamate, Int 12c, (670 mg, 693 μmol, 1 .00 eq) in dimethyl formamide (3.00 mL) was added /V^-diisopropylethylamine (134 mg, 1.04 mmol, 181 yL, 1.50 eq) and bis(4-nitrophenyl) carbonate (422 mg, 1.39 mmol, 2.00 eq). The mixture was stirred at 25 °C for 2 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC (Cl 8, 80 g; condition: water/ acetonitrile = 1/0 - 0/1, 0 l%formic acid) and lyophilized to afford tert-butyl ((37R,40S,43S)-40,43-dimethyl-44- ((4-((((4-nitrophenoxy)carbonyl) oxy)methyl)phenyl)amino)-38,41,44- trioxo- 2,5,8,l l,14,17,20,23,26,29,32-undecaoxa-35-thia-39,42-diazatetratetracontan-37-yl)carbamate, Int 12d, (700 mg, 618 μmol, 89% yield) as colorless oil. 1H NMR (400 MHz, CDCh) δ = 8.69 (s, 1H), 8.27 (d, J= 9.2 Hz, 2H), 7.83 (br d, J= 8.4 Hz, 2H), 7.65 - 7.48 (m, 2H), 7.38 (dd, J= 2.8, 8.9 Hz, 4H), 5.71 (br d, J= 6.0 Hz, 1H), 5.25 (s, 2H), 4.62 (quin, J= 7.2 Hz, 1H), 4.45 (q, J = 6.8 Hz, 1H), 4.35 - 4.27 (m, 1H), 3.68 - 3.60 (m, 40H), 3.57 - 3.54 (m, 2H), 3.38 (s, 3H), 2.91
(br d, J= 6.8 Hz, 2H), 2.88 - 2.74 (m, 2H), 1.51 (dd, J= 1.6, 7.3 Hz, 6H), 1.46 (s, 9H).
Step E. Preparation of Int 12e
Figure imgf000312_0001
Int 12e
To a solution of tert-butyl ((37R,40S,43S)-40,43-dimethyl-44-((4-((((4- nitrophenoxy)carbonyl)oxy)methyl) phenyl)amino)-38,41 ,44-trioxo- 2,5,8,11,14,17,20,23,26,29,32- undecaoxa-35-thia-39,42-diazatetratetracontan-37-yl)carbamate, Int 12d, (470 mg, 415 μmol, 1.00 eq) in dimethyl formamide (3.00 mL) was added triethylamine (84.0 mg, 830 μmol, 116 μL, 2.00 eq) and l-(3-chloro-4-(2-(2- (methylamino)ethoxy) ethyl)phenyl)-3 -((2-(2, 6-dioxopiperi din-3 -yl)- 1 -oxoisoindolin-5- yl)methyl)urea, Compound IG-4. The mixture was stirred at 25 °C for 1 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed- phase HPLC (C1 8, 40 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1%formic acid) and lyophilized to afford 4-((377?,40S,43S)-37-((tert-butoxycarbonyl)amino)-40,43-dimethyl-38,41- dioxo-2,5,8,1 l,14,17,20,23,26,29,32-undecaoxa-35-thia-39,42-diazatetratetracontan-44- amido)benzyl (2-(2-chloro-4-(3-((2-(2, 6-dioxopiperi din-3 -yl)- 1 -oxoisoindolin-5- yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int 12e, (600 mg, 390 μmol, 94% yield, 99% purity) as colorless oil. MS (ESI) m/z 1521.5 [M+H]+
Step F. Preparation of Int 12
Figure imgf000313_0001
Int 12f
To a solution of 4-((377?,401S',43)S)-37-((tert-butoxycarbonyl)amino)-40,43-dimethyl- 38,41-dioxo-2,5,8,l l,14,17,20,23,26,29,32-undecaoxa-35-thia-39,42-diazatetratetracontan-44- amido)benzyl (2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int 12e, (300 mg, 197 μmol, 1 00 eq) in dichloromethane (3.00 mL) was added trifluoroacetic acid (0.600 mL). The mixture was stirred at 25 °C for 1 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC (Cl 8, 40 g; condition: water/ acetonitrile = 1/0 - 0/1, 0 l%formic acid) and lyophilized to afford 4-((377?,405,435)-37-amino-40,43-dimethyl- 38,41-dioxo-2,5,8,l l,14,17,20,23,26,29,32-undecaoxa-35-thia-39,42-diazatetratetracontan-44- amido)benzyl (2-(2-chloro-4-(3-((E)-3-(l-(2,6-dioxopiperidin-3-yl)-4-methyl-5-oxo-2,5- dihydro- I H-pyrrol-3-yl) allyl)ureido) phenethoxy)ethyl)(methyl)carbamate, Int 12f, (220 mg, 155 μmol, 78 % yield) as yellow oil. JHNMR (400 MHz, DMSO-cZ6) δ = 10.98 (br d, J= 4.3 Hz, 1H), 9 94 (s, 1H), 8 78 (s, 1H), 8 33 - 8 22 (m, 1H), 8 17 (d, J= 7.2 Hz, 1H), 7 71 - 7 65 (m, 2H), 7.59 (br d, J= 8.0 Hz, 2H), 7.51 (s, 1H), 7.44 (d, J= 7.6 Hz, 1H), 7.29 (br d, J= 7.2 Hz,
2H), 7.21 - 7.11 (m, 2H), 6.81 (t, J= 6.0 Hz, 1H), 5.10 (dd, J= 5.2, 13.2 Hz, 1H), 4 98 (s, 2H), 4.47 - 4 28 (m, 7H), 3.50 (s, 48H), 3.43 - 3.42 (m, 2H), 3.37 - 3.34 (m, 2H), 3.23 (s, 3H), 2.96 - 2.87 (tn, 1H), 2.83 (br d, J= 8.4 Hz, 5H), 2.69 - 2.67 (m, 2H), 2.62 - 2.56 (m, 1H), 2.42 - 2.34 (m, 1H), 2.03 - 1.95 (m, 1H), 1.30 (d, J = 7.2 Hz, 3H), 1.24 (d, J= 7.0 Hz, 3H).
Step G. Preparation of Compound IG-L-18
Figure imgf000314_0001
To a solution of 4-((377?,40S,435)-37-amino-40,43-dimethyl-38,41-dioxo-
2,5,8,l l,14,17,20,23,26,29,32-undecaoxa-35-thia-39,42-diazatetratetracontan-44-amido)benzyl (2-(2-chloro-4-(3-((E)-3-(l-(2,6-dioxopiperidin-3-yl)-4-methyl-5-oxo-2,5-dihydro-177-pyrrol-3- yl)allyl)ureido)phenethoxy)ethyl)(methyl) carbamate, Int 12f, (20.0 mg, 14.1 μmol, 1.00 eq) in dimethyl formamide (2.00 mL) was added f9-('7-Azabenzotriazol- l-yl )-/V,A'',Ar’jV’- tetramethyluronium Hexafluorophosphate (5.89 mg, 15.5 μmol, 1 10 eq), 2-(2-(2-(3-(2,5-dioxo- 2,5-dihydro-l//-pyrrol-l-yl)propanamido)ethoxy)ethoxy)acetic acid (5.31 mg, 16.9 μmol, 1.20 eq) and AW-diisopropylethylamine (3.64 mg, 28 2 μmol, 4.90 μL, 2.00 eq). The mixture was stirred at 25 °C for 2 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by /vep-HPLC (column: Waters Xbridge 150*25mm* 5um;mobile phase: [Water- ACN];gradient:23%-53% B over 10 min). The desired fraction was collected and lyophilized to afford 4-((377?,40S,43S)-37-(2-(2-(2-(3-(2,5-dioxo-2,5-dihydro-17/-pyrrol-l- to o
Figure imgf000315_0001
To a solution of (S)-2-amino-A-((5)-l-((4-(hydroxymethyl)phenyl)amino)-l -oxopropan- 2-yl)propanamide (1.27 g, 4.79 mmol, 1.00 eq) in dimethyl formamide (8.00 mL) was added N6- ((benzyloxy)carbonyl)-A2-(ter/-butoxycarbonyl)-Z-lysine (2.00 g, 5.27 mmol, 1.10 eq), O-(J- Azabenzotriazol-l-yl)-A,A,A’,lV’-tetramethyluronium Hexafluorophosphate (2.37 g, 6.22 mmol, 1.30 eq) and A,A-diisopropylethylamine (1.24 g, 9.57 mmol, 1.67 mL, 2.00 eq). The mixture was stirred at 25 °C for 2 h. The reaction mixture was filtered to give the filtrate The filtrate was purified by reversed-phase HPLC ( 0. 1% FA ) to give benzyl tert-butyl ((>S)-6-(((5)- 1 -(((£)- l-((4-(hydroxymethyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl)amino)-6- oxohexane-l,5-diyl)dicarbamate, Int 13a, (1 90 g, 3 03 mmol, 63% yield) as a white solid 1H NMR (400 MHz, DMSO-d6) 3 = 9.85 (s, 1H), 8.08 (br d, J= 7.2 Hz, 1H), 7.89 (br d, J= 7.2 Hz, 1H), 7.54 (br d, 8.4 Hz, 2H), 7.38 - 7.30 (m, 5H), 7.23 (br d, J= 8.4 Hz, 3H), 6.91 (br d, J= 7.6 Hz, 1H), 5.75 (s, 2H), 5.09 (t, J= 5.6 Hz, 1H), 4.99 (s, 2H), 4.42 (d, J= 5.6 Hz, 2H), 4.37 (br t, J= 7.2 Hz, 1H), 4.28 (br t, J= 7.2 Hz, 1H), 3.91 - 3.79 (m, 1H), 2.96 (br d, J= 5.6 Hz, 2H), 1.67 - 1.54 (m, 1H), 1.49 - 1.43 (m, 1H), 1.37 (s, 11H), 1.29 (br d, J= 7.2 Hz, 3H), 1.21 (d, J= 7.2 Hz, 3H). MS (ESI) m/z 510.3 [M+H-100-18]+
Figure imgf000316_0001
To a solution of benzyl tert-butyl ((5)-6-(((5)- 1 -(((*S)-l-((4- (hydroxymethyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl)amino)-6- oxohexane-l,5-diyl)dicarbamate, Int 13a, (1.80 g, 2.87 mmol, 1.00 eq) in dichloromethane (20.0 mL) was added trifluoroacetic acid (2.00 mL). The mixture was stirred at 25 °C for 2 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC (0.1% FA) to give benzyl ((5)-5-amino-6-(((5)-l-(((5)-l- ((4-(hydroxymethyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l- oxopropan-2-yl)amino)-6- oxohexyl) carbamate, Int 13b, (1.10 g, 682 μmol, 66% yield, 90% purity) as a yellow solid. 1H NMR (400 MHz, DMSO-^) 3 = 9.96 (s, 1H), 8 46 (br d, J= 7.2 Hz, 1H), 8 22 (d, .7= 7 2 Hz, 1H), 7.54 (d, J= 8.4 Hz, 2H), 7.39 - 7.29 (m, 5H), 7.27 - 7. 19 (m, 3H), 5.00 (s, 3H), 4.47 - 4.35 (m, 4H), 3.58 (br t, J= 6 4 Hz, 2H), 2.97 (q, J= 6.4 Hz, 2H), 1.71 - 1.52 (m, 2H), 1.45 - 1.19
(m, 10H). MS (ESI) m/z 528.3 [M+H]+
Step C. Preparation of Int 13c
Figure imgf000317_0001
To a solution of benzyl ((<S)-5-amino-6-(((»S)-l-(((5)-l-((4- (hydroxymethyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl)amino)-6- oxohexyl)carbamate, Int 13b, (1 10 g, 2.08 mmol, 1.00 eq) in dimethyl formamide (3 00 mL) was added l-(9H-fluoren-9-yl)-3-oxo-2,7,10-trioxa-4-azadodecan-12-oic acid (884 mg, 2.29 mmol, 1.10 eq), <9-(7-Azabenzotriazol-l-yl)-Ar,A,A’,A’-tetramethyluronium Hexafluorophosphate (1.19 g, 3.13 mmol, 1.50 eq) and A,A-diisopropylethylamine (808 mg, 6.25 mmol, 1.09 mL, 3.00 eq). The mixture was stirred at 25 °C for 2 h. The reaction mixture was filtered and the filtrate was purified by reversed-phase HPLC (0.1% FA) to give (9/7- fluoren-9-yl)methyl ((5)-9-(((5)- 1 -l(GS')- 1 -((4-(hydroxymethyl)phenyl)amino)-l -oxopropan-2- yl)amino)- 1 -oxopropan-2-yl) carbamoyl)-3 , 11 -di oxo- 1 -phenyl-2, 13, 16-trioxa-4, 10- diazaoctadecan-18-yl)carbamate, Int 13c, (1.05 g, 1.06 mmol, 51% yield, 90% purity) as a white solid. LH NMR (400 MHz, DMSO-J6) δ = 9.88 (s, 1H), 8.21 (br d, J= 7.2 Hz, 1H), 8.04 (d, J= 7.2 Hz, 1H), 7.88 (d, J= 7.6 Hz, 2H), 7.68 (d, J= 7.6 Hz, 2H), 7 62 (br d, J= 7.6 Hz, 1H), 7.54 (d, J= 8.4 Hz, 2H), 7.43 - 7.38 (m, 2H), 7.36 - 7.29 (m, 8H), 7.25 - 7.19 (m, 3H), 5.10 (t, J= 5.6 Hz, 1H), 4.98 (s, 2H), 4.42 (d, J= 5.6 Hz, 2H), 4.38 - 4.26 (m, 5H), 4.23 - 4.18 (m, 1H), 3.91 (s, 2H), 3.60 - 3.52 (m, 4H), 3.44 - 3.40 (m, 2H), 3.17 - 3.12 (m, 2H), 2.95 (br d, J= 6.0 Hz, 2H), 1.70 - 1 62 (m, 1H), 1.58 - 1.50 (m, 1H), 1.37 (br d, J= 7.2 Hz, 2H), 1.30 - 1.21 (m, 8H). MS (ESI) m/z 877.3 [M+H-18]+
Step D. Preparation of Int 13d
Figure imgf000318_0001
Int 13d
Int 13c
To a solution of (9//-fluoren-9-y I (methyl ((S)-9-(((1S)-l-(((S)-l-((4- (hydroxymethyl)phenyl)amino)- 1 -oxopropan-2-yl)amino)-l -oxopropan-2-yl)carbamoyl)-3 , 11- dioxo-1- phenyl-2,13,16-trioxa-4,10-diazaoctadecan-18-yl)carbamate, Int 13c, (300 mg, 335 umol, 1 .00 eq) in dimethyl formamide (5.00 mL) was added A-diisopropylethylamine (85.6 mg, 670 nmol, 117 μL, 2.00 eq) and palladium on carbon (100 mg, 10% purity) under nitrogen. The suspension was degassed under vacuum and purged with hydrogen several times. The mixture was stirred under hydrogen (15 psi) at 25°C for 2 h. The reaction mixture was filtered and the filtrate was concentrated under vacuum to give a residue. The residue was purified by reversed-phase HPLC(H2O/ACN) to give (92/-fluoren-9-yl)methyl((2S,55',85)-8-(4-aminobutyl)- l-((4-(hydroxymethyl)phenyl)amino)-2,5-dimethyl-l,4,7,10-tetraoxo-12,15-dioxa-3,6,9- triazaheptadecan- 17-yl)carbamate, Int 13d, (250 mg, 328 μmol, 98% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-<76) 3 = 9.90 (s, 1H), 8.22 (br d, J= 7.2 Hz, 1H), 8.09 (br d, J= 6.8 Hz, 1H), 7.89 (d, J= 7.4 Hz, 2H), 7.70 - 7.64 (m, 3H), 7.53 (br d, J = 8.4 Hz, 2H), 7.40 (br d, J = 7.2 Hz, 2H), 7.36 - 7.30 (m, 3H), 7.24 (br d, J= 8.4 Hz, 2H), 5.28 - 4.96 (m, 1H), 4.43 (s, 2H),
4.38 - 4 26 (m, 5H), 4.24 - 4.17 (m, 1H), 3.94 - 3.90 (m, 2H), 3.61 - 3.53 (m, 4H), 3.42 (br d, J = 6.0 Hz, 2H), 3.18 - 3.12 (m, 2H), 2.73 (br t, J= 7.2 Hz, 2H), 1.73 - 1.64 (m, 1H), 1.57 - 1.44 (m, 3H), 1.34 - 1.19 (m, 9H), 1.05 (br d, J= 3.6 Hz, 1H). MS (ESI) m/z 761.3 [M+H]+
Step E. Preparation of Int 13e
Figure imgf000319_0001
To a solution of2,5,8, l l,14,17,20,23,26,29-decaoxahentriacontan-31-oic acid (160 mg, 329 gmol, 1.00 eq) in dimethyl formamide (3 ml) was added O-(7-Azabenzotriazol-l-yl)- A', A',.V', .A’-tctramcthyluronium Hexafluorophosphate (187 mg, 493 gmol, 1.50 eq), N,N- diisopropylethylamine (127 mg, 986 gmol, 172 gL, 3.00 eq) and (9//-fluoren-9-yl)m ethyl ((21S',55',86)-8-(4-aminobutyl)-l-((4-(hydroxymethyl)phenyl)amino)-2,5-dimethyl-l,4,7,10- tetraoxo-12,15-dioxa-3,6,9-triazaheptadecan-17-yl)carbamate, Int 13d, (250 mg, 328 gmol, 1.00 eq). The mixture was stirred at 25 °C for 2 h. The reaction mixture was filtered to give filtrate. The filtrate was purified by reversed-phase HPLC ( 0. 1% FA ) to give (9/7-fluoren-9-yl)methyl ((S)-37-(((5)-l -(((>5)- 1 -((4-(hydroxymethyl)phenyl)amino)- 1 -oxopropan-2-yl)amino)- 1 - oxopropan-2-yl)carbamoyl)-31,39-dioxo-2,5,8, l l,14,17,20,23,26,29,41,44-dodecaoxa-32,38- diazahexatetracontan-46-yl)carbamate, Int 13e, (280 mg, 228 gmol, 69% yield) as yellow oil. 1H NMR (400 MHz, DMSO-rfe) b = 9.88 (s, 1H), 8.20 (br d, J = 7.2 Hz, 1H), 8.03 (d, J = 7.2 Hz, 1H), 7.88 (d, J= 7.6 Hz, 2H), 7.68 (br d, J= 7.6 Hz, 2H), 7.65 - 7.58 (m, 2H), 7.54 (d, J= 8.4 Hz, 2H), 7.44 - 7.38 (m, 2H), 7.37 - 7.28 (m, 3H), 7.23 (d, J= 8.4 Hz, 2H), 5.09 (t, J= 5.6 Hz, 1H), 4.44 - 4.26 (m, 7H), 4.24 - 4.16 (m, 1H), 3.91 (s, 2H), 3.87 - 3.77 (m, 2H), 3 58 (br d, J = 4.0 Hz, 2H), 3.57 - 3.52 (m, 6H), 3.52 - 3.46 (m, 27H), 3.45 - 3.39 (m, 4H), 3.23 (s, 3H), 3.15 (q, J= 6.0 Hz, 2H), 3.09 - 3.02 (m, 2H), 1.71 - 1.61 (m, 1H), 1.59 - 1.50 (m, 1H), 1.43 - 1.35 (m, 2H), 1.32 - 1.19 (m, 8H). MS (ESI) m/z 1211.5 [M+H-18]+
Step F. Preparation of Int 13f
Figure imgf000320_0001
To a solution of (9H/-fluoren-9-yl)methyl ((S)-37-(((5)-l-(((5)-l-((4- (hydroxymethyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl)carbamoyl)- 31,39- dioxo-2,5,8,1 l,14,17,20,23,26,29,41,44-dodecaoxa-32,38-diazahexatetracontan-46- yl)carbamate, Int 13e, (180 mg, 146 μmol, 1.00 eq) in dimethyl formamide (2.00 mL) was added bis(4-nitrophenyl) carbonate (53.5 mg, 176 μmol, 1.20 eq) and N,N- diisopropylethylamine (28.4 mg, 220 μmol, 38 3 μL, 1.5 eq). The mixture was stirred at 25 °C for 2 h The reaction mixture was filtered to give filtrate. The filtrate was purified by reversed- phase HPLC ( 0.1% FA ) to (9//-fluoren-9-yl)methyl ((5)-37-(((5)-l-(((5)-l-((4-((((4- nitrophenoxy)carbonyl)oxy)methyl)phenyl) amino)- 1 -oxopropan-2-yl)amino)- 1 -oxopropan-2- yl)carbamoyl)-31 ,39-dioxo-2,5, 8, 11,14,17,20,23 ,26,29,41 , 44-dodecaoxa-32,38- diazahexatetracontan-46-yl)carbamate, Int 13f, (100 mg, 68.1 ymol, 47% yield, 95% purity) as colorless oil. MS (ESI) m/z 1394.6 [M+H]+
Step G. Preparation of Int 13g
Figure imgf000321_0001
To a solution of (9//-fluoren-9-yl)rneLhyl ((S)-37-(((5)-l-(((5)-l-((4-((((4- nitrophenoxy)carbonyl)oxy)methyl) phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2- yl)carbamoyl)-31 ,39-dioxo-2,5, 8, 11,14,17,20,23 ,26, 29,41 ,44-dodecaoxa-32,38- diazahexatetracontan-46-yl)carbamate, Int 13f, (80.0 mg, 57.4 ymol, 1.00 eq) in dimethyl formamide (1.00 mL) was added l-(3-chloro-4-(2-(2-(methylamino)ethoxy)ethyl)phenyl)-3-((2- (2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)urea, Compound IG-4, (30.3 mg, 57.4y.mol, 1.00 eq) and triethylamine (17.4 mg, 172 ymol, 24.0 yL, 3.00 eq). The mixture was stirred at 25 °C for 2 h. The reaction mixture was filtered to give filtrate. The crude product was purified by reversed-phase HPLC (0.1% FA) to give 4-((375,403',43S)-37-(l-(9ZZ-fluoren-9- yl)-3-oxo-2,7,10-trioxa-4-azadodecan-12-amido)-40,43-dimethyl-31,38, 41-trioxo- 2,5,8,l l,14,17,20,23,26,29-decaoxa-32,39,42-triazatetratetracontan-44-amido)benzyl (2-(2-
hl((((diiidil)iidli432263l5 coroooppernoosononxyx-----------,
Sif H P I 13htttepreparaon on.
Figure imgf000322_0001
ifd b prie reuyv ih)t amnoeoexy diid)bl ((hl((((323942442243226ttttttecaoaraaeraeraconanamoencoroxzzy-----------,,, diiidil)iidlil)hl)id)hh)hl)(hl)b3l5tttttooppernoosononmereopeneoemecaramaexyxyyuxyyy------, Int 13h, (30.0 mg, 12.1 μmol, 54% yield, 63% purity) as a yellow solid. MS (ESI) m/z 1560.8 [M+H]+
Step I. Preparation of Compound IG-L-19
Figure imgf000323_0001
Compound IG-L-19 To a solution of 4-((375, 405, 435)-37-(2-(2-(2 -aminoethoxy )ethoxy)acetamido)-40, 43- dimethyl-31,38,41-trioxo-2,5,8,l l,14,17,20,23,26,29-decaoxa-32,39,42-triazatetratetracontan- 44-amido)benzyl (2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl) methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Int 13h, (30.0 mg, 19.2 μmol, 1.00 eq) in dimethyl formamide (0.50 ml) was added (2,5-dioxopyrrolidin-l-yl) 3-(2,5-dioxopyrrol-l- yl)propanoate (5.12 mg, 19.2 μmol, 1.00 eq) and ACV-diisopropyl ethyl amine (4.97 mg, 38.4 μmol, 6 69 μL, 2.00 eq). The mixture was stirred at 25 °C for 2 h The reaction mixture was filtered to give filtrate. The residue was purified by prep-HPLC (column: Waters Xbridge 150*25mm* 5um; mobile phase: [Water-ACN]; gradient: 25%-55% B over 9 min) to give 4- ((375,405,435)-37-(2-(2-(2-(3-(2,5-dioxo-2,5-dihydro-177-pyrrol-l- yl)propanamido)ethoxy)ethoxy)acetamido)-40,43-dimethyl-31,38,41-trioxo-2,5,8,l 1, 14, 17,20,23,26,29-decaoxa-32,39,42-triazatetratetracontan-44-amido)benzyl (2-(2-chloro-4-(3-((2- (2,6-dioxopiperidin-3 -yl)- 1 -oxoisoindolin-5- yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate, Compound IG-L-19, (19.2 mg, 11.0 μmol, 57% yield, 97% purity) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) δ = 10.96 (br s, 1H), 9.96 (s, 1H), 8.77 (s, 1H), 8.20 (br d, J= 7.2 Hz, 1H), 8.07 - 7.97 (m, 2H), 7.72 - 7.65 (m, 2H), 7.64 - 7.55 (m, 4H), 7.51 (s, 1H), 7.44 (d, J= 8.0 Hz, 1H), 7.28 (br d, J= 7.6 Hz, 2H),
7.19 - 7.11 (m, 2H), 6.99 (s, 2H), 6.80 (br t, J= 5.6 Hz, 1H), 5.10 (dd, J= 5.2, 13.2 Hz, 1H), 4.98 (s, 2H), 4.47 - 4.39 (m, 3H), 4.38 - 4.25 (m, 4H), 3.91 (s, 2H), 3.84 (s, 2H), 3.59 (br d, J= 6.8 Hz, 4H), 3.55 - 3.47 (m, 41H), 3.44 - 3.35 (m, 6H), 3.23 (s, 3H), 3.19 - 3.13 (m, 2H), 3.06 (q, J= 6 8 Hz, 2H), 2 96 - 2 80 (m, 6H), 2 63 - 2 56 (m, 1H), 2 41 - 2.31 (m, 3H), 2 02 - 1 96 (m, 1H), 1.71 - 1.62 (m, 1H), 1.58 - 1.50 (m, 1H), 1.40 (br dd, J= 4.4, 6.8 Hz, 2H), 1.29 (br d, J =
7.2 Hz, 3H), 1.22 (br d, J= 7.2 Hz, 5H). MS (ESI) m/z 1711.8 [M+H]+
EXAMPLE L-14: Synthesis of (32S)-32-(2-(4-(2-(4-((S)-2-((S)-2- acetamidopropanamido)propanamido)phenyl)-2-(((2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3- yl)-l-oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamoyl)oxy)ethyl)-l/7- l,2,3-triazol-l-yl)ethyl)-45-(2,5-dioxo-2,5-dihydro-l/f-pyrrol-l-yl)-6,12,18,24,30-pentamethyl-
7,13,19, 25, 31,34, 43-heptaoxo-3, 9, 15, 21, 27,36, 39-heptaoxa-6, 12,18,24,30,33,42- heptaazapentatetracontanoic acid (IG-L-14)
Figure imgf000324_0001
Step A. Preparation of Int 14a
Figure imgf000325_0001
Figure imgf000325_0002
Tetrakis(acetonitrile)copper(l) tetrafluoroborate
NMP/DCM = 2/1, 25 °C, 12 h
Figure imgf000325_0003
To a solution of l-l-(4-((S)-2-((S')-2-acetamidopropanamido)propanamido)phenyl)but-3- yn- 1 -yl (2-(2-chloro-4-(3 -((2-(2, 6-dioxopiperi din-3 -yl)- 1 -oxoi soindolin-5 - yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamate (100 mg, 111 umol, 1.00 eq) in /V-methyl pyrrolidone (1.50 mL) and dichloromethane (1 50 mL) was added tert-butyl (S)-5-(2- azidoethyl)-l-(9/7-fluoren-9-yl)-7,13,19,25,31-pentamethyl-3,6,12, 18,24,30-hexaoxo- 2,10,16,22,28,34-hexaoxa-4,7,13,19,25,31 -hexaazahexatri acontan-36 -oate (122 mg, 122 umol, 1.10 eq) and cuprous;acetonitrile;tetrafluoroborate (105 mg, 334 umol, 3.00 eq). The mixture was stirred at 25 °C for 12 h. The reaction mixture was filtered and concentrated to remove the dichloromethane to afford tert-butyl (55)-5-(2-(4-(2-(4-((5)-2-((5)-2- acetamidopropanamido)propanamido)phenyl)-2-(((2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3- yl)-l-oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl) (methyl)carbamoyl)oxy)ethyl)-l//- l,2,3-triazol-l-yl)ethyl)-l-(9/7-fluoren-9-yl)-7,13,19,25,31- pentamethyl-3,6, 12,18,24,30- hexaoxo-2,10, 16,22,28,34-hexaoxa-4,7,13,19,25,31-hexaazahexatriacontan-36-oate, Int 14a, (200 mg, crude) as yellow oil. MS (ESI) m/z 949.6 [1/2 M+H]+
Figure imgf000326_0001
To a solution of tert-butyl (55)-5-(2-(4-(2-(4-((5)-2-((5)-2- acetamidopropanamido)propanamido)phenyl)-2-(((2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3- yl)-l- oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl) (methyl)carbamoyl)oxy)ethyl)-l/7- l,2,3-triazol-l-yl)ethyl)-l-(97/-fluoren-9-yl)-7,13,19,25,31-pentamethyl-3,6,12,18,24,30- hexaoxo-2,10,16,22,28,34-hexaoxa-4,7,13,19,25,3 l-hexaazahexatriacontan-36-oate, Int 14a, (200 mg, 105 umol, 1 00 eq) in A-methyl pyrrolidone (1 50 mb) was added piperidine (0 30 mb). The mixture was stirred at 20 °C for 1 h. The reaction mixture was filtered to give filtrate. The filtrate was purified by reversed-phase HPLC ( 0. 1% FA ) to give tert-butyl (325)-34-(4-(2- (4-((S)-2-((5)-2-acetamidopropanamido) propanamido)phenyl)-2-(((2-(2-chloro-4-(3-((2- (2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl) ureido)phenethoxy)ethyl)(methyl)carbamoyl)oxy)ethyl)- 1H-l,2,3-triazol-l-yl)-32-amino- 6,12,18,24,30-pentamethyl-7,13,19,25,3 l-pentaoxo-3,9,15,21,27-pentaoxa-6,12,18,24,30- pentaazatetratriacontanoate, Int 14b, (100 mg, 59.7 umol, 57% yield) as a black solid. MS (ESI) m/z 838.3 [1/2 M+H]+ Step C. Preparation of Int 14c
Figure imgf000327_0001
To a solution of 2-(2-(2-(3-(2,5-dioxo-2,5-dihydro-l//-pyrrol-l- yl)propanamido)ethoxy)ethoxy)acetic acid (22.5 mg, 71.6 umol, 1.20 eq) in dimethyl formamide (2.00 mL) was added tert-butyl (32S)-34-(4-(2-(4-((S)-2-((S)-2- acetamidopropanamido)propanamido)phenyl)-2-(((2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3- yl)-l-oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl) (methyl)carbamoyl )oxy)ethyl )-17/- l,2,3-triazol-l-yl)-32-amino-6,12,18,24,30-pentamethyl-7,13,19,25,3 l-pentaoxo-3,9,15,21,27- pentaoxa-6,12,18,24,30-pentaazatetratriacontanoate, Int 14b, (100 mg, 59.7 umol, 1.00 eq), O- (7-Azabenzotriazol-l-yl)-N,N,N,N ’,N’-tetramethyluronium hexafluorophosphate (29.5 mg, 77.6 umol, 1.30 eq) and /V,A-diisopropylethylamine (15.4 mg, 119 umol, 20.8 uL, 2.00 eq) The mixture was stirred at 25 °C for 2 h. The reaction mixture was filtered. The filtrate was purified by reversed-phase HPLC(0.1% FA) to give tert-butyl (325)-32-(2-(4-(2-(4-((>S)-2-((5)-2- acetamidopropanamido)propanamido)phenyl)-2-(((2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3- yl)-l-oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamoyl)oxy)ethyl)- \H- 1,2,3-triazol-l-yl) ethyl)-45-(2,5-dioxo-2,5-dihydro-l//-pyrrol-l-yl)-6,12,18,24,30-pentamethyl- 7,13,19,25,31,34,43-heptaoxo-3,9, 15,21,27,36,39-heptaoxa-6,12,18,24,30,33,42- heptaazapentatetracontanoate, Int 14c (40.0 mg, 20.3 μmol, 34% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) 3 = 11.02 - 10.95 (m, 1H), 9.89 - 9.83 (m, 1H), 8.80 - 8.75 (m, 1H), 8.13 (d, J= 7.6 Hz, 1H), 8.08 (d, J= 7.6 Hz, 1H), 7.94 - 7.86 (m, 1H), 7.81 - 7.75 (m, 1H), 7.70 - 7 65 (m, 2H), 7.58 - 7.49 (m, 3H), 7.43 (d, J= 7.6 Hz, 1H), 7.28 - 7.20 (m, 3H), 7.16 - 7.11 (m, 2H), 6.99 (s, 1H), 6.83 - 6.77 (m, 1H), 6.74 - 6.62 (m, 1H), 5.79 - 5.70 (m, 1H), 5.10 (dd, .7= 4.8, 13.6 Hz, 1H), 4 42 - 4.10 (m, 18H), 4.00 - 3.91 (m, 4H), 3 58 - 3 45 (m, 20H), 3 24 - 3.04 (m, 7H), 2.94 - 2.77 (m, 24H), 2.03 - 1.97 (m, 2H), 1.84 (s, 3H), 1.75 (s, 3H), 1.40 (s, 9H), 1.29 (br d,
Figure imgf000328_0001
7.2 Hz, 3H), 1.19 (d,
Figure imgf000328_0002
7.2 Hz, 3H). MS (ESI) m/z 986.5 [1/2 M+H]+
Step E. Preparation of Compound IG-L-14
Figure imgf000328_0003
To a solution of tert-butyl (325)-32-(2-(4-(2-(4-((5)-2-((5)-2- acetamidopropanamido)propanamido)phenyl)-2-(((2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3- yl)-l-oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl) (methyl)carbamoyl)oxy)ethyl)-l//- l,2,3-triazol-l-yl)ethyl)-45-(2,5-dioxo-2,5-dihydro-17/-pyrrol-l-yl)-6,12,18,24,30-pentamethyl- 7,13,19,25,31,34,43-heptaoxo-3,9, 15,21,27,36,39-heptaoxa-6,12,18,24,30,33,42- heptaazapentatetracontanoate, Int 14c, (20.0mg, 10.1 μmol, 1.00 eq) in dichloromethane (2.00 mb) was added trifluoroacetic acid (0.40 mb). The mixture was stirred at 25 °C for 1 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (column: Waters Xbridge 150 * 25 mm * 5 um; mobile phase: [Water - ACN]; B%: 10%-40%, 9 min) to give (32S)-32-(2-(4-(2-(4-((X)-2-((5)-2- acetamidopropanamido)propanamido)phenyl)-2-(((2-(2-chloro-4-(3-((2-(2,6-dioxopiperidin-3- yl)-l-oxoisoindolin-5-yl)methyl)ureido)phenethoxy)ethyl)(methyl)carbamoyl)oxy)ethyl)-l/7- l,2,3-triazol-l-yl)ethyl)-45-(2,5-dioxo-2,5-dihydro-l//-pyrrol-l-yl)-6,12,18,24,30-pentamethyl- 7,13,19, 25,31,34,43-heptaoxo-3,9,15,21,27,36,39-heptaoxa-6,12,18,24,30,33,42- heptaazapentatetracontanoic acid, Compound IG-L-14, (7.48 mg, 3.67 μmol, 36% yield, 94% purity) as a yellow solid 1H NMR (400 MHz, DMSO-iA) δ = 9 91 (br s, 1H), 8 23 - 8 15 (m, 1H), 8.09 (d, J= 7.2 Hz, 1H), 8.06 - 7.98 (m, 1H), 7.96 - 7.85 (m, 1H), 7.82 - 7.76 (m, 1H), 7.73 - 7.66 (m, 2H), 7.63 - 7.54 (m, 2H), 7.51 (s, 1H), 7.48 - 7.40 (m, 1H), 7.25 (br d, J = 8.1 Hz, 2H), 7.21 - 7.10 (m, 2H), 6.99 (s, 1H), 5.76 (br t, J= 6.4 Hz, 1H), 5.14 - 5.03 (m, 1H), 4.92 - 4.65 (m, 1H), 4.48 - 4.02 (m, 17H), 3.94 (br d, J= 5.6 Hz, 2H), 3.85 (br s, 2H), 3.63 - 3.48 (m, 20H), 3.43 (br s, 12H), 3.23 - 3.06 (m, 7H), 2.94 - 2.87 (m, 9H), 2.84 - 2.79 (m, 9H), 2 74 - 2.67 (m, 2H), 2.64 - 2.54 (m, 2H), 2.41 - 2.34 (m, 2H), 2.32 - 2.11 (m, 2H), 2.06 - 1.96 (m, 2H), 1.85 (s, 3H), 1.30 (d, J= 7.2 Hz, 3H), 1.20 (d, J= 7.2 Hz, 3H). MS (ESI) m/z 958.5 [1/2 M+H]+
EXAMPLE L-35: Synthesis of 34-(2-(3-(((2S)-l-(((2S)-l-((4-(10-(3-(5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l-yl)-4-methoxy-3,8- dioxo-2,9-dioxa-4,7-diazadecyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2- yl)amino)-3 -oxopropyl)-5-(2, 5 -dioxo-2, 5 -dihydro- 1 H-pyrrol- 1 -yl)phenoxy)-
3 ,6,9, 12, 15, 18,21 ,24,27,3 O-decamethyl-4,7, 10, 13 , 16, 19,22,25,28,31-decaoxo- 3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid (Compound IG-L-35)
Figure imgf000329_0001
Step A. Preparation of Int 35a ■
Figure imgf000330_0002
To a solution of (9-m ethylhydroxylamine (891 mg, 10.7 mmol, 809 μL, 1.50 eq) in dichloromethane (20.0 mL) was added .V,.V-diisopropyl ethyl amine (2.76 g, 21.3 mmol, 3.72 mL, 3.00 eq) and (97/-fluoren-9-yl)methyl (2-oxoethyl)carbamate (2.00 g, 7.11 mmol, 1.00 eq). The mixture was stirred at 25 °C for 12 h. Then the mixture was concentrated to afford a residue. The residue was dissolved in dichloromethane (20 mL) and acetic acid (5.00 mL), then sodium cyanoborohydride (670 mg, 10.7 mmol, 1.50 eq) was added to the mixture at 0 °C. The mixture was stirred at 25 °C for 12 h. The mixture was filtered and the filtrate was concentrated to give a residue. The residue was purified by reversed-phase column (C1 8, 120 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1% formic acid) and lyophilized to afford (9//-fluoren-9-yl)methyl (2- (methoxyamino)ethyl)carbamate Int 35a (900 mg, 2.88 mmol, 40% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6) 3 = 7.89 (d, J= 7.6 Hz, 2H), 7.69 (d, J= 7.6 Hz, 2H), 7.45 - 7.37 (m, 2H), 7.36 - 7.29 (m, 2H), 7.22 (br t, J= 5.6 Hz, 1H), 6.57 (br t, J= 5.6 Hz, 1H), 4 34 - 4.27 (m, 2H), 4.25 - 4.18 (m, 1H), 3.37 (s, 3H), 3.10 (q, J= 6.4 Hz, 2H), 2.80 (q, J= 6.4 Hz, 2H). MS (ESI) m/z 313.1 [M+H]+
Step B. Preparation of Int 35b
Figure imgf000330_0001
To a solution of (9/7-fluoren-9-yl)methyl (2-(methoxyamino)ethyl)carbamate Int 35a (147 mg, 471 μmol, 1.00 eq) and tert-butyl ((5)-l-(((5)-l-((4-((((4- nitrophenoxy)carbonyl)oxy)methyl)phenyl)amino)- 1 -oxopropan-2-yl)amino)- 1 -oxopropan-2- yl)carbamate Int lOp (250 mg, 471 μmol, 1.00 eq) in N,N-dimethylformamide (2.00 mL) were added 1 -hydroxybenzotri azole (127 mg, 942 μmol, 2.00 eq) and diisopropylethylamine (183 mg, 1.41 mmol, 246 μL, 3.00 eq) at 0 °C. The mixture was stirred at 25 °C for 12 h. Six parallel reactions was combined and concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (C1 8, 120 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1% formic acid) and lyophilized to afford 4-((S)-2-((M-2-((tert- butoxycarbonyl)amino)propanamido)propanamido)benzyl (2-((((97T-fluoren-9- yl)methoxy)carbonyl)amino)ethyl)(methoxy)carbamate Int 35b (720 mg, 1.02 mmol, 36% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6) 3 = 10.08 - 9 91 (m, 1H), 8.00 (d, J = 7.2 Hz, 1H), 7.88 (d, J= 1.6 Hz, 2H), 7.67 (d, J= 7.6 Hz, 2H), 7.59 (d, J= 8.4 Hz, 2H), 7.46 - 7.38 (m, 3H), 7.33 - 7.29 (m, 4H), 6.97 (br d, J= 7.2 Hz, 1H), 5.03 (s, 2H), 4.45 - 4.34 (m, 1H), 4.28 (d, 6.8 Hz, 2H), 4.23 - 4.16 (m, 1H), 3.99 (quin, J= 7.2 Hz, 1H), 3.59 (s, 3H), 3.51 (br t, J=
6.4 Hz, 2H), 3.16 (q, J= 5.6 Hz, 2H), 1.37 (s, 9H), 1.29 (d, J= 7.2 Hz, 3H), 1.18 (br d, J= 7.2 Hz, 3H). MS (ESI) m/z 704 3 [M+H]+
Step C. Preparation of Int 35c
Figure imgf000331_0001
To a solution of 4-((5)-2-((S)-2-((tert-butoxycarbonyl)amino)propanamido)propanamido)benzyl (2-((((9//-fluoren-9-yl)methoxy)carbonyl)amino)ethyl)(methoxy)carbamate Int 35b (600 mg, 852 ptmol. 1.00 eq) in ?V,.V-dimethylformamide (1.00 mb) was added piperidine (1.03 g, 12.2 mmol, 1.20 mL, 14.3 eq). The mixture was stirred at 25 °C for 0.5 h. The mixture was adjusted with formic acid (50%) to pH=7 and concentrated to give a residue. The residue was purified by reversed-phase column (acetonitrile -water) and lyophilized to afford 4-((5)-2-((5)-2-((/er/- butoxycarbonyl)amino)propanamido)propanamido)benzyl (2-aminoethyl)(methoxy)carbamate Int 35c (320 mg, 664 μmol, 78% yield) as a white solid. 1 H NMR (400 MHz, DMSO-t/g) δ = 10.06 (s, 1H), 8.08 (d, J= 7.2 Hz, 1H), 7.61 (d, J= 8.4 Hz, 2H), 7.33 (d, J= 8.4 Hz, 2H), 6.98 (br d, J= 7.2 Hz, 1H), 5.07 (s, 2H), 4.41 - 4.36 (m, 1H), 4.03 - 3.95 (m, 1H), 3.61 (s, 3H), 3.57 (t, J = 6.4 Hz, 2H), 2 83 (t, J= 6.4 Hz, 2H), 1 37 (s, 9H), 1 30 (d, J= 7 2 Hz, 3H), 1.18 (br d, J = 7.2 Hz, 3H). MS (ESI) m/z 482.2 [M+H]+
Step D. Preparation of Int 35d
Figure imgf000332_0001
To a solution of 4-((S)-2-((S)-2-((tert- butoxycarbonyl)amino)propanamido)propanamido)benzyl (2-aminoethyl)(methoxy)carbamate Int 35c (363 mg, 755 μmol, 1.00 eq) in N,N-dimethylformamide (4.00 mL) was added triethylamine (229 mg, 2.26 mmol, 315 μL, 3.00 eq) and (3-(5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l-yl)methyl (4- nitrophenyl) carbonate (480 mg, 758 prnol, 1.00 eq). The mixture was stirred at 25 °C for 5 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (C18, 80 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1% formic acid) and lyophilized to afford 4-((A)-2-((S)-2-((tert- butoxycarbonyl)amino)propanamido)propanamido)benzyl (2-((((3-(5-((3-(3-chloro-4- methylphenyl) ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methoxy)carbonyl)amino)ethyl) (methoxy) carbamate Int 35d (510 mg, 521 μmol, 69% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6) δ = 9.99 (s, 1H), 8.75 (s, 1H), 8.00 (d, J = 7.2 Hz, 1H), 7.70 (d, J= 7.6 Hz, 1H), 7.66 (d, J= 1.6 Hz, 1H), 7 58 (d, J= 8.4 Hz, 2H), 7.52
(s, 1H), 7.48 - 7.38 (m, 2H), 7.31 (d, J= 8.8 Hz, 2H), 7.20 - 7 15 (m, 1H), 7.15 - 7.10 (m, 1H), 6.97 (br d, J= 7.2 Hz, 1H), 6.80 (t, J= 6.0 Hz, 1H), 5.64 - 5.51 (m, 2H), 5.22 (br dd, J= 5.2, 13.5 Hz, 1H), 5.05 (s, 2H), 4 49 - 4.25 (m, 5H), 4.03 - 3.93 (m, 1H), 3.60 - 3.56 (m, 3H), 3.53 - 3.45 (m, 2H), 3.19 - 3.04 (m, 3H), 2.88 - 2.77 (m, 1H), 2.38 (br dd, J= 3.6, 14.1 Hz, 1H), 2.23 (s, 3H), 2.13 - 2.08 (m, 1H), 1.37 (s, 9H), 1.30 (d, J= 7.2 Hz, 3H), 1.18 (br d, J= 7.2 Hz, 3H).
MS (ESI) m/z 978.5 [M+H]+
Step E. Preparation of Int 35e
Figure imgf000333_0001
To a solution of 4-((S)-2-((5)-2-((tert butoxycarbonyl)amino)propanamido)propanamido)benzyl (2-((((3-(5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methoxy)carbonyl)amino)ethyl)(methoxy)carbamate Int 35d (510 mg, 521 μmol, 1.00 eq) in dichloromethane (5.00 mL) was added trifluoroacetic acid (1.54 g, 13.5 mmol, 1.00 mL, 25.8 eq). The mixture was stirred at 25 °C for 6 min The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (Cl 8, 12 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1% formic acid) and lyophilized to afford 4-((S)-2- ((S)-2-aminopropanamido)propanamido)benzyl (2-((((3-(5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methoxy)carbonyl)amino)ethyl)(methoxy)carbamate Int 35e (90.0 mg, 99.4 μmol, 19% yield, 97% purity) as a white solid. ’H NMR (400 MHz, DMSCM,) 3 = 10.14 (s, 1H), 9.04 - 8.89 (m, 1H), 8.51 - 8.33 (m, 1H), 7.72 - 7.65 (m, 2H), 7.59 (d, J= 8.4 Hz, 2H), 7.52 (s, 1H), 7.47 - 7.39 (m, 2H), 7.32 (d, J= 8.4 Hz, 2H), 7.20 - 7.12 (m, 2H), 7.08 - 6.97 (m, 1H), 5.57 (q, J= 9.2 Hz, 2H), 5.22 (br dd, J= 52, 13.2 Hz, 1H), 5.05 (s, 2H), 4.56 - 4.18 (m, 6H), 3.58 (s, 3H), 3.49 (br s, 3H), 3.14 - 3.05 (m, 3H), 2.86 - 2.79 (m, 1H), 2.54 (br s, 1H), 2.47 - 2.35 (m, 1H), 2.22 (s, 3H), 2.13 - 1.97 (m, 1H), 1.32 (d, J= 7.2 Hz, 3H), 1.25 (d, J= 6.8 Hz, 3H). MS (ESI) m/z 878.4 [M+H]+
Step F. Preparation of Compound IG-L-35
Figure imgf000334_0001
Compound IG-L-35
To a solution of 4-((S)-2-((5)-2-aminopropanamido)propanamido)benzyl (2-((((3-(5-((3-
(3-chloro-4-methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methoxy)carbonyl)amino) ethyl)(methoxy)carbamate Int 35e (20.0 mg, 22.8 μmol, 1.00 eq) and 34-(5-(2,5-dioxo-2,5-dihydro- 1H-pyrrol-l-yl)-2-(3-oxo-3-(2, 3,5,6- tetrafluorophenoxy)propyl)phenoxy)-3,6,9, 12, 15, 18,21,24,27,30-decamethyl-4,7, 10, 13, 16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid (24.7 mg, 20.5 gmol, 0.900 eq) in JV,Mdimethylformamide (1.00 mL) was added diisopropylethylamine (8.83 mg, 68.3 μmol, 11.9 uL, 3.00 eq). The mixture was stirred at 0 °C for 1 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (C1 8, 40 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1% formic acid), reversed-phase column (acetonitrile -water) and lyophilized to afford 34-(2-(3-(((2S)-l-(((25)-l- ((4-( 10-(3 -(5-((3 -(3 -chi oro-4-m ethylphenyl )ureido)m ethyl)- 1 -oxoi soindolin-2-yl)-2,6- dioxopiperidin-l-yl)-4-methoxy-3,8-dioxo-2,9-dioxa-4,7-diazadecyl)phenyl)amino)-l- oxopropan-2-yl)amino)-l-oxopropan-2-yl)amino)-3-oxopropyl)-5-(2,5-dioxo-2,5-dihydro-l 1/H7- pyrrol-l-yl)phenoxy)-3,6,9,12,15,18,21,24,27,30-decamethyl-4,7,10,13,16,19,22,25,28,31- decaoxo-3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid Compound IG-L-35 (4.34 mg, 2 19 μmol, 9% yield, 97% purity) as a yellow solid. XH NMR (400 MHz, DMSO-d6) D δM =SO-d6 10.06 - 9.90 (m, 1H), 8.34 - 8.00 (m, 2H), 7.72 - 7.65 (m, 2H), 7.62 (br d, J= 8.4 Hz, 2H), 7.51 (br s, 1H), 7.47 - 7.38 (m, 2H), 7.31 (br d, J= 8.4 Hz, 2H), 7.23 - 7.11 (m, 5H), 6.89 (br d, J = 8.8 Hz, 1H), 6.77 (br t,
Figure imgf000335_0001
4.8 Hz, 1H), 5.64 - 5.51 (m, 2H), 5.26 - 5.17 (m, 1H), 5. 10 - 4.98 (m, 2H), 4 50 - 4 13 (m, 16H), 4 12 - 3 85 (m, 12H), 3 58 (s, 3H), 3 52 - 3 45 (m, 2H), 3 17 - 3 10 (m, 2H), 3.10 - 2.69 (m, 36H), 2.46 - 2.41 (m, 2H), 2.22 (s, 3H), 2.11 - 1.84 (m, 4H), 1 30 (br d, J= 7.2 Hz, 3H), 1.19 (br d, J= 7.2 Hz, 3H). MS (ESI) m/z 960.2 [M/2+2H]
The compounds in Table 16 were prepared in a manner similar to that described for Compound IG-L-35 using the appropriate compound as starting material.
Table 16
Figure imgf000336_0001
Figure imgf000337_0001
Figure imgf000338_0001
EXAMPLE L-36: Synthesis of 34-(6-((6S,9S)-l-((3-chloro-4-methylphenyl)amino)-2-((2-
(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)-6,9-dimethyl-l,5,8,l 1 -tetraoxo-2, 4,7,10- tetraazatridecan-13-yl)-3-(2,5-dioxo-2,5-dihydro-lH-pyrrol-l-yl)-2-fluorophenoxy)-
3,6,9,12,15,18,21,24,27,30-decamethyl-4,7,10,13,16,19,22,25,28,31-decaoxo-
3 ,6,9, 12, 15, 18,21 ,24,27, 3 O-decaazatetratri acontanoic acid, IG-L-36
Figure imgf000339_0001
Int 36a
To a solution of 2-fluoro-3-methoxyaniline (11.0 g, 77.9 mmol, 1.00 equiv) in N,N- dimethyl formamide (40.0 mL) was added a solution of 1 -bromopyrrolidine-2, 5-dione (13.9 g, 78.0 mmol, 1.00 equiv) dropwise. The mixture was stirred at 15 °C for 3 h. The mixture was diluted with brine (300 mL) and extracted with ethyl acetate (3 x 300 mL). The organic layers were collected and dried over anhydrous sodium sulfate. After filtration, the filtrate was concentrated under reduced pressure to give a crude product, which was purified by column chromatography on silica gel (SiOz, petroleum ether/ethyl acetate=l/O to 3/1) and concentrated to afford 4-bromo-2-fluoro-3-methoxyaniline, Int. 36a, (26.0 g, 118 mmol, 75% yield) as yellow oil. 1H NMR (400 MHz, DMSO-tfe) δ = 7.03 (dd, J= 8.8, 1.2 Hz, 1H), 6.47 (t, J= 8.8 Hz, 1H), 5.38 (s, 2H), 3.86 - 3.78 (m, 3H).
Step B. Preparation of Int 36b
Figure imgf000339_0002
Int 36a Int 36b To a solution of 4-bromo-2-fluoro-3-methoxyaniline, Int. 36a, (10.0 g, 45.5 mmol, 1.00 equiv) in dichloromethane (100 mL) was added borontribromide (171 g, 682 mmol, 65.7 mb, 15.0 equiv) at 0 °C. The mixture was stirred at 15 °C for 0.5 h. The reaction mixture was quenched by addition water (300 mL) at 0 °C. After filtration, the filtrate was extracted with ethyl acetate (3 x 200 mL). The organic layers were collected and dried over anhydrous sodium sulfate After filtration, the filtrate was concentrated under reduced pressure to afford 3-amino- 6-bromo-2-fluorophenol, Int. 36b, (22.5 g, crude) as yellow oil. 1 H NMR (400 MHz, DMSO-<7()) δ = 9.95 - 9.35 (m, 1H), 6 90 (dd, J= 8.8, 1.6 Hz, 1H), 6.20 - 6.16 (m, 1H), 5.15 (br s, 2H). MS (ESI) m/z 205.9 [M+H]+
Step C. Preparation of Int 36c
Figure imgf000340_0001
Int 36b Int 36c
To a solution of 3-amino-6-bromo-2-fluorophenol, Int. 36b, (16.0 g, 77.7 mmol, 1.00 equiv), cesium carbonate (50.6 g, 155 mmol, 2 00 equiv) and potassium iodide (1.29 g, 7.77 mmol, 0.100 equiv) in N, /V-dimethyl formamide (50.0 mL) was added /crt-butyl 4- bromobutanoate (19.1 g, 85 4 mmol, l. lO equiv). The mixture was stirred at 85 °C for 12 h. The mixture was diluted with brine (300 mL) and extracted with ethyl acetate (3 x 200 mL). The organic layers were collected and dried over anhydrous sodium sulfate. After filtration, the filtrate was concentrated under reduced pressure to give a crude product, which was purified by column chromatography on silica gel (SiO2, petroleum ether/ethyl acetate=l/O to 3/1) and concentrated to afford tert-butyl 4-(3-amino-6-bromo-2-fluorophenoxy)butanoate, Int. 36c, (17.0 g, 48.8 mmol, 62% yield) as brown oil. 1 H NMR (400 MHz, DMSCW<>) δ = 7.03 (dd, J= 8.8, 1 6 Hz, 1H), 6.46 (t, J= 8.8 Hz, 1H), 5.36 (s, 2H), 3.98 - 3.93 (m, 2H), 2.43 (t, J= 7.2 Hz, 2H), 1.91 (br t, J= 6.8 Hz, 2H), 1.40 (s, 9H).
Step D. Preparation of Int 36d
Figure imgf000341_0001
Int 36c Int 36d
To a solution of tert-butyl 4-(3-amino-6-bromo-2-fluorophenoxy)butanoate, Int. 36c, (12.0 g, 34.5 mmol, 1.00 equiv) and ethyl (E)-3-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2- yl)acrylate (19.5 g, 86.2 mmol, 2.50 equiv) in dioxane (100 mL) and water (10.0 mb) was added 2-dicyclohexylphosphino-2,6-dimethoxybiphenyl (1.41 g, 3.45 mmol, 0.100 equitv), potassium phosphate (11.0 g, 51.7 mmol, 1.50 equiv) and bis(dibenzylideneacetone)-palladium(0) (1.58 g, 1.72 mmol, 0.050 equiv.). The mixture was stirred at 90 °C for 12 h under nitrogen atmosphere. The mixture was concentrated under reduced pressure to give a crude product, which was purified by column chromatography on silica gel ( Si O2, petroleum ether / ethyl acetate=l/O to 3/1) and concentrated to afford tert-butyl (E)-4-(3-amino-6-(3-ethoxy-3-oxoprop-l-en-l-yl)-2- fluorophenoxy)butanoate, Int. 36d, (11.0 g, 30.0 mmol, 86% yield) as yellow solid. H NMR (400 MHz, DMSO-ds) 6 = 7.70 (d, J= 16.0 Hz, 1H), 7.30 (dd, J= 8.8, 1.2 Hz, 1H), 6.50 (t, J = 8.4 Hz, 1H), 6.32 (d, J= 16 0 Hz, 1H), 5 87 (s, 2H), 4.14 (q, J= 7.2 Hz, 2H), 4.01 (t, <7= 6.4 Hz, 2H), 2.40 (t, J= 7.2 Hz, 2H), 1.92 (quin, J= 6.8 Hz, 2H), 1.38 (s, 9H), 1.25 - 1.22 (m, 3H).
Step E. Preparation of Int 36e
Figure imgf000341_0002
A mixture of tert-butyl (/.')-4-(3 -am ino-6-(3 -ethoxy-3 -oxoprop- l -en- l -yl)-2- fluorophenoxy)butanoate, Int. 36d, (5.00 g, 13.6 mmol, 1.00 equiv) in methanol (100 mL) was added palladium on activated carbon (5.00 g, 10% purity). The mixture was stirred at 25 °C for 12 h under hydrogen (50 Psi) atmosphere. The reaction mixture was filtered concentrated under reduced pressure to afford tert-butyl 4-(3-amino-6-(3 -ethoxy-3 -oxopropyl)-2- fluorophenoxy)butanoate, Int. 36e, (3.40 g, crude) as black oil. XH NMR (400 MHz, DMSO-c/f,) δ = 6.64 (dd, .7= 8.4, 1.6 Hz, 1H), 6.39 (t, J= 8.4 Hz, 1H), 5.01 - 4.91 (m, 2H), 4.03 (q, J= 6.8 Hz, 2H), 3.93 (t, J= 6.8 Hz, 2H), 2.74 - 2.64 (m, 2H), 2.47 - 2.44 (m, 2H), 2.39 (t, J= 6.8 Hz, 2H), 1.90 (quin, J = 6.8 Hz, 2H), 1.40 (s, 9H), 1.15 (t, J= 6.8 Hz, 3H).
Step F. Preparation of Int 36f
Figure imgf000342_0001
Int 36e Int 36f
To a solution of /m-butyl 4-(3-amino-6-(3 -ethoxy-3 -oxopropyl)-2- fluorophenoxy)butanoate, Int. 36e, (5.00 g, 13 5 mmol, 1.00 equiv) in methanol (10.0 mL), tetrahydrofuran (10.0 mL) and water (10 0 mL) was added lithium hydroxide monohydrate (852 mg, 20.3 mmol, 1.50 equiv). The mixture was stirred at 15 °C for 1 h. The mixture was quenched with hydrochloric acid (IM) until pH=7. The mixture was concentrated to remove tetrahydrofuran and methanol. The mixture was diluted with water (150 mL) and extracted with ethyl acetate (3 * 150 mL). The organic layers were collected and dried over anhydrous sodium sulfate After filtration, the filtrate was concentrated under reduced pressure to afford 3-(4- amino-2-(4-(/t77-butoxy)-4-oxobutoxy)-3-fluoropheriyl)propanoic acid, Int. 36f, (4.00 g, crude) as yellow oil. ^ NMR (400 MHz, DMSCM,) 8 = 12.45 - 11.77 (m, 1H), 6.65 (dd, J= 8.4, 1.2 Hz, 1H), 6.39 (t, J= 8.4 Hz, 1H), 4.96 (s, 2H), 3.93 (t, J= 6.4 Hz, 2H), 2.66 (t, J= 7.2 Hz, 2H), 2.41 - 2 36 (m, 4H), 1.90 (quin, J= 6.8 Hz, 2H), 1.40 (s, 9H).
Step G. Preparation of Int 36g
Figure imgf000342_0002
To a solution of 3-(4-amino-2-(4-(z‘erLbutoxy)-4-oxobutoxy)-3-fluorophenyl)propanoic acid, Int. 36f, (4.00 g, 11.7 mmol, 1.00 equiv) in dichloromethane (50.0 mL) was added triethylamine (3.56 g, 35.2 mmol, 4.89 mL, 3.00 equiv) and methyl 2,5-dioxo-2,5-dihydro-l/7- pyrrole-l-carboxylate (2.00 g, 12.9 mmol, 2.00 mL, 1.10 equiv) at 0 °C. The mixture was stirred at 15 °C for 2 h. The mixture was diluted with water (100 mL) and extracted with dichloromethane (3 x 80 mL). The organic layers were collected and dried over anhydrous sodium sulfate After filtration, the filtrate was concentrated under reduced pressure to afford 3- (2-(4-(tert-butoxy)-4-oxobutoxy)-4-(2,5-dioxo-2,5-dihydro-H/-pyrrol-l-yl)-3- fluorophenyl)propanoic acid, Int. 36g, (4.50 g, crude) as brown oil. 1H NMR (400 MHz, DMSO-c/g) 3 = 7 25 (s, 2H), 7 16 (d, J= 8.8 Hz, 1H), 7.08 - 7 03 (m, 1H), 4 01 (br t, J= 6.4 Hz, 2H), 2.87 (br t, J= 7.6 Hz, 2H), 2.52 - 2.51 (m, 2H), 2.42 - 2.36 (m, 4H), 1.39 (s, 9H)
Step H. Preparation of Int 36h
Figure imgf000343_0001
To a solution of 3-(2-(4-(terZ-butoxy)-4-oxobutoxy)-4-(2,5-dioxo-2,5-dihydro-l//-pyrrol- l-yl)-3-fluorophenyl)propanoic acid, Int. 36g, (4.50 g, 10.7 mmol, 1.00 equiv) and 2, 3,5,6- tetrafluorophenol (3.55 g, 21.4 mmol, 2.00 equiv) in dichloromethane (50.0 mL) and Ay.V- dimethylacetamide (5.00 mL) was added l-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (4.09 g, 21 .4 mmol, 2.00 equiv) at 0 °C. The mixture was stirred at 15 °C for 1 h. The mixture was concentrated under reduced pressure to give a crude product, which was purified by reversed-phase HPLC (column: spherical C1 8, 20-45 um, 100A, SW 330, mobile phase: [0.1% formic acid - acetonitrile]; B%: 85%-100%, 60 min). The desired fraction collected and lyophilized to afford tert-butyl 4-(3-(2, 5-dioxo-2,5-dihydro-l //-pyrrol - I -yl)-2- fluoro-6-(3-oxo-3-(2,3,5,6-tetrafluorophenoxy)propyl)phenoxy)butanoate, Int. 36h, (3.00 g, 5.27 mmol, 49 %yield) as a brown solid. H NMR (400 MHz, DMSCM,) 3 = 7.97 - 7 91 (m, 1H), 7.26 (s, 2H), 7.24 (s, 1H), 7.13 - 7.08 (m, 1H), 4.06 (t, J= 6.4 Hz, 2H), 3.18 - 3.12 (m, 2H), 3.10 - 3 04 (m, 2H), 2.43 - 2.39 (m, 2H), 1.97 - 1.92 (m, 2H), 1.37 (s, 9H). MS (ESI) m/z 587.1 [M+H2O]+
Step I. Preparation of Int 36i
Figure imgf000344_0001
To a solution of tert-butyl 4-(3-(2,5-dioxo-2,5-dihydro-l//-pyrrol-l-yl)-2-fluoro-6-(3- oxo-3-(2,3,5,6-tetrafluorophenoxy)propyl)phenoxy)butanoate, Int. 36h, (1.00 g, 1.76 mmol, 1.00 equiv) in dichloromethane (15.0 mL) was added trifluoroacetic acid (76.8 g, 673 mmol, 50 0 mL, 383 equiv). The mixture was stirred at 15 °C for 0 5 h. The reaction mixture was lyophilized to give a crude product, which was triturated with methyl tert-butyl ether (10 mL) at 25 °C. Then filtered, the filter cake was dried in vacuum to afford 4-(3-(2,5-dioxo-2,5-dihydro- l/Z-pyrrol-l-yl)-2-fluoro-6-(3-oxo-3-(2,3,5,6-tetrafluorophenoxy)propyl)phenoxy)butanoic acid, Int. 36i, (300 mg, 584 μmol, 33% yield) as a pink solid. rH NMR (400 MHz, DMSO-c/e) δ = 13.15 - 11.06 (m, 1H), 7.94 (tt, J= 7.6, 10.8 Hz, 1H), 7.26 (s, 2H), 7.24 (s, 1H), 7.15 - 7.06 (m, 1H), 4.08 (t, J= 6.0 Hz, 2H), 3.23 - 3.13 (m, 2H), 3.11 - 3.02 (m, 2H), 2.42 (t, J= 7.4 Hz, 2H), 1.96 (quin, J= 6.8 Hz, 2H).
Figure imgf000344_0002
To a solution of 4-(3-(2,5-dioxo-2,5-dihydro-177-pyrrol-l-yl)-2-fluoro-6-(3-oxo-3- (2,3,5,6-tetrafluorophenoxy)propyl)phenoxy)butanoic acid, Int. 36i, (100 mg, 195 μmol, 1.00 equiv) in dichloromethane (3.00 mL) was added l -chloro-;V,.'V,2-trimethylprop- l -en- l-amine, Int. 36j, (52. 1 mg, 390 umol, 51.5 μL, 2.00 equiv). The mixture was stirred at 25 °C for 0.5 h. The reaction mixture was used in next step directly.
Step K. Preparation of Int 36k
Figure imgf000345_0001
To a solution of 5,8,ll,14,17,20,23,26,29-nonamethyl-4,7,10,13,16,19,22,25,28- nonaoxo-2,5,8,l l, 14,17,20,23,26,29-decaazahentriacontan-31-oic acid, Int lOf, (137 mg, 188 μmol, 1 00 equiv) in dichloromethane (2.00 mL) and ;V,/V-di isopropyl ethylamine (72.9 mg, 564 μmol, 98.3 μL, 3.00 equiv). The mixture was stirred at 25 °C for 10 min. Then to the mixture was added 2,3,5,6-tetrafluorophenyl 3-(2-(4-chloro-4-oxobutoxy)-4-(2,5-dioxo-2,5-dihydro-l/7- pyrrol-l-yl)-3-fluorophenyl)propanoate, Int. 36j, (100 mg, 188 μmol, 1.00 equiv) at 0 °C. The mixture was stirred at 25 °C for 20 min. The reaction mixture was concentrated under reduced pressure to give a crude product, which was purified by prep-HPLC (column: UniSil 3-100 C1 8 Ultra (150*25mm*3um); mobile phase: [water (formic acid)-acetonitrile]; gradient: 20%-50% B over 40 min). The desired fraction collected and lyophilized to afford 34-(3-(2,5-dioxo-2,5- dihy dro- 17f-pyrrol- 1 -yl)-2-fluoro-6-(3 -oxo-3 -(2,3 , 5 ,6-tetrafluorophenoxy)propyl)phenoxy)- 3 ,6,9, 12, 15, 18,21 ,24,27,30-decamethyl-4,7, 10, 13 , 16, 19,22,25,28,31-decaoxo- 3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid, Int. 36k, (30.0 mg, 24.3 μmol, 12 % yield, 99% purity) as a white solid. ^ NMR (400 MHz, DMSO-d6) δ = 13.48 - 12.07 (m, 1H), 8.00 - 7 87 (m, 1H), 7.26 (s, 2H), 7.25 - 7.20 (m, 1H), 7.13 - 7.06 (m, 1H), 4.34 - 4.19 (tn, 8H), 4.15 - 3 98 (m, 11H), 3.93 (br d, J = 4.4 Hz, 2H), 3.16 (br d, J= 6.0 Hz, 2H), 3.11 - 3.06 (m, 2H), 2.95 - 2.71 (m, 31H), 2.35 - 2 29 (m, 2H), 1 99 - 1.89 (m, 2H). MS (ESI) m/z 1246.4 [M+Na]+
Step L. Preparation of Int 361
Figure imgf000346_0001
Int 361
To a solution of (2S)-2-[[(2S)-2-(9H-fluoren-9- ylmethoxycarbonylamino)propanoyl]amino]propanoic acid (10 g, 26.2 mmol, 1 equiv) in DCM (100 mL) was added 1 -hydroxypyrrolidine-2, 5-dione (9.03 g, 78.5 mmol, 3 equiv) and DCC (16.2 g, 78.5 mmol, 15.9 mL, 3 equiv) at 0°C. The mixture was allowed to warm to 20°C and stirred for 14 hours. The reaction solution was filtered and the filtrate was concentrated under reduced pressure to give a residue. Compound (2,5-dioxopyrrolidin-l-yl) (2S)-2-[[(2S)-2-(9H- fluoren-9-ylmethoxycarbonylamino)propanoyl]amino]propanoate, Int. 361, (22.5 g, crude) was obtained as a white solid.
Step M. Preparation of Int 50m
Figure imgf000346_0002
3, , ,
Int 361 Int 36m
To a solution of (2,5-dioxopyrrolidin-l-yl) (2S)-2-[[(2S)-2-(9H-fluoren-9- ylmethoxycarbonylamino)propanoyl]amino]propanoate, Int. 361, (45 g, 93.9 mmol, 1 equiv) and 2-aminoacetic acid (7.05 g, 93.9 mmol, 1 equiv) in DMF (250 mL) was added the solution of NaHCCL (23 7 g, 282 mmol, 11 0 mL, 3 equiv) in H2O (250 mL) at 0°C. The mixture was stirred at 20°C for 12 hours. The reaction mixture was quenched with HC1 (1 M) until pH = -2, and diluted with H2O (500 mL). The aqueous was extracted with EtOAc (400 ml *3). The organic s were combined, and washed with brine (800 mL), dried over Na2SO4 , filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 220 g SepaFlash® Silica Flash Column, Eluent of 0-100% Ethyl acetate/Petroleum ether then 0-25% MeOH/Ethyl acetate gradient @ 100 mL/min). Compound 2- [[(2S)-2-[[(2 S)-2-(9H-fluoren-9- ylmethoxycarbonylamino)propanoyl]amino]propanoyl]amino]acetic acid, Int. 36m, (12.6 g, 28.7 mmol, 30.6 % yield) was obtained as a white solid. 1H NMR (400 MHz, DMSO-fife) 58. 19- 7.98 (m, 2H), 7.89 (d, J= 7.6 Hz, 2H), 7.72 (t, J= 7.2 Hz, 2H), 7.62-7.48 (m, 1H), 7.44-7.38 (m, 2H), 7.36-7.29 (m, 2H), 4.36-4.18 (m, 4H), 4.12-4.02 (m, 1H), 3.78-3.69 (m, 2H), 1.25-1.17 (m, 6H).
Step N. Preparation of Int 36n
Figure imgf000347_0001
Figure imgf000347_0002
Int 36m
Figure imgf000347_0004
Int 36n
To a solution of 2-[[(2S)-2-[[(2S)-2-(9H-fluoren-9-ylmethoxycarbonylamino)propanoyl] amino]propanoyl]amino]acetic acid, Int. 36m, (7.60 g, 17.3 mmol, 1.0 equiv) in THF (90 mb) and toluene (30 mL) was added pyridine (1.64 g, 20.8 mmol, 1.68 mL, 1.2 equiv) and triacetoxyplumbyl acetate (9.20 g, 20.8 mmol, 1.2 equiv) at 25°C under N2. The reaction mixture was heated to 80°C and stirred for 14 hours. The reaction mixture was filtered and the filtrate was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO2, Petroleum ether/Ethyl acetate=10/l to 0/1). Compound [[(2S)- 2-[[(2S)-2-(9H-fluoren-9-ylmethoxycarbonylamino)propanoyl]amino] propanoyl-] amino]methyl acetate, Int. 36m, (4.0 g, 8 82 mmol, 51.0% yield) was obtained as a white solid. 1H NMR: (400 MHz, DMSO-d6) 5 8.88-8.79 (m, 1H), 7.89 (d, J= 7.6 Hz, 2H), 7.72 (t, J= 7.2 Hz, 2H), 7.45-7.38 (m, 2H), 7.36-7.29 (m, 2H), 5.19-4.99 (m, 2H), 4.35-4.17 (m, 4H), 4.12-4.04 (m, 1H), 2.01-1.93 (m, 3H), 1.25-1.18 (m, 6H)
Step O. Preparation of Int 36o
Figure imgf000347_0003
Int 36n Int 36o
To a solution of [[(2S)-2-[[(2S)-2-(9H-fluoren-9- ylmethoxycarbonylamino)propanoyl]amino]propanoyl]amino]methyl acetate, Int. 36n, (0.6 g, 1.32 mmol, 1 equiv) in DCM (6 mL) was added TMSI (794 mg, 3.97 mmol, 540 μL, 3 equiv) at 0°C. The mixture was warmed to 25°C and stirred for 1 hour. LC-MS showed Int 36n was consumed and ~80% of desired compound was detected (quenched with MeOH). The reaction mixture was concentrated under reduced pressure to give a residue. Compound 9H-fluoren-9- ylmethyl N-[(lS)-2-[[(lS)-2-(iodomethylamino)-l-methyl-2-oxo-ethyl]amino]-l-methyl-2-oxo- ethyl]carbamate, Int. 36o, (0.75 g, crude) was obtained as a red solid.
Step P. Preparation of Int 36p
Figure imgf000348_0001
To a solution of l-(3-chloro-4-methyl-phenyl)-3-[[2-(2,6-dioxo-3-piperidyl)-l-oxo- isoindolin-5-yl]methyl]urea, Compound IG-1, (0.15 g, 340 μmol, 1 equiv) in NMP (5 mL) was added Ag2C0h (187 mg, 680 μmol, 30 9 μL, 2 equiv) and 9H-fluoren-9-ylmethyl N-[(lS)-2- [[(1 S)-2-(iodomethylamino)-l-methyl-2-oxo-ethyl]amino]- 1 -methyl-2-oxo-ethyl]carbamate, Int. 50o, (709 mg, 1.36 mmol, 4 equiv) at 25°C. The mixture was heated to 60°C and stirred for 16 hours under N2 atmosphere. After that, the reaction mixture was cooled to 25°C, piperidine (127 mg, 1 50 mmol, 148 μL, 5 equiv) was added to the above mixture, and stirred at 25°C for another 1 hour. The resulting mixture was filtered and purified by prep-HPLC (column: Phenomenex Luna C18 75 x 30mm x 3um; mobile phase: [H2O (0.1% TFA)-ACN]; gradient: 10%-40% B over 8.0 min). Compound (2S)-2-amino-N-((2S)-l-(((3-(3-chloro-4- methylphenyl)- l-((2-(2,6-dioxopiperi din-3 -yl)-l-oxoisoindolin-5- yl)methyl)ureido)methyl)amino)-l-oxopropan-2-yl)propanamide, Int. 36p, (30 mg, 49 0 μmol, 16.4% yield) was obtained as a white solid. 1H NMR (400 MHz, DMSO-d6) 510.99 (s, 1H), 9.59 (d, J= 16.4 Hz, 1H), 9.19-9.17 (m, 1H), 8.74-8.69 (m, 1H), 8.19-8.05 (m, 2H), 7.75-7.71 (m, 1H), 7.62 (d, J= 2.0 Hz, 1H), 7.52-7.50 (m, 1H), 7.45-7.43 (m, 1H), 7.28-7.24 (m, 2H), 5.14- 5.09 (m, 1H), 4.70-4.65 (m, 4H), 4.48-4.30 (m, 3H), 3.87-3.86 (m, 1H), 2.92-2.79 (m, 1H), 2.68- 2.58 (m, 1H), 2.41-2.34 (m, 1H), 2.26 (s, 3H), 2.07-2.00 (m, 1H), 1.36-1.24 (m, 6H). Step Q. Preparation of Compound IG-L-36
Figure imgf000349_0001
Compound IG-L-36
To a solution of (2S)-2-amino-N-((2S)-l-(((3-(3-chloro-4-methylphenyl)-l-((2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)ureido)methyl)amino)-l-oxopropan-2- yl)propanamide, Int. 36p, (25 mg, 34.4 μmol, 1 equiv, TFA) in DMF (1 mL) was added DIEA (13.3 mg, 103 μmol, 18.00 μL, 3 equiv) and 2-[[2-[[2-[[2-[[2-[[2-[[2-[[2-[[2-[[2-[4-[3-(2,5- dioxopyrrol-l-yl)-2-fluoro-6-[3-oxo-3-(2,3,5,6-tetrafluorophenoxy)propyl]phenoxy]butanoyl- methyl-amino]acetyl]-methyl-amino]acetyl]-methyl-amino]acetyl]-methyl-amino]acetyl]- methyl-amino]acetyl]-methyl-amino]acetyl]-methyl-amino]acetyl]-methyl-amino]acetyl]- methyl-amino]acetyl]-methyl-amino]acetic acid, Int. 36k, (42.2 mg, 34.4 μmol, 1 equiv) at 0°C. The mixture was warmed to 25°C and stirred for 1 hour. The reaction solution was quenched with TFA until pH = 6. The resulting mixture was filtered and purified by prep-HPLC (column: Phenomenex Luna C18 75 x 30 mm x 3 um; mobile phase: [HjO (0.1% TFA)-ACN]; gradient: 20%-50% B over 8.0 min). Compound 34-(6-((6S,9S)-l-((3-chloro-4-methylphenyl)amino)-2- ((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)-6,9-dimethyl-l,5,8, 11-tetraoxo-
2, 4, 7, 10-tetraazatridecan-l 3-yl)-3-(2,5-di oxo-2, 5-dihydro-lH-pyrrol-l-yl)-2 -fluorophenoxy)-
3 ,6,9, 12, 15, 18,21 ,24,27,3 O-decamethyl-4,7, 10, 13 , 16, 19,22,25,28,31-decaoxo- 3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid, Compound IG-L-36, (31 mg, 18.6 μmol, 53.9% yield) was obtained as a white solid. H NMR (400 MHz, DMSO-d6) 510.98 (d, J = 4.0 Hz, 1H), 9.80-9.64 (m, 1H), 9.12-8.93 (m, 1H), 8.50-8.07 (m, 2H), 7.76-7.67 (m, 1H), 7.65-7.59 (m, 1H), 7.55-7.49 (tn, 1H), 7.45 (d, 7= 8.0 Hz, 1H), 7.29-7.18 (m, 3H), 7.14-6.98 (m, 2H), 5.17-5.04 (m, 1H), 4.74-4.50 (m, 4H), 4.47-3.84 (m, 26H), 3.10-2.50 (m, 35H), 2.45-2.30 (m, 3H), 2.22 (ks, 3H), 2.05-1.81 (m, 3H), 1.34-1.10 (m, 6H). MS (ESI): mass calcd. For C76H98CIFN18O22 1668.68, m/z found 1669.6 [M+H] +
EXAMPLE L-37: Synthesis of 34-(6-((9S,12S)-l-((3-chloro-4-methylphenyl)amino)-2-((2- (2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)-9,12-dimethyl-l,5,8,l 1,14-pentaoxo- 2,4,7,10,13-pentaazahexadecan-16-yl)-3-(2,5-dioxo-2,5-dihydro-lH-pyrrol-l-yl)-2- fluorophenoxy)-3,6,9,12,15,18,21,24,27,30-decamethyl-4,7, 10,13, 16,19,22,25,28,31-decaoxo- 3 ,6,9, 12, 15, 18,21 ,24,27, 3 O-decaazatetratri acontanoic acid, IG-L-37)
Figure imgf000350_0001
0-25-C, 12 hr
Int 37a
To a stirred reaction mixture of 2- [(2-aminoacetyl)amino] acetic acid (5.00 g, 37.9 mmol, 1.0 equiv) and NaHCOa (6 36 g, 75.7 mmol, 2.95 mL, 2.0 equiv) in H2O (50 mL) was added allyl carbonochloridate (5.47 g, 45.4 mmol, 4.82 mL, 1.2 equiv) in THF (25 mL) dropwise at 0°C. The resulting mixture was warmed to 25°C and stirred for 12 hours. The reaction mixture was concentrated to remove THF, the aqueous phase was acidified to pH = ~5 with HC1 (aq. 1 N) The precipitated solid was collected by filtration and washed with HO (aq. 1 N) (50 mL x 2). Compound 2-[[2-(allyloxycarbonylamino)acetyl]amino]acetic acid, Int. 37a, (3.00 g, 13.9 mmol, 36.7% yield) was obtained as a white solid. 1H NMR (400 MHz, DMSO-Ts) 612.55 (s, 1H), 8.13 (t, 7= 5.6 Hz, 1H), 7.43 (t, 7= 6.0 Hz, 1H), 5.99-5.82 (m, 1H), 5.29 (dd, J= 1.6, 17.2 Hz, 1H), 5.17 (dd, J= 1.2, 10.4 Hz, 1H), 4.47 (td, J= 1.6, 5.2 Hz, 2H), 3.75 (d, J= 6.0 Hz, 2H), 3.63 (d, J= 6.0 Hz, 2H)
Step B. Preparation of Int 37b
CU(OAC)
Figure imgf000351_0002
A mixture of 2-[[2-(allyloxycarbonylamino)acetyl]amino]acetic acid, Int. 37a, (2.80 g, 12.9 mmol, 1.0 equiv) and Cu(OAc)2 (235 mg, 1 30 mmol, 0.1 equiv) in THF (30 mL) was stirred for 1 hour at 60°C under nitrogen atmosphere. The mixture was allowed to cool down to 25°C. To the above mixture was added triacetoxyplumbyl acetate (6.89 g, 15.5 mmol, 1.2 equiv) at 25°C. The resulting mixture was stirred for an additional 12 hours at 25°C. The resulting mixture was filtered, the filter cake was washed with MeOH (50 mL x 3). The filtrate was concentrated under reduced pressure. The residue was purified by silica gel column chromatography (SiO2, Petroleum ether/Ethyl acetate=100/l to 10/1). Compound [[2- (allyloxycarbonylamino)acetyl]amino]methyl acetate, Int. 37b, (2.40 g, 10.4 mmol, 80.5% yield) was obtained as a white solid. 1H NMR (400 MHz, DMSO-d6) D 5M 8S.9O1-d (t, J= 6.8 Hz, 1H), 7.42 (t, J = 6.0 Hz, 1H), 5.97-5.83 (m, 1H), 5.29 (dd, J= 1.6, 17.2 Hz, 1H), 5.18 (dd, J= 1.2, 10.4 Hz, 1H), 5.09 (d, J = 12 Hz, 2H), 4.47 (td, J= 1.2, 5.2 Hz, 2H), 3.63 (d, J= 6.4 Hz, 2H), 1.99 (s, 3H)
Step C. Preparation of Int 37c
Figure imgf000351_0001
Int 37b Int 37c
To a stirred mixture of [[2-(allyloxycarbonylamino)acetyl]amino]methyl acetate, Int. 37b, (0.9 g, 3.91 mmol, 1.0 equiv) in DCM (10 mL) was added TMSC1 (1.70 g, 15.6 mmol, 1.98 mL, 4.0 equiv) dropwise at 0°C, and stirred for 1 hour, the reaction mixture was concentrated under reduced pressure. The crude product allyl N-[2-(chloromethylamino)-2-oxo-ethyl] carbamate, Int. 37c, (1 g crude) was used in the next step without further purification.
Step D. Preparation of Int 37d
Figure imgf000352_0003
Figure imgf000352_0001
A mixture of l-(3-chloro-4-methyl-phenyl)-3-[[2-(2,6-dioxo-3-piperidyl)-l-oxo- isoindolin-5-yl]methyl]urea, Compound IG-1, (0.15 g, 340 μmol, 1.0 equiv) and K2CO3 (94.0 mg, 680 μmol, 2.0 equiv) in NMP (5 mL) was stirred for 10 min at 25°C. To the above mixture was added allyl N-[2-(chloromethylamino)-2-oxo-ethyl]carbamate, Int. 37c, (422 mg, 2.04 mmol, 6.0 equiv) at 25°C. The resulting mixture was stirred for additional 12 hours at 60°C. The reaction mixture was poured into ice-water (w/w = 1/1) (15 mL) and stirred for 2 min. The aqueous phase was extracted with ethyl acetate (20 mL x 3). The combined organic phase was dried with anhydrous Na2SCL. filtered and concentrated in vacuum. The crude product allyl (2-(((3-(3- chloro-4-methylphenyl)-l-((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)methyl)ureido)methyl)amino)-2-oxoethyl)carbamate, Int. 37d, (200 mg, crude) was used into the next step without further purification.
Step E. Preparation of Int 37 e
Figure imgf000352_0002
To a stirred mixture of allyl (2-(((3-(3-chloro-4-methylphenyl)-l-((2-(2,6-dioxopiperidin-3-yl)- l-oxoisoindolin-5-yl)methyl)ureido)methyl)amino)-2-oxoethyl)carbamate, Int 37d, (250 mg, 409 μmol, 1.0 equiv) and Pd(PPhs)4 (47.3 mg, 40.9 μmol, 0.1 equiv) in THF (3 mL) was added phenylsilane (88.6 mg, 818 μmol, 101 μL, 2.0 equiv) dropwise at 25°C under nitrogen atmosphere. The resulting mixture was stirred for 1 hour at 25°C under nitrogen atmosphere. The residue was poured into ice-water (w/w = 1/1) (4 mL) and stirred for 2 min. The aqueous phase was extracted with ethyl acetate (10 mL x 3) and filtered. The aqueous phase was purified by prep-HPLC (column: Phenomenex Luna C18 75 x 30mm x 3um; mobile phase: [H2O (0.1% TFA)-ACN]; gradient: 5 %-35% B over 8.0 min). Compound 2-amino-N-((3-(3-chloro-4- methylphenyl)- l-((2-(2,6-dioxopiperi din-3 -yl)-l-oxoisoindolin-5- yl)methyl)ureido)methyl)acetamide, Int. 37e, (12.0 mg, 22.8 μmol, 5.57% yield) was obtained as a white solid. ‘H NMR (400 MHz, DMSO-d6) 810.98 (s, 1H), 9.27 (s, 1H), 9.18 (s, 1H), 8.02 (s, 3H), 7.74 (d, J= 8.0 Hz, 1H), 7.64 (d, J= 2.0 Hz, 1H), 7.52 (s, 1H), 7.44 (d, J= 8.0 Hz, 1H), 7.33 (dd, 2.0, 8.4 Hz, 1H), 7.24 (d, J= 8.4 Hz, 1H), 5.11 (dd, J= 5.2, 13.2 Hz, 1H), 4.76 (d, J= 6.4 Hz, 2H), 4.70 (s, 2H), 4.44 (s, 1H), 4.36-4.28 (m, 1H), 3.65 (s, 2H), 2.97-2.86 (m, 2H), 2.68-2.65 (m, 1H), 2.35-2.30 (m, 1H), 2.26 (s, 3H), 2.03-1.98 (m, 1H).
Step F. Preparation of Int 37f
Figure imgf000353_0001
To a stirred mixture of (2S)-2-[[(2S)-2-(9H-fluoren-9- ylmethoxycarbonylamino)propanoyl] amino]propanoic acid (7.98 mg, 20.9 μmol, 1.0 equiv), HATU (9.52 mg, 25.1 μmol, 1.2 equiv) and HOBt (3.38 mg, 25.1 μmol, 1.2 equiv) in DMF (1 mb) was added 2-amino-N-((3-(3-chloro-4-methylphenyl)-l-((2-(2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl) ureido) methyl)acetamide, Int. 37e, (11.0 mg, 20.9 μmol, 1.0 equiv), DIEA (8.09 mg, 62.6 μmol, 10.9 μL, 3.0 equiv) at 0°C. The resulting mixture was warm to 25°C and stirred for 1 hour. After that, piperidine (7.64 mg, 89.8 μmol, 8.86 μL, 5.0 equiv) was added above mixture and stirred at 25°C for 30 min. The mixture was quenched with TFA until pH = -6 at 0°C. The resulting mixture was filtered and purified by prep-HPLC (column: Phenomenex Luna C18 75 x 30mm x 3um; mobile phase: [HzO (0.1% TFA)-ACN]; gradient: 7%-37% B over 8.0 min). Compound (2S)-2-amino-N-((2S)-l-((2-(((3-(3-chloro-4- methylphenyl)- l-((2-(2,6-dioxopiperi din-3 -yl)-l-oxoi soindolin-5- yl)methyl)ureido)methyl)amino)-2-oxoethyl)amino)-l-oxopropan-2-yl)propanamide, Int. 37f, (5.00 mg, 7.47 μmol, 41.6% yield) was obtained as a white solid.
Step G. Preparation of Compound IG-L-37
Figure imgf000354_0001
To a solution of (2S)-2-amino-N-((2S)-l-((2-(((3-(3-chloro-4-methylphenyl)-l-((2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)ureido)methyl)amino)-2-oxoethyl)amino) -1- oxopropan-2-yl)propanamide, Int. 37f, (5.0 mg, 6.38 umol, 1.0 equiv, TFA) in DMF (1 mL) was added DIEA (2.48 mg, 19.2 μmol, 3.34 μL, 3.0 equiv) and 2-[[2-[[2-[[2-[[2-[[2-[[2-[[2-[[2- [[2-[4-[3-(2,5-dioxopyrrol-l-yl)-2-fluoro-6-[3-oxo-3-(2,3,5,6-tetrafluorophenoxy)propyl]pheno xy]butanoyl-methyl-amino]acetyl]-methyl-amino]acetyl]-methyl-amino]acetyl]-methyl-ami no]acetyl]-methyl-amino]acetyl]-methyl-amino]acetyl]-methyl-amino]acetyl]-methyl-amin o]acetyl]-methyl-amino]acetyl]-methyl-amino]acetic acid, Int. 36k, (7.82 mg, 6.38 μmol, 1.0 equiv) at 0°C. The mixture was warm to 25°C and stirred for 1 hour. The mixture was quenched with TFA until pH = ~6 at 0°C. The resulting mixture was filtered and purified by prep-HPLC (column: Phenomenex Luna C18 75 x 30mm x 3um; mobile phase: [H2O (0.1% TFA)-ACN]; gradient: 15%-45% B over 8.0 min). Compound 34-(6-((9S, 12S)-l-((3-chloro-4- methylphenyl)amino)-2-((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)-9,12- dimethyl-1,5,8,1 l,14-pentaoxo-2,4,7,10,13-pentaazahexadecan-16-yl)-3-(2,5-dioxo-2,5-dihydro- lH-pyrrol-l-yl)-2-fluorophenoxy)-3,6,9,12,15,18,21,24,27,30-decamethyl- 4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid, Compound IG-L-37, (4.5 mg, 2.61 μmol, 40 8% yield) was obtained as a white solid. 1H NMR (400 MHz, DMSO-Jc,) 5 = 10.97 (s, 1H), 9.67-9.58 (m, 1H), 8.98-8.89 (m, 1H), 8.26-8.19 (m, 1H), 8.17-8.05 (m, 2H), 7.71 (d, J= 8.0 Hz, 1H), 7.61 (d, J= 2.0 Hz, 1H), 7.52 (s, 1H), 7.45 (d, J= 8.4 Hz, 1H), 7.28-7.19 (m, 4H), 7.12-7.07 (m, 1H), 7.05-6.99 (m, 1H), 5.10 (dd, J= 5.2, 13.2 Hz, 1H), 4.70-4.60 (m, 4H), 4.49-4.42 (m, 1H), 4.36-3.96 (m, 24H), 3.82-3.78 (m, 2H), 2.97-2.52 (m, 38H), 2.48-2.44 (m, 3H), 2.24 (s, 3H), 2.02-1.86 (m, 3H), 1.24 (d, J= 7.2 Hz, 3H), 1.17 (d, J= 7.2 Hz, 3H). MS (ESI): mass calcd. For C78H101CIFN19O23 1725.70, m/z found 1726.7 [M+H] +
EXAMPLE L-38: Synthesis of 34-(6-((9S)-9-benzyl-2-((2-(2,6-dioxopiperidin-3-yl)-4- hydroxy-l-oxoisoindolin-5-yl)methyl)-l-((3-isopropyl-4-methylphenyl)amino)-l,5,8,ll,14,17- hexaoxo-2,4,7, 10,13,16-hexaazanonadecan- 19-yl)-3-(2,5-dioxo-2,5-dihydro-lH-pyrrol-l-yl)-2- fluorophenoxy)-3,6,9,12,15,18,21,24,27,30-decamethyl-4,7, 10,13, 16,19,22,25,28,31-decaoxo- 3 ,6,9, 12, 15, 18,21 ,24,27, 3 O-decaazatetratri acontanoic acid, IG-L-38
Figure imgf000355_0001
Step A. Preparation of Int 38a
Figure imgf000356_0001
Int 38a
A solution of (((9//-fluoren-9-yl)methoxy)carbonyl)glycylglycine (10.0 g, 28.2 mmol, 1.00 eq) in dichloromethane (200 mL) was added to 2-chlorotrityl chloride resin, low crosslink, swellable polystyrene (60 0 g). Then diethylamine (9.12 g, 70.6 mmol, 12.3 mL, 2.50 eq) was added slowly and the mixture was agitated with nitrogen for 2 h at 25 °C. The mixture was filtered and washed with dimethyl formamide (2 x 150 mL) and di chloromethane/ methanol/diethylamine (150 mL, 80/15/5). Then the resin in piperidine (80.0 mL) and dimethyl formamide (80.0 mL) was agitated with nitrogen for 5 min at 25°C. The mixture was filtered and washed with dimethyl formamide (6 x 150 mL) to give product on the resin.
A solution of (((9Z/-fluoren-9-yl)methoxy)carbonyl)-Z,-phenylalanine (14.7 g, 37.9 mmol, 1.50 eq), diethylamine (6.54 g, 50.6 mmol, 8.82 mL, 2.00 eq) and O-(7-azabenzotriazol- l-yl)-A,A,7V’,A’-tetramethyluronium hexafluorophosphate (17.3 g, 45.6 mmol, 1.80 eq) in dimethyl formamide (150 mL) was added to the resin. Then the mixture was agitated with nitrogen for 2 h at 25°C. The mixture was filtered and washed with dimethyl formamide (3 x 150 mL). The resin in piperidine (80.0 mL) and dimethyl formamide (80.0 mL) was agitated with nitrogen for 5 min at 25°C. The mixture was filtered and washed with dimethyl formamide (6 x 150 mL) to give product on the resin.
A solution of (((9Z/-fluoren-9-yl)methoxy)carbonyl)glycylglycine (13.4 g, 37.7 mmol, 1.50 eq), diethylamine (6.50 g, 50.3 mmol, 8.76 mL, 2.00 eq) and O-(7-Azabenzotriazol-l-yl)- A,A,A’,A’-tetramethyluronium hexafluorophosphate (17.2 g, 45.3 mmol, 1.80 eq) in dimethyl formamide (150 mL) was added to the resin. The mixture was agitated with nitrogen for 2 h at 25°C. The mixture was filtered and washed with dimethyl formamide (3 x 150 mL) and dichloromethane (3 x 150 mL). The resin in dichloromethane (150 mL) and hexafluoroisopropanol (30 mL) was agitated with nitrogen for 1 h at 25°C. The mixture was filtered. The filtrate was concentrated to give (((9//-fluoren-9- yl)methoxy)carbonyl)glycylglycyl-Z-phenylalanylglycylglycine, Int-38a (15.0 g, crude) as an off-white solid. 1H NMR (400 MHz, DMSO-d6) 3 = 8.36 (brt, J = 5.4 Hz, 1H), 8.17 (br d, J= 8.0 Hz, 1H), 8.10 - 7.98 (m, 1H), 7.97 - 7.83 (m, 2H), 7.77 - 7.56 (m, 2H), 7.46 - 7.09 (m, 6H), 5.18 (td, J= 6.8, 13.5 Hz, 1H), 4.63 - 4.44 (m, 1H), 4.35 - 4.11 (m, 2H), 3.87 - 3.51 (m, 6H), 3 20 - 2 89 (m, 2H), 2 84 - 2 72 (m, 2H) LCMS (ESI) m/z 616.3 [M+H]+
Step B. Preparation of Int 38b
Figure imgf000357_0001
Int 38a Int 38b
To a solution of (((9//-fluoren-9-yl)methoxy)carbonyl)glycylglycyl-L- phenylalanylglycylglycine (2.00 g, 3.25 mmol, 1.00 eq) and copper acetate (59.0 mg, 324 prnol, 0.10 eq) in dimethyl formamide (20.0 mL) were added acetic acid (390 mg, 6.50 mmol, 372 μL, 2.00 eq) and triacetoxyplumbyl acetate (2. 16 g, 4.87 mmol, 1.5 eq). Then the mixture was stirred at 60 °C for 1 h. The reaction mixture was filtered. The filtrate was purified by reversed phase (C18, 330 g; condition: water/acetonitrile = 100/0 to 0/100, 0.1% formic acid) and lyophilized to afford (5)-l l-benzyl-l-(9//-fluoren-9-yl)-3,6,9,12,15-pentaoxo-2-oxa- 4,7,10,13,16-pentaazaheptadecan-17-yl acetate, Int 38b (1.50 g, 2.38 mmol, 73% yield) as a white solid, 'l l NMR (400 MHz, DMSO-d6 ) δ = 8.86 (br t, J= 6.8 Hz, 1H), 8.35 (br t, J= 5.6 Hz, 1H), 8.17 (br d, J= 8.4 Hz, 1H), 8.03 (br t, J= 5.4 Hz, 1H), 7 89 (d, J= 7.6 Hz, 2H), 7.71 (d, J= 7.6 Hz, 2H), 7.61 (br t, J= 6.0 Hz, 1H), 7.46 - 7.37 (m, 2H), 7.36 - 7.29 (m, 2H), 7.28 - 7.21 (m, 4H), 7.20 - 7.13 (m, 1H), 5.16 - 5.05 (m, 2H), 4.62 - 4.45 (m, 1H), 4.34 - 4.12 (m, 3H), 3.74 (br t, J= 6.4 Hz, 3H), 3.70 - 3.51 (m, 3H), 3.05 (br dd, J= 4.0, 13.8 Hz, 1H), 2.85 - 2.71 (m, 1H), 1.99 (s, 3H). LCMS (ESI) m/z 570.3 [M-OAc]+
Step C. Preparation of Int 38c
Figure imgf000357_0002
Int 38b Int 38c To a solution of (<S)-1 l-benzyl-l-(9.H-fluoren-9-yl)-3,6,9,12,15-pentaoxo-2-oxa-4,7,10,13,16- pentaazaheptadecan- 17-yl acetate (200 mg, 318 μmol. 1.00 eq) in dichloromethane (4 00 mL) was added trimethylchlorosilane (1.00 mL). The mixture was stirred at 25 °C for 1 h. The reaction mixture was concentrated under reduced pressure to give (97/-fluoren-9-yl)m ethyl (5)- (7-benzyl-l-chloro-3,6,9, 12-tetraoxo-2,5,8,l l-tetraazatridecan-13-yl)carbamate, Int 38c (180 mg, 297 μmol, 94% yield) as white solid. MS (ESI) m/z 570.2 [M-C1]+
Step D. Preparation of Int 38d
Figure imgf000358_0001
To a solution of l-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5-yl)methyl)-3-(3- isopropyl-4-methylphenyl)urea, IG-50, (250 mg, 538 μmol, 1.00 eq) in dimethyl formamide (5.00 mL) were added silver oxide (624 mg, 2.69 mmol, 5.00 eq) and benzyl bromide (276 mg, 1.61 mmol, 192 μL, 3.00 eq) The mixture was stirred at 25 °C for 2 h. The mixture was filtered. The filtrate was purified by reversed-phase HPLC (0.1% formic acid condition) The desired fraction was collected and lyophilized to give l-((4-(benzyloxy)-2-(2,6-dioxopiperidin- 3-yl)-l-oxoisoindolin-5-yl)methyl)-3-(3-isopropyl-4-methylphenyl)urea, Int 38d (165 mg, 297 μmol, 27% yield) as a white solid. ’H NMR (400 MHz, DMSO-d6) d = 11.01 (br s, 1H), 8.64 - 8.57 (m, 1H), 7.54 (br d, J= 7.2 Hz, 2H), 7.48 - 7.35 (m, 5H), 7.24 (d, J= 2.0 Hz, 1H), 7.13 (dd, J= 2.0, 8.4 Hz, 1H), 6 95 (d, J= 8.4 Hz, 1H), 6.60 (br t, J= 5.6 Hz, 1H), 5.22 (s, 2H), 5.17 - 5.06 (m, 1H), 4.67 (br d, J= 17.2 Hz, 1H), 4.56 - 4.47 (m, 1H), 4.41 (br d, J= 6.0 Hz, 2H), 3.02 (td, J= 6.8, 13.2 Hz, 1H), 2 95 - 2.89 (m, 1H), 2.63 (br d, J= 2.4 Hz, 1H), 2.47 - 2.42 (m, 1H), 2.19 (s, 3H), 2.05 - 1.98 (m, 1H), 1.13 (d, J= 6.8 Hz, 6H). LC-MS (ESI) m/z 555.3 [M+H]+
Step E. Preparation of Int 38e
Figure imgf000359_0001
To a solution of l-((4-(benzyloxy)-2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)-3- (3-isopropyl-4-methylphenyl)urea, Int 38d (300 mg, 541 μmol, 1.00 eq) and (9//-fluoren-9- yl)methyl (5)-(7-benzyl-l-chloro-3,6,9,12-tetraoxo-2,5,8,l l-tetraazatridecan-13-yl)carbamate (656 mg, 1 08 mmol, 2 00 eq) in tetrahydrofuran (10 0 mL) was added silver carbonate (447 mg, 1.62 mmol, 73.6 μL, 3.00 eq). The mixture was stirred at 60 °C for 1 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase HPLC (0. 1% formic acid condition). The desired fraction was collected and lyophilized to give (9H-fluoren-9-yl) methyl ((95)-9-benzyl-2-((4-(benzyloxy)-2-(2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)-l-((3-isopropyl-4-methylphenyl)amino)- l,5,8,l l,14-pentaoxo-2,4,7,10,13-pentaazapentadecan-15-yl)carbamate, Int 38e (100 mg, 88.9 μmol, 16% yield). ‘HNMR (400 MHz, DMSO-d6) δ = 11.00 (br s, 1H), 9.37 - 9.28 (m, 1H), 8.87 (br d, J= 5.2 Hz, 1H), 8.43 (br d, J= 6.4 Hz, 1H), 8.15 (br d, J= 8.4 Hz, 1H), 8.02 - 7.97 (m, 1H), 7.88 (d, J= 7.6 Hz, 2H), 7.69 (br d, J= 7.2 Hz, 2H), 7.57 - 7.52 (m, 3H), 7.46 (d, J = 7.6 Hz, 1H), 7.43 - 7.38 (m, 5H), 7.34 - 7.28 (m, 5H), 7.23 - 7.21 (m, 4H), 7.16 (br d, J= 2.0 Hz, 1H), 6.96 (d, J= 8.0 Hz, 1H), 5.23 (s, 2H), 5.13 (dd, J= 5.2, 12.8 Hz, 1H), 4.74 (br d, J= 6.4 Hz, 2H), 4.71 (br d, J= 3.6 Hz, 2H), 4.55 - 4.49 (m, 2H), 4.29 - 4.26 (m, 2H), 4.22 (br d, J= 6.4 Hz, 1H), 3.77 (br t, J= 5.6 Hz, 2H), 3.72 (br d, J= 5.2 Hz, 1H), 3 60 (br d, J= 5.6 Hz, 2H), 3.09 - 2.89 (m, 4H), 2.76 (br s, 2H), 2.59 (br s, 1H), 2.45 - 2.41 (m, 1H), 2.19 (s, 3H), 2.02 - 1.96 (m, 1H), 1 .09 (d, - 6.8 Hz, 6H). LC-MS (ESI) m/z 1124.5 [M UI]
Step F. Preparation of Int 38f
Figure imgf000360_0002
To a solution of (9Z7-fluoren-9-yl)methyl ((9SS-9-benzyl-2-((4-(benzyloxy)-2-(2,6- dioxopiperidin-3-yl)- 1 -oxoisoindolin-5-yl)methyl)- 1 -((3-isopropyl-4-methylphenyl)amino)- l,5,8,H,14-pentaoxo-2,4,7,10,13-pentaazapentadecan-15-yl)carbamate Int 38e (80.0 mg, 71.2 μmol, 1 00 eq) in dichloromethane (5.00 mL) was added boron trichloride (1 M, 712 μL, 10.0 eq). The mixture was stirred at 0 °C for 1 h. The reaction mixture was diluted water (20 0 mL). The mixture was extracted with ethyl acetate (3 x20 mL). The combined organic extracts were washed with brine (20.0 mL), dried over sodium sulfate and filtered. The filtrate was purified by reversed-phase HPLC (0.1% formic acid condition). The desired fraction was collected and lyophilized to give (9H-fluoren-9-yl)methyl ((95)-9-benzyl-2-((2-(2,6-dioxopiperidin-3-yl)-4- hydroxy-l-oxoisoindolin-5-yl)methyl)-l-((3-isopropyl-4-methylphenyl)amino)-l,5,8,l l,14- pentaoxo-2,4,7,10,13-pentaazapentadecan-15-yl)carbamate, Int 38f (30.0 mg, 29.0 μmol, 41% yield) as a white solid. LC-MS (ESI) m/z 1034.8 [M+H]+
Step G. Preparation of Int 38g
Figure imgf000360_0001
To a solution of (9/7-fluoren-9-yl)methyl ((9S)-9-benzyl-2-((2-(2,6-dioxopiperidin-3-yl)-4- hydroxy-l-oxoisoindolin-5-yl)methyl)-l-((3-isopropyl-4-methylphenyl)amino)-l,5,8,l l,14- pentaoxo-2,4,7,10,13-pentaazapentadecan-15-yl)carbamate Int 38f (50.0 mg, 48.4 μmol, 1.00 eq) in piperidine (0.500 mL) and dimethyl formamide (2.50 mL) The mixture was stirred at 25 °C for 0.5 h. The mixture was filtered. The filtrate was purified by /vcy-HPLC (column: Phenomenex luna Cl 8 150*25mm* lOum; mobile phase: [water (formic acid) - acetonitrile]; gradient:24%-54% B over 10 min). The desired fraction was collected and lyophilized to give (25)-2-(2-(2-aminoacetamido) acetamido)-2V-(2-(((l-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l- oxoisoindolin-5-yl)methyl)-3-(3-isopropyl-4-methylphenyl)ureido)methyl)amino)-2-oxoethyl)- 3-phenylpropanamide, Int 38g (20.0 mg, 24.6 μmol, 51% yield). LC-MS (ESI) m/z 812.6 [M+H]+
Step H. Preparation of Compound IG-L-38
Figure imgf000361_0001
To a solution of (25)-2-(2-(2-aminoacetamido)acetamido)-JV-(2-(((l-((2-(2,6- dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5-yl)methyl)-3-(3 -isopropyl-4- methylphenyl)ureido)methyl)amino)-2-oxoethyl)-3-phenylpropanamide, Int 38g (20.0 mg, 24.6 μmol, 1 00 eq) and 34-(3-(2,5-dioxo-2,5-dihydro-l/7-pyrrol-l-yl)-2-fluoro-6-(3-oxo-3-(2,3,5,6- tetrafluorophenoxy)propyl)phenoxy)-3,6,9, 12,15, 18,21,24,27,30-decamethyl- 4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid, Int 36k (30.2 mg, 24.6 μmol, 1.00 eq) in dimethyl formamide (2 00 mL) was added triethylamine (7.48 mg, 73 9 μmol, 10.3 μL, 3.00 eq). The mixture was stirred at 25 °C for 0.5 h The mixture was filtered The filtrate was purified by prep-HPLC (column: Phenomenex luna C1 8 150*25mm* lOum; mobile phase: [water (formic acid) - acetonitrile]; gradient:25%- 55% B over 20 min). The desired fraction was collected and lyophilized to give 34-(6-((9S)-9- benzyl-2-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5-yl)methyl)-l-((3-isopropyl- 4-methylphenyl)amino)- 1,5,8,11,14, 17-hexaoxo-2,4, 7, 10,13,16-hexaazanonadecan- 19-yl)-3- (2, 5-dioxo-2,5-dihydro-12/-pyrrol-l-yl)-2-fluorophenoxy)-3, 6, 9, 12,15,18,21,24,27,30- decamethyl-4,7,10,13, 16, 19,22,25,28, 31-decaoxo-3,6,9,12,15,18,21,24,27,30- decaazatetratriacontanoic acid, Compound IG-L-38 (16.49 mg, 8.73 μmol, 35% yield, 99% purity) as a white solid. 1H NMR (400 MHz, DMSCM,) 6 - 12.74 (s, 1H), 10.97 (s, 1H), 10.68 (br s, 1H), 9 75 - 9 62 (m, 1H), 9 14 - 9 02 (m, 1H), 8 55 - 8 44 (m, 1H), 8 25 - 8 03 (m, 3H), 7.44 (br d, J= 7.6 Hz, 1H), 7.26 - 7.22 (m, 8H), 7.19 - 7.14 (m, 2H), 7.13 - 7.09 (m, 1H), 7.04 - 6.98 (tn, 2H), 5.09 (dd, J= 4 8, 13.2 Hz, 1H), 4.64 (br d, J= 4.8 Hz, 2H), 4.51 (br s, 3H), 4.36 - 4.17 (m, 12H), 4.11 - 3.91 (m, 13H), 3.85 - 3.62 (m, 6H), 3.03 (br d, J= 6.8 Hz, 1H), 2.96 - 2.71 (m, 37H), 2.61 (br d, J= 2.8 Hz, 2H), 2.45 (br d, J= 0.8 Hz, 1H), 2.20 (s, 3H), 2.03 - 1.87 (m, 3H), 1.10 (d, J= 6.8 Hz, 6H). LC-MS (ESI) m/z 1870.7 [M+2H]
The compounds in Table 17 were prepared in a manner similar to that described for Compound IG-L-38 using the appropriate compound as starting material.
Table 17
Figure imgf000363_0001
Figure imgf000364_0001
Figure imgf000365_0001
Figure imgf000366_0001
EXAMPLE L-40: Synthesis of 34-(6-((7S)-7-benzyl-l-(3-(4-hydroxy-l-oxo-5-((3-(3-(l- (trifluoromethyl)cyclopropyl)phenyl)ureido)methyl)isoindolin-2-yl)-2,6-dioxopiperidin-l-yl)- 3,6,9,12,15-pentaoxo-2,5,8,l l,14-pentaazaheptadecan-17-yl)-3-(2,5-dioxo-2,5-dihydro-lH- pyrrol-l-yl)-2-fluorophenoxy)-3,6,9,12,15,18,21,24,27,30-decamethyl- 4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid,
IG-L-40
Figure imgf000367_0001
Figure imgf000368_0001
Compound IG-L-40
Step A. Preparation of Int 40a
To a solution of l-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5-yl)methyl)-3-(3- (l-(trifluoromethyl)cyclopropyl)phenyl)urea, IG-50 (1.70 g, 3.29 mmol, 1.00 eq) in dimethyl formamide (20.0 mL) were added silver oxide (3.81 g, 16.5 mmol, 5.00 eq) and benzyl bromide (1.41 g, 8.23 mmol, 977 μL, 2.50 eq). The mixture was stirred at 25 °C for 2 h under darkness The reaction mixture was filtered to give filtrate. The filtrate was purified by reversed-phase HPLC (0.1% formic acid) and lyophilized to give l-((4-(benzyloxy) -2-(2,6-dioxopiperidin-3- yl)-l-oxoisoindolin-5-yl)methyl)-3-(3-(l-(trifluoromethyl)cyclopropyl)phenyl)urea, Int 40a (700 mg, 1.15 mmol, 35% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-fifc) δ = 11.01 (s,
1H), 8.77 (s, 1H), 7.60 (s, 1H), 7.54 (br d, J= 7.2 Hz, 2H), 7.48 - 7.35 (m, 6H), 7.23 - 7 20 (m, 1H), 6.99 (br d, J= 7.6 Hz, 1H), 6.61 (br t, J= 5.6 Hz, 1H), 5.23 (s, 2H), 5.15 - 5.10 (m, 1H), 4.70 - 4 65 (m, 1H), 4.56 - 4.49 (m, 1H), 4.47 - 4.37 (m, 2H), 2.98 - 2.90 (m, 1H), 2.62 (br d, J= 17.2 Hz, 1H), 2.49 - 2.42 (m, 1H), 2.03 - 1.97 (m, 1H), 1.33 - 1.28 (m, 2H), 1.07 (br s, 2H). MS (ESI) m/z 607.2 [M+H]+
Step B. Preparation of Int 40b
Figure imgf000369_0001
Int 40b
To a solution of tert-butyl carbamate (3.00 g, 25.6 mmol, 1.00 eq) in water (40.0 mb) and methanol (40.0 mL) were added sodium benzene sulfinate (8.41 g, 51.2 mmol, 2.00 eq), carbinol (20.0 mL), formic acid (3.08 g, 64.0 mmol, 2.50 eq) and formaldehyde (1.54 g, 51.2 mmol, 1.41 mL, 2.00 eq). The mixture was stirred at 25 °C for 12 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 3/1). The desired fraction was concentrated under reduced pressure to give tert-butyl ((phenylsulfonyl)methyl)carbamate, Int 40b (4.50 g, 16.4 mmol, 64% yield, 99% purity) as a white solid 1 H NMR (400 MHz, DMSO-ufc) δ = 8.06 (br t, J = 6.8 Hz, 1H), 7.82 (br d, J= 7.6 Hz, 2H), 7.75 - 7 70 (m, 1H), 7.66 - 7.60 (m, 2H), 4.50 (d, J= 6.8 Hz, 2H), 1.22 (s, 9H). MS (ESI) m/z 294 0 [M+Na]+
Step C. Preparation of Int 40c
To a solution of l-((4-(benzyloxy)-2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)-3- (3-(l-(trifluoromethyl)cyclopropyl)phenyl)urea, Int 40a (450 mg, 742 umol, 1.00 eq) in dimethyl formamide (10.0 mL) were added tert-butyl ((phenylsulfonyl)methyl)carbamate, Int 40b (221 mg, 816 μmol, 1.10 eq) and cesium carbonate (483 mg, 1.48 mmol, 2.00 eq). The mixture was stirred at 25 °C for 2 h. The reaction mixture was filtered to give filtrate. The filtrate was purified by reversed-phase HPLC ( 0.1% formic acid) and lyophilized to give tertbutyl ((3-(4-(benzyloxy)-l-oxo-5-((3-(3-(l-(trifluoromethyl)cyclopropyl)phenyl)ureido)methyl) soindolin-2-yl)-2,6-dioxopiperidin-l-yl)methyl)carbamate, Int 40c (300 mg, 408 μmol, 55% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6) δ = 8.77 (s, 1H), 7.60 (br s, 1H), 7.52 (br d, J= 7.2 Hz, 2H), 7.49 - 7.33 (m, 6H), 7.23 (br d, J= 7.6 Hz, 1H), 6.99 (br d, J= 7.2 Hz, 2H), 6.61 (br t, J= 5.6 Hz, 1H), 5.27 - 5.16 (m, 3H), 4.98 (br dd, J= 5.6, 12.4 Hz, 1H), 4.91 - 4.84 (m, 1H), 4.67 (br d, J= 17.2 Hz, 1H), 4.53 - 4.37 (m, 3H), 3.05 - 2.94 (m, 1H), 2.78 (br d, J= 17.2 Hz, 1H), 2.43 - 2.33 (m, 1H), 2.06 - 2.00 (m, 1H), 1.35 (s, 9H), 1.33 - 1.27 (m, 2H), 1.07 (br s, 2H). MS (ESI) m/z 680.2 [M+H-56]+
Step D. Preparation of Int 40d
To a solution of tert-butyl ((3-(4-(benzyloxy)-l-oxo-5-((3-(3-(l- (trifluoromethyl)cyclopropyl)phenyl)ureido) methyl)isoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methyl)carbamate, Int 40c (300 mg, 408 prnol, 1.00 eq) in dioxane (2.00 mL) was added hydrochloric acid/dioxane (10.0 mL). The mixture was stirred at 25 °C for 2 h. The reaction mixture was concentrated under reduced pressure to give l-((2-(l-(aminomethyl)-2,6- dioxopiperidin-3-yl)-4-(benzyloxy)-l-oxoisoindolin-5-yl)methyl)-3-(3-(l-
(trifluoromethyl)cyclopropyl)phenyl)urea, Int 40d (250 mg, crude) as white solid MS (ESI) m/z 636.3 [M+H]+
Step E. Preparation of Int 40e
To a solution of (((977-fluoren-9-yl)methoxy)carbonyl)glycine (15.0 g, 50.5 mmol, 1.00 eq) in dichloromethane (300 mL) was added 2-Chlorotritylchlorideresin (60.0 g) and N,N- diisopropylethylamine (16.3 g, 126 mmol, 22.0 mL, 2.50 eq). Then deprotection and acid-amine condensation in turn by solid-phase synthesis (((9/f-fluoren-9-yl)methoxy)carbonyl)-Z- phenylalanine (29.0 g, 74.9 mmol, 1.50 eq) and (((9/f-fluoren-9- yl)methoxy)carbonyl)glycylglycine (9.50 g, 46.3 mmol, 1.00 eq) were be used for the acid- amine condensation. Condition of acid-amine condensation: <9-(7-Azabenzotriazol-l-yl)-N,N,N,N ’,N’-tetramethyluronium Hexafluorophosphate (1.80 eq), A)JV-diisopropylethylamine (3.00 eq), dimethyl formamide (150 mL), 25 °C for 2 h. Condition of deprotection: a. dimethyl formamide (100 mL) / piperidine (100 mL), 25 °C for 5 min; b. dichloromethane (160 mL) I hexafluoroisopropanol (40.0 mL), 25 °C for 1 h to give (((9//-fluoren-9- yl)methoxy)carbonyl)glycylglycyl-Z-phenylalanylglycine, Int 40e (13.0 g, 23.3 mmol, 50% yield) as a white solid MS (ESI) m/z 559 2 [M+H]+
Step F. Preparation of Int 40f
To a solution of l-((2-(l-(aminomethyl)-2,6-dioxopiperidin-3-yl)-4-(benzyloxy)-l- oxoisoindolin-5-yl)methyl)-3-(3-(l-(trifluoromethyl)cyclopropyl)phenyl)urea, Int 40d (250 mg, 393 μmol, 1.00 eq) in dimethyl formamide (3.00 mL) were added (((9/7-fluoren-9- yl)methoxy)carbonyl)glycylglycyl-Z-phenylalanylglycine, Int 53e (220 mg, 393 μmol, 1.00 eq), triethylamine (79.6 mg, 787 μmol, 109 μL, 2.00 eq) 3-(ethyliminomethylideneamino)propyl- dimethylazanium;chloride (113 mg, 590 μmol, 1.50 eq) and l//-benzo[<7][l,2,3]triazol-l-ol (79.7 mg, 590 μmol, 1.50 eq). The mixture was stirred at 25 °C for 1 h. The reaction mixture was filtered to give a filtrate. The filtrate was purified by reversed-phase HPLC (0. 1% formic acid) and lyophilized to give (9/7-fluoren-9-yl)methyl ((75)-7-benzyl-l-(3-(4-(benzyloxy)-l-oxo-5- ((3-(3-(l-(trifluoromethyl)cyclopropyl)phenyl)ureido)methyl)isoindolin-2-yl)-2,6- dioxopiperidin-l-yl)-3,6,9,12-tetraoxo-2,5,8,l l-tetraazatridecan-13-yl)carbamate, Int 40f (240 mg, 204 μmol, 52% yield) as a white solid. 1 H NMR (400 MHz, DMSO-tfe) d = 8.95 (s, 1H), 8.38 (br t, J= 5.2 Hz, 1H), 8.32 - 8.21 (m, 2H), 8.13 (br d, J= 4.4 Hz, 1H), 8.01 (d, J= 7.6 Hz, 2H), 7.83 (br d, J= 7.2 Hz, 2H), 7.74 - 7.69 (m, 2H), 7.65 (br d, J= 7.2 Hz, 2H), 7.63 - 7.58 (m, 2H), 7.57 - 7.50 (m, 5H), 7.48 - 7.42 (m, 3H), 7.38 - 7.33 (m, 5H), 7.30 (br d, J= 6.4 Hz, 1H), 7.12 (d, J= 7.6 Hz, 1H), 6.78 (br t, J= 5.6 Hz, 1H), 5.37 - 5 29 (m, 4H), 5.12 (td, J= 6.0, 12.4 Hz, 1H), 4.85 - 4.78 (m, 1H), 4.69 - 4.60 (m, 2H), 4.55 (br d, J= 5.2 Hz, 2H), 4.46 - 4.38 (m, 2H), 4.36 (br d, J= 6.4 Hz, 1H), 3.90 - 3.72 (m, 6H), 3.19 - 3.11 (m, 2H), 2.97 - 2.86 (m, 2H), 2.60 - 2.50 (m, 1H), 2.21 - 2.13 (m, 1H), 1.47 - 1.39 (m, 2H), 1.20 (br s, 2H). MS (ESI) m/z 1176.4 [M+H]+
Step G. Preparation of Int 40g
To a solution of (9//-fluoren-9-yl)methyl ((7S)-7-benzyl-l-(3-(4-(benzyloxy)-l-oxo-5-((3-(3-(l- (trifluoromethyl)cyclopropyl)phenyl) ureido)methyl)isoindolin-2-yl)-2,6-dioxopiperidin-l-yl)- 3,6,9,12-tetraoxo-2,5,8,l l-tetraazatridecan-13-yl)carbamate, Int 40f (240 mg, 204 μmol, 1.00 eq) in dichloromethane (5 00 mL) was added boron trichloride (2 M, 1 02 mb, 10 0 eq) at 0 °C The mixture was stirred at 25 °C for 0.5 h. The reaction mixture was quenched by addition water (5 mL) at 0 °C and filtered to give (9//-fluoren-9-yl)m ethyl ((75)-7-benzyl-l-(3-(4- hydroxy-l-oxo-5-((3-(3-(l-(trifluoromethyl)cyclopropyl) phenyl)ureido) methyl)isoindolin-2- yl)-2,6-dioxopiperidin-l-yl)-3,6,9,12-tetraoxo-2,5,8,l l-tetraazatridecan-13-yl)carbamate, Int 40g (200 mg, crude) as white solid. MS (ESI) m/z 1086.4 [M+H]+
Step H. Preparation of Int 40h
To a solution of (97/-fluoren-9-yl)m ethyl ((75)-7-benzyl-l-(3-(4-hydroxy-l-oxo-5-((3-(3-(l- (trifluoromethyl)cyclopropyl)phenyl)ureido)methyl)isoindolin-2-yl)-2,6-dioxopiperidin-l-yl)- 3,6,9,12-tetraoxo-2,5,8,l l-tetraazatridecan-13-yl)carbamate, Int 40g (200 mg, 184 μmol, 1 00 eq) in dimethyl formamide (2.00 mL) was added piperidine (0.500 mL). The mixture was stirred at 25 °C for 0.5 h. The reaction mixture was filtered. The filtrate was purified by /wc/i-HPLC (column: Phenomenex luna C1 8 150 * 25 mm * 10 um; mobile phase: [water(formic acid) - acetonitrile]; gradient: 18% - 48% B over 9 min) and lyophilized to give (25)-2-(2-(2- aminoacetamido)acetamido)-/V-(2-(((3-(4-hydroxy-l-oxo-5-((3-(3-(l -(tri fluoromethyl) cyclopropyl)phenyl)ureido)methyl)isoindolin-2-yl)-2,6-dioxopiperidin-l-yl)methyl)amino)-2- oxoethyl)-3-phenylpropanamide, Int 40h (60.0 mg, 69.5 umol, 38% yield) as a white solid. 'l l NMR (400 MHz, DMSO-d6) 3 = 9.09 (s, 1H), 8.39 - 8.28 (m, 2H), 8.28 - 8.11 (m, 3H), 7.62 (s, 1H), 7.40 (br d, J= 7.2 Hz, 2H), 7.30 - 7.21 (m, 7H), 7.04 (br d, J= 12 Hz, 2H), 5.25 - 5.15 (m, 2H), 5.07 - 4.97 (m, 1H), 4.59 - 4.50 (m, 1H), 4.45 - 4.36 (m, 3H), 4.32 - 4.25 (m, 1H), 3.85 - 3.65 (m, 6H), 3.24 (s, 2H), 3 09 - 3.02 (m, 2H), 2.85 - 2.72 (m, 2H), 2.38 (br d, J= 8.8 Hz, 1H), 2.12 - 2.06 (m, 1H), 1.38 - 1.32 (m, 2H), 1.11 (br s, 2H). MS (ESI) m/z 864.3 [M+H]+
Step I. Preparation of Compound IG-L-40
To a solution of (25)-2-(2-(2-aminoacetamido)acetamido)-/V-(2-(((3-(4-hydroxy-l-oxo-5-((3-(3- (l-(trifluoromethyl)cyclopropyl)phenyl)ureido)methyl)isoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methyl)amino)-2-oxoethyl)-3-phenylpropanamide, Int 40h (30.0 mg, 34.7 nmol, 1.00 eq) in dimethyl formamide (1.00 mL) were added triethylamine (10.5 mg, 104 μmol, 14.5 μL, 3.00 eq) and 34-(3-(2,5-dioxo-2,5-dihydro-l//-pyrrol-l-yl)-2-fluoro-6-(3-oxo-3-(2,3,5,6- tetrafluorophenoxy)propyl)phenoxy)-3,6,9, 12,15, 18,21,24,27,30-decamethyl- 4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid, Int 36k (42.5 mg, 34.7 μmol, 1.00 eq). The mixture was stirred at 25 °C for 0.5 h. The reaction mixture was filtered. The filtrate was purified by p/rp-HPLC (column: UniSil 3 - 100 C1 8 Ultra (150 * 25 mm * 3 um); mobile phase: [water(formic acid) - acetonitrile]; gradient:20%-50% B over 40 min) and lyophilized to give 34-(6-((75)-7-benzyl-l-(3-(4-hydroxy-l-oxo-5-((3-(3-(l- (trifluoromethyl)cyclopropyl)phenyl) ureido)methyl) isoindolin-2-yl)-2,6-dioxopiperidin-l-yl)- 3,6,9,12,15-pentaoxo-2,5,8,ll,14-pentaazaheptadecan-17-yl)-3-(2,5-dioxo-2,5-dihydro-lH- pyrrol-l-yl)-2-fluorophenoxy)-3,6,9,12,15,18,21,24,27,30-decamethyl-4,7,10,13, 16,19,22,25, 28,3 l-decaoxo-3,6,9, 12, 15,18,21,24,27,30-decaazatetratriacontanoic acid, Compound IG-L-40 (22.93 mg, 11.8 μmol, 34% yield, 99% purity) as a white solid. 1H NMR (400 MHz, DMSO-<U) δ = 10.62 - 10.01 (m, 1H), 9.15 - 8.89 (m, 1H), 8.30 - 8.01 (m, 5H), 7.58 (br s, 1H), 7.38 - 7.33 (m, 2H), 7.27 - 7.11 (m, 10H), 7.06 - 6.99 (m, 2H), 6.95 - 6.84 (m, 1H), 5.23 - 5.11 (m, 2H), 4.99 (dt, J= 5.2, 13.2 Hz, 1H), 4.53 - 4.46 (m, 1H), 4.39 - 3.87 (m, 27H), 3.79 - 3.67 (m, 5H), 3.59 (br dd, J= 5.4, 16.8 Hz, 1H), 3.05 - 2.70 (m, 38H), 2.37 - 2.21 (m, 2H), 2.07 - 2.00 (m, 1H), 1.98 - 1.86 (m, 2H), 1.35 - 1.29 (m, 2H), 1.07 (br s, 2H). MS (ESI) m/z 1922.6 [M+2H]
The compounds in Table 18 were prepared in a manner similar to that described for Compound IG-L-40 using the appropriate compound as starting material.
Table 18
Figure imgf000373_0001
Figure imgf000374_0001
Figure imgf000375_0001
Figure imgf000376_0001
Figure imgf000377_0001
EXAMPLE L-44: Synthesis of 34-(3-(2,5-dioxo-2,5-dihydro-lH-pyrrol-l-yl)-6-(3-(((2S)-l- (((2S)-l-((4-((((2-((((2-(2,6-dioxopiperidin-3-yl)-5-((3-(3-isopropyl-4- methylphenyl)ureido)methyl)-l-oxoisoindolm-4- yl)oxy)carbonyl)(methyl)amino)ethyl)(methoxy)carbamoyl)oxy)methyl)phenyl)amino)-l- oxopropan-2-yl)amino)- 1 -oxopropan-2-yl)amino)-3-oxopropyl)-2-fluorophenoxy)-
3.6.9.12.15.18.21.24.27.30-decamethyl-4,7,10,13,16,19,22,25,28,31-decaoxo-
3.6.9.12.15.18.21.24.27.30-decaazatetratri acontanoic acid, IG-L-44
Figure imgf000378_0001
Figure imgf000379_0001
Step A. Preparation of Int 54a
Figure imgf000379_0002
Int 44a
To a solution of (((9//-fluoren-9-yl)methoxy)carbonyl)-Z-alanyl-Z-alanine (20.0 g, 52.3 mmol, 1.00 eq) and (4-aminophenyl)methanol (7.73 g, 62.8 mmol, 1.20 eq) in dichloromethane (300 mL) and methanol (300 mL) was added (97T-fluoren-9-yl)m ethyl ((5)-3-methyl-l-(((5)-l-((4- ((((4-nitrophenoxy)carbonyl)oxy) methyl)phenyl)amino)-l-oxo-5-ureidopentan-2-yl)amino)-l- oxobutan-2-yl)carbamate (38.8 g, 157 mmol, 3.00 eq), the mixture was stirred at 25°C for 12 h. The mixture concentrated in vacuum to give a residue. The residue was triturated with tetrahydrofuran (300 mL) and filtered to afford (9H-fluoren-9-yl)m ethyl ((5)-l-(((5)-l-((4- (hydroxymethyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl)carbamate, Int 44a (18.0 g, 36.9 mmol, 71% yield) as a yellow solid 1H NMR (400 MHz, D\fSO-Lj d = 9.89 (s, 1H), 8.11 (br d, J = 7.3 Hz, 1H), 7.90 (d, J = 7.5 Hz, 2H), 7.73 (br t, J = 8.1 Hz, 2H), 7.59 - 7.53 (m, 3H), 7.42 (br t, J = 7.4 Hz, 2H), 7.37 - 7.31 (m, 2H), 7.24 (d, J = 8.4 Hz, 2H), 5.11 (t, J = 5.7 Hz, 1H), 4.48 - 4.39 (m, 3H), 4.30 - 4.21 (m, 3H), 4.15 - 4 06 (m, 1H), 1.31 (d, J = 7.1 Hz, 3H), 1.25 (d, J = 7.1 Hz, 3H).
Step B. Preparation of Int 44b
Figure imgf000380_0001
Int 44a
Int 44b
To a solution of (9//-fluoren-9-yl)m ethyl ((S)-l-(((S)-l-((4- (hydroxymethyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl)carbamate Int 44a (4.20 g, 8.61 mmol, 1.00 eq) and bis(4-nitrophenyl) carbonate (2.62 g, 8.61 mmol, 1.00 eq) in ACV-dimethylformamide (20.0 mL) was added diisopropylethylamine (3.34 g, 25.8 mmol, 4.50 mL, 3.00 eq). The mixture was stirred at 25 °C for 1 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (Cl 8, 220 g; condition: water/ acetonitrile = 1/0 -0/1, 0. l%formic acid) and lyophilized to afford (977- fluoren-9-yl)methyl ((5)- 1 -(((5)- 1 -((4-((((4-nitrophenoxy)carbonyl)oxy)methyl)phenyl)amino)- l-oxopropan-2-yl)amino)-l-oxopropan-2-yl)carbamate Int 44b (3.15 g, 4.83 mmol, 56% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6) 3 = 10.04 (s, 1H), 8.38 - 8.24 (m, 2H), 8.13 (br d, J= 7.2 Hz, 1H), 7.88 (d, J= 7.2 Hz, 2H), 7 72 (br t, J= 7.6 Hz, 2H), 7.64 (br d, J= 8.4 Hz, 2H), 7 59 - 7 52 (m, 3H), 7 44 - 7 38 (m, 4H), 7 35 - 7 29 (m, 2H), 5 24 (s, 2H), 4 46 - 4 34 (m, 1H), 4.30 - 4.18 (m, 3H), 4.12 - 4.06 (m, 1H), 1.31 (d, J= 7.2 Hz, 3H), 1.23 (br d, J= 7.2 Hz, 3H).
Step C. Preparation of Int 44c
Figure imgf000381_0002
Int 44c
To a solution of (9-methylhydroxylamine (1.45 g, 17.3 mmol, 1.32 mL, 1.50 eq) in dichloromethane (20.0 mL) were added diisopropylethylamine Int 44b (4.48 g, 34.6 mmol, 6.03 mL, 3.00 eq) and tert-butyl methyl(2-oxoethyl)carbamate (2.00 g, 11.6 mmol, 1.00 eq). The mixture was stirred at 25 °C for 12 h. Then the mixture was concentrated to afford a residue. The residue was dissolved in acetic acid (5.00 mL) and dichloromethane (20.0 mL), then sodium cyanoborohydride (1.09 g, 17.3 mmol, 1.50 eq) was added to the mixture at 0 °C. The mixture was stirred at 25 °C for 5 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO2. petroleum ether/ethyl acetate=l/0 to 2/1) to afford tert-butyl (2-(methoxyamino)ethyl)(methyl)carbamate Int 44c (1.40 g, 4.80 mmol, 41% yield, 70% purity) as yellow oil. 1H NMR (400 MHz, DMSO-tsfc) δ = 6.77 - 6.20 (m, 1H), 3.38 (s, 3H), 3.24 (t, J= 6.4 Hz, 2H), 2.85 (br t, J= 6.4 Hz, 2H), 2.78 (br s, 3H), 1.38 (s, 9H).
Step D. Preparation of Int 44d
Figure imgf000381_0001
To a solution of tert-butyl (2-(methoxyamino)ethyl)(methyl)carbamate Int 44c (400 mg, 1.37 mmol, 1.00 eq) and (9//-fluoren-9-yl)methyl ((5)-l-(((5)-l-((4-((((4- nitrophenoxy)carbonyl)oxy)methyl)phenyl)amino)- 1 -oxopropan-2-yl)amino)- 1 -oxopropan-2- yl)carbamate Int 44b (895 mg, 1.37 mmol, 1.00 eq) in .V,/V-dimethylformamide (10.0 mL) were added 1 -hydroxybenzotri azole (370 mg, 2.74 mmol, 2.00 eq) and diisopropylethylamine (531 mg, 4 11 mmol, 716 μL, 3.00 eq) at 0 °C. The mixture was stirred at 25 °C for 12 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (C1 8, 120 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1%formic acid) and lyophilized to afford 4-((5)-2-((S)-2-((((9H-fluoren-9- yl)methoxy)carbonyl)amino)propanamido) propanamido)benzyl (2-((tert- butoxycarbonyl)(methyl)amino)ethyl)(methoxy)carbamate Int 44d (593 mg, 496 μmol, 36% yield, 60% purity) as a white solid. MS (ESI) m/z 740.4 [ M+Na |
Step E. Preparation of Int 44e
Figure imgf000382_0001
Int 44d Int 44e
To a solution of 4-((S)-2-((5)-2-((((9Z/-fluoren-9- yl)methoxy)carbonyl)ammo)propanamido)propanamido) benzyl (2-((lerl- butoxycarbonyl)(methyl)amino)ethyl)(methoxy)carbamate Int 44d (593 mg, 496 μmol, 1.00 eq) in dichloromethane (10.0 mL) was added trifluoroacetic acid (1.54 g, 13.5 mmol, 1.00 mL, 27.2 eq) at 0 °C. The mixture was stirred at 0 °C for 0.5 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (Cl 8, 80 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1%formic acid) and lyophilized to afford 4-((5)-2- ((S)-2-((((9//-fluoren-9-yl)methoxy)carbonyl)amino)propanamido)propanamido)benzyl methoxy(2-(methylamino)ethyl)carbamate Int 44e (120 mg, 192 μmol, 39% yield, 99% purity) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) 8 = 10.07 - 9.98 (m, 1H), 8.31 (br s, 1H), 8.16 (br d, J= 6.8 Hz, 1H), 7.89 (d, J= 7.6 Hz, 2H), 7.72 (br t, J= 7.6 Hz, 2H), 7.60 (br d, J= 8.4 Hz, 2H), 7.44 - 7.38 (m, 2H), 7.36 - 7.29 (m, 4H), 5.06 (s, 2H), 4.40 (br t, J= 7.2 Hz, 1H), 4.29 - 4.19 (m, 3H), 4.12 - 4.06 (m, 1H), 3.60 (s, 3H), 3.57 (br t, J= 6.4 Hz, 2H), 2.74 (br t, J= 6.4 Hz, 2H), 2.32 (s, 3H), 1.31 (d, J= 7.2 Hz, 3H), 1.23 (br d, J= 7.2 Hz, 3H). MS (ESI) m/z 618.3 [M+H]+
Step F. Preparation of Int 44f
To a solution of l-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5- yl)methyl)-3-(3-isopropyl-4-methylphenyl)urea IG-50 (100 mg, 215 μmol, 1.00 eq) in N,N- dimethylformamide (2.00 mL) was added tri ethylamine (174 mg, 1.72 mmol, 239 μL, 8.00 eq) and 4-nitrophenyl carbonochloridate (65.1 mg, 323 μmol, 1.50 eq). The mixture was stirred at 0 °C for 0.5 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (Cl 8, 80 g; condition: water/ acetonitrile = 1/0 - 0/1, 0 1%formic acid) and lyophilized to afford 2-(2,6-dioxopiperidin-3-yl)-5-((3-(3-isopropyl- 4-methylphenyl)ureido)methyl)-l-oxoisoindolin-4-yl (4-nitrophenyl) carbonate Int 44f (100 mg,
79.4 μmol, 37% yield, 50% purity) as a white solid. MS (ESI) m/z 630.2 [M+H]+
Step G. Preparation of Int 44g
To a solution of 2-(2,6-dioxopiperidin-3-yl)-5-((3-(3-isopropyl-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-4-yl (4-nitrophenyl) carbonate Int 44f (80.0 mg,
63.5 μmol, 1.00 eq) and 4-((5)-2-((5)-2-((((9ff-fluoren-9- yl)methoxy)carbonyl)ammo)propanamido)propanamido)benzyl methoxy(2-(methylamino) ethyl)carbamate Int 44e (39.2 mg, 63.5 μmol, 1.00 eq) in A'./V-dimethylformamide (1.00 mL) was added diisopropyl ethyl amine (16.4 mg, 127 μmol, 22.1 μL, 2.00 eq). The mixture was stirred at 0 °C for 0.5 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by /7ey>-I IPLC (column: Phenomenex Luna C1 8 150*25mm* 10um;mobile phase: [water(formic acid)- acetonitrile], gradient: 50%-80% B over 10 min) and lyophilized to afford 4-((5)-2-((1$)-2-((((9/f-fluoren-9- yl)methoxy)carbonyl)amino)propanamido)propanamido)benzyl (2-((((2-(2,6-dioxopiperidin-3- yl)-5-((3-(3-isopropyl-4-methylphenyl)ureido)methyl)-l-oxoisomdolin-4- yl)oxy)carbonyl)(methyl)amino)ethyl) (methoxy)carbamate Int 44g (15.0 mg, 13.4 μmol, 21% yield, 99% purity) as a yellow solid. MS (ESI) m/z 1108.3 [M+H]+
Step H. Preparation Int 44h
To a solution of 4-((S)-2-((<S)-2-((((927-fluoren-9- yl)methoxy)carbonyl)ammo)propanamido)propanamido) benzyl(2-((((2-(2,6-dioxopiperidin-3- yl)-5-((3-(3-isopropyl-4-methylphenyl)ureido)methyl)-l-oxoisomdolin-4- yl)oxy)carbonyl)(methyl)amino)ethyl)(methoxy)carbamate Int 44g (15.0 mg, 13.5 μmol, 1.00 eq) in /v,.V-dimethylformamide (1.00 mL) was added piperidine (259 mg, 3.04 mmol, 0.300 mL, 224 eq). The mixture was stirred at 25 °C for 0.5 h. The mixture was adjusted with formic acid (50%) to pH=7 and concentrated to give a residue. The residue was purified by /wp-HPhC (column: Waters xbridge 150*25mm lOum; mobile phase: [water (ammonium bicarbonate) - acetonitrile]; gradient: 37% - 57% B over 8 min) and lyophilized to afford 4-((S)-2-((S)-2- ((((9B-fluoren-9-yl)methoxy)carbonyl)amino)propanamido) propanamido)benzyl (2-((((2-(2,6- dioxopiperidin-3-yl)-5-((3-(3-isopropyl-4-methylphenyl)ureido)methyl)-l-oxoisoindolin-4- yl)oxy)carbonyl)(methyl)amino)ethyl)(methoxy)carbamate Int 44h (5.00 mg, 5.59 μmol, 41% yield, 99% purity) as a white solid. MS (ESI) m/z 886.4 [M+H] Step I. Preparation of Compound IG-L-44
To a solution of 4-((S)-2-((5)-2-((((9ZZ-fluoren-9- yl)methoxy)carbonyl)amino)propanamido)propanamido) benzyl (2-((((2-(2,6-dioxopiperidin-3- yl)-5-((3-(3-isopropyl-4-methylphenyl)ureido)methyl)-l-oxoisoindolin-4- yl)oxy)carbonyl)(methyl)amino)ethyl)(methoxy)carbamate Int 44h (5.00 mg, 5.64 μmol, 1.00 eq) and 34-(3 -(2, 5 -dioxo-2, 5 -dihydro- 177-pyrrol- 1 -yl)-2-fluoro-6-(3 -oxo-3 -(2,3 ,5,6- tetrafluorophenoxy)propyl)phenoxy)-3,6,9, 12, 15, 18,21,24,27,30-decamethyl- 4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid (6.22 mg, 5 08 μmol, 0 900 eq) in AlA-dimethylformamide (0 500 mL) was added diisopropylethylamine (2.19 mg, 16.9 μmol, 2.95 μL, 3.00 eq). The mixture was stirred at 0 °C for 1 h The mixture was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (column: Phenomenex luna C18 150*25mm* lOum; mobile phase: [water (formic acid) - acetonitrile]; gradient: 25% - 55% B over 20 min) and lyophilized to afford 34-(3-(2,5-dioxo-2,5-dihydro-l^-pyrrol-l-yl)-6-(3-(((2A)-l-(((25)-l-((4-((((2-((((2-(2, 6- dioxopiperidin-3-yl)-5-((3-(3-isopropyl-4-methylphenyl)ureido)methyl)-l-oxoisoindolin-4- yl)oxy)carbonyl)(methyl)amino)ethyl)(methoxy)carbamoyl)oxy)methyl)phenyl)amino)-l- oxopropan-2-yl)amino)-l-oxopropan-2-yl)amino)-3-oxopropyl)-2-fluorophenoxy)- 3 ,6,9, 12, 15, 18,21 ,24,27,3 O-decamethyl-4,7, 10, 13 , 16, 19,22,25,28,31-decaoxo- 3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid, compound IG-L-44 (1.29 mg, 0.61 μmol, 11% yield, 92% purity) as a white solid. XH NMR (400 MHz, DMSO-cA) δ = 10.99 (br s, 1H), 10.08 (br s, 1H), 9.13 (br s, 1H), 8.49 - 8.08 (m, 3H), 7.63 - 7.48 (m, 4H), 7.29 (br d, J= 7.6 Hz, 2H), 7.24 (s, 3H), 7.17 - 7.09 (m, 2H), 7.06 - 6.99 (m, 1H), 6 93 (br d, J= 8.8 Hz, 1H), 5.14 - 5.01 (m, 3H), 4.39 - 3.88 (m, 30H), 3.69 - 3.58 (m, 6H), 3.17 (d, J= 5.2 Hz, 4H), 3.06 (br s, 2H), 2.98 - 2.70 (m, 36H), 2.18 (s, 3H), 1.99 - 1.89 (m, 3H), 1.30 (br d, J= 5.4 Hz, 3H), 1.19 (br d, J= 7.2 Hz, 3H), 1.12 (br d, J= 6.4 Hz, 6H). MS (ESI) m/z 972.8 [M/2+H]+
EXAMPLE L-45: Synthesis of 34-(6-(3-(((2S)-l-(((2S)-l-((4-((((2-(4-(3-((2-(l-(((((4- (((2S,3R,4S,5S,6S)-6-carboxy-3,4,5-trihydroxytetrahydro-2H-pyran-2- yl)oxy)benzyl)oxy)carbonyl)amino)methyl)-2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)methyl)ureido)-2-chlorophenethoxy)ethyl)(methyl)carbamoyl)oxy)methyl)phenyl)amino)-l- oxopropan-2-yl)amino)-l-oxopropan-2-yl)amino)-3-oxopropyl)-3-(2,5-dioxo-2,5-dihydro-lH- pyrrol-l-yl)-2-fluorophenoxy)-3,6,9,12,15,18,21,24,27,30-decamethyl- 4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid, IG-L-45
Figure imgf000385_0001
Figure imgf000386_0001
Compound IG-L-45
Step A. Preparation of Int 45a
Figure imgf000386_0002
Int 45a
To a solution of (2R, 3R, 45,55, 65)-2-bromo-6-(methoxycarbonyl)tetrahydro-2/7-pyran- 3,4,5-triyl triacetate (30.0 g, 75.5 mmol, 1.00 eq) and 4-hydroxybenzaldehyde (10.2 g, 83.1 mmol, 1.10 eq) in acetonitrile (300 mL) was added silver oxide (26.3 g, 113 mmol, 1.50 eq), the mixture was stirred at 20 °C for 4 h under darkness. The mixture was concentrated to give a residue. The residue was purified by column chromatography (SiO2, Petroleum ether/Ethyl acetate=5/l to 1/1) and concentrated to afford (25,37?,45,55,65)-2-(4-formylphenoxy)-6- (methoxycarbonyl )tetrahydro-2//-pyran-3, 4, 5-triyl triacetate Int 45a (26.0 g, 59.3 mmol, 79% yield) as a yellow solid. H NMR (400 MHz, DMSCM,) 3 = 9.92 (s, 1H), 7.92 (d, J= 8.8 Hz, 2H), 7.20 (d, J= 8.8 Hz, 2H), 5.86 (d, J= 7.6 Hz, 1H), 5.52 - 5.46 (m, 1H), 5.21 - 5.04 (tn, 2H), 4.77 (d, J= 9.6 Hz, 1H), 3.64 (s, 3H), 2.04 - 2.00 (m, 9H).
Step B. Preparation of Int 45b
Figure imgf000387_0001
Int 45a Int 45b
To a solution of (25,37?,45,55,65)-2-(4-formylphenoxy)-6-(methoxycarbonyl)tetrahydro- 2//-pyran-3,4,5-triyl triacetate Int 45a (10.0 g, 22.8 mmol, 1.00 eq) in dichloromethane (100 mL) and isopropanol (20.0 mL) was added sodium borohydride (2.15 g, 56.8 mmol, 2.49 eq) at 0 °C, the mixture was stirred at 0 °C for 1 h. The mixture was quenched with water (200 mL) and extracted with dichloromethane (100 mL x 3). The organic phase was collected and concentrated to afford (25, 3R, 45,55, 65)-2-(4-(hydroxymethyl)phenoxy)-6- (mcthoxycarbonyl)tctrahydro-27/-pyran-3,4,5-triyl triacetate Int 45b (10.0 g, crude) as yellow oil. ‘H NMR (400 MHz, DMSO-d6) 3 = 7 ,T1 (d, J= 8.8 Hz, 2H), 6.95 (d, J= 8.8 Hz, 2H), 5.62 (d, J= 7.6 Hz, 1H), 5.47 (t, J= 9.6 Hz, 1H), 5.16 - 5.03 (m, 3H), 4.70 (d, J= 9.6 Hz, 1H), 4.43 (s, 2H), 3.64 (s, 3H), 2.03 - 1.99 (m, 9H).
Step C. Preparation of Int 45c
Figure imgf000387_0002
Int 45b Int 45c
To a solution of (25,37?,45,55,65)-2-(4-(hydroxymethyl)phenoxy)-6- (methoxycarbonyl)tetrahydro-2//-pyran-3,4,5-triyl triacetate Int 45b (10.0 g, 22.7 mmol, 1.00 eq) in dimethylformamide (100 mL) was added fert-butyl-chloro-dimethylsilane (5.13 g, 34.1 mmol, 4.19 mL, 1.50 eq) and imidazole (3.09 g, 45.4 mmol, 2.00 eq), the mixture was stirred at 25 °C for 12 h. The reaction mixture was diluted with water (300 mL) and exacted with ethyl acetate (3 x 100 mL). The organic phase was separated, washed with brine (2 x 100 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure to give a residue The residue was purified by column chromatography (SiC>2, petroleum ether/ethyl acetate=5/l to 1/1) and concentrated to afford (2S,3R,4S,5S,6S)-2-(4-(((terl- butyldimethylsilyl)oxy)methyl)phenoxy)-6-(methoxycarbonyl)tetrahydro-2/7-pyran-3,4,5-triyl triacetate Int 45c (9.00 g, 16 2 mmol, 71% yield) as yellow oil 1H NMR (400 MHz, DMSO-flfe) δ = 7.26 (d, J= 8.8 Hz, 2H), 6.96 (d, J= 8.8 Hz, 2H), 5.62 (d, J= 8.0 Hz, 1H), 5.46 (t, J = 9.6 Hz, 1H), 5.11 - 5.01 (m, 2H), 4.69 (d, J= 10.0 Hz, 1H), 4.64 (s, 2H), 3.63 (s, 3H), 2.02 - 1.98 (m, 9H), 0.89 (s, 9H), 0 06 (s, 6H).
Step D. Preparation of Int 45d
Figure imgf000388_0001
Int 45c Int 45d
To a solution of (25,37?,45,55,65)-2-(4-(((tert-butyldimethylsilyl)oxy)methyl)phenoxy)-6- (methoxycarbonyl)tetrahydro-2//-pyran-3,4,5-triyl triacetate Int 45c (10.0 g, 18.0 mmol, 1.00 eq) in methanol (100 mL) was added sodium methanolate (1.95 g, 36.1 mmol, 2.00 eq), the mixture was stirred at 25 °C for 3 h. The mixture was filtered to give filtrate. The filtrate was purified by reversed-phase column (column: spherical Cl 8, 20-45 um, 100A, SW 40, mobile phase: [water (0.1% ammonium hydrogen carbonate) - acetonitrile) and lyophilized to afford (2S, 35, 4,S’.5/<6.S’)-6-(4-(((tert-butyl dimethyl silyl)oxy)methyl)phenoxy) -3,4,5- trihydroxytetrahydro-277-pyran-2-carboxylic acid Int 45d (6.00 g, 14.5 mmol, 80% yield) as yellow oil. MS (ESI) m/z 437.1 [M+Na]+
Step E. Preparation of Int 45e
Figure imgf000388_0002
Int 45d Int 45e
To a solution of (25,37?,45,55,65)-2-(4-(((tert-butyldimethylsilyl)oxy)methyl)phenoxy)-6- (methoxycarbonyl)tetrahydro-27/-pyran-3,4,5-triyl triacetate Int 45d (10.0 g, 18.0 mmol, 1.00 eq) in methanol (100 mL) was added sodium methanolate (1.95 g, 36.1 mmol, 2.00 eq), the mixture was stirred at 25 °C for 3 h. The mixture was filtered to give filtrate The filtrate was purified by reversed-phase column (column: spherical Cl 8, 20-45 um, 100A, SW 40, mobile phase: [water (0.1% ammonium hydrogen carbonate) - acetonitrile) and lyophilized to afford (IS, 3S, 45,57?,6S)-6-(4-(((/erZ-butyl dimethyl silyl)oxy)methyl)phenoxy) -3,4,5- trihydroxytetrahydro-27/-pyran-2-carboxylic acid Int 45e (6.00 g, 14.5 mmol, 80% yield) as yellow oil. MS (ESI) m/z 437.1 [M+Na]+
Step F. Preparation of Int 45f
Figure imgf000389_0001
Int 45e Int 45f
To a solution of (2S,3S,4S,57?,6y)-6-(4-(((tert-butyldimethylsilyl)oxy)methyl)phenoxy)-3,4,5- trihydroxytetrahydro-2//-pyran-2-carboxylic acid Int 45e (6.00 g, 14.5 mmol, 1.00 eq) in dimethylformamide (30.0 mL) was added 2,3,4,6,7,8,9,10-octahydropyrimido[l,2-a]azepine (4.41 g, 29.0 mmol, 4.36 mL, 2.00 eq) and 3 -bromoprop- 1-ene (5.25 g, 43.4 mmol, 3.00 eq), the mixture was stirred at 40 °C for 2 h under nitrogen atmosphere. The mixture was filtered to give a filtrate. The filtrate was purified by reversed-phase column (column: spherical C18, 20-45 um, 100A, SW 40, mobile phase: [water (0.1%ammonium acid carbonate)) - acetonitrile) and lyophilized to afford (A)-prop- 1 -en- 1 -yl (2S,3S,4S,5A,65)-6-(4-(((ter/-butyldimethylsilyl)oxy) methyl) phenoxy)-3,4,5-trihydroxytetrahydro-277-pyran-2-carboxylate Int 45f (4.00 g, 8.80 mmol, 61% yield) as yellow oil. ’H NMR (400 MHz, DMSO-tfc) δ = 7.16 (d, J= 8.8 Hz, 2H), 6.92 (d, J= 8.8 Hz, 2H), 5.84 (tdd, J= 5.2, 10.4, 17.2 Hz, 1H), 5.42 (d, J= 4.8 Hz, 1H), 5.38 (d, J= 5.6 Hz, 1H), 5.29 - 5.23 (m, 1H), 5.21 (d, J= 5.2 Hz, 1H), 5.13 (dd, J= 1.6, 10.4 Hz, 1H), 5.01 (d, .7= 7.6 Hz, 1H), 4.64 - 4.50 (m, 4H), 4.01 (d, J= 9.6 Hz, 1H), 3.36 (br d, J= 5.6 Hz, 1H), 3.22 (br dd, J= 5.2, 7.6 Hz, 2H), 0.83 (s, 9H), 0.00 (s, 6H).
Step G. Preparation of Int 45g
Figure imgf000389_0002
Int 45f Int 45g
To a solution of (A’)-prop- l -en- l -yl (2.S,3S,4S,5R,6S)-6-(4-(((tert- butyldimethylsilyl)oxy)methyl)phenoxy)-3,4,5-trihydroxytetrahydro-27/-pyran-2-carboxylate Int 45f (4.00 g, 8.80 mmol, 1.00 eq) in pyridine (50.0 mL) was added allyl carbonochloridate (31 .8 g, 264 mmol, 28.0 mL, 30.0 eq) at 0 °C, the mixture was stirred at 25 °C for 3 h under nitrogen atmosphere. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (column: spherical Cl 8, 20-45 um, 100A, SW 40, mobile phase: [water (0.1% ammonium hydrogen carbonate) - acetonitrile) and lyophilized to afford (A)-prop- 1 -en- l -yl (2S, 35,45,57?, 65)-3, 4, 5-tris(((allyloxy)carbonyl)oxy)-6- (4-((i7c7/-butyldimethylsilyl) oxy)methyl)phenoxy)tetrahydro-277-pyran-2-carboxylate Int 45g (3.50 g, 4.95 mmol, 56% yield) as yellow oil. 1H NMR (400 MHz, DMSO-d6) 3 = 7.21 (d, J = 8.8 Hz, 2H), 6.90 (d, J= 8.8 Hz, 2H), 5.89 - 5.76 (m, 4H), 5.61 (d, J= 8.0 Hz, 1H), 5.38 - 5.32 (m, 1H), 5.28 - 5.25 (m, 1H), 5.22 (tdd, J= 1.6, 3.2, 5.2 Hz, 3H), 5.19 - 5.17 (m, 3H), 5.16 (dd, J = 1.2, 2.0 Hz, 1H), 5 07 - 4 99 (m, 2H), 4 74 (d, 10 0 Hz, 1H), 4 61 - 4 44 (m, 10H), 0 83 (s,
9H), 0.00 (s, 6H). MS (ESI) m/z 724.3 [M+H20]+
Step H. Preparation of Int 45h
Figure imgf000390_0001
Int 45g Int 45h
To a solution of (E)-prop-l-en-l-yl (25,35,45,57?,65)-3,4,5-tris(((allyloxy)carbonyl)oxy)- 6-(4-(((ter/-butyldimethylsilyl)oxy)methyl)phenoxy)tetrahydro-277-pyran-2-carboxylate Int 45g (3.50 g, 4.95 mmol, 1.00 eq) in tetrahydrofuran (20.0 mb) was added pyridine;hydrofluoride (6.42 g, 45.3 mmol, 5.83 mb, 70% purity, 9.15 eq), the mixture was stirred at 25 °C for 3 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (column: spherical Cl 8, 20-45 um, 100A, SW 40, mobile phase: [water (0.1% Formic Acid) - acetonitrile) and lyophilized to afford (E)-prop-l-en-l-yl (25,35,45,57?,65)-3,4,5-tris(((allyloxy)carbonyl)oxy)-6-(4-(hydroxymethyl)phenoxy)tetrahydro- 277-pyran-2-carboxylate Int 45h (2.30 g, 3.88 mmol, 78% yield) as yellow oil. I I NMR (400 MHz, DMSO-<7<>) δ = 7.28 (d, J= 8.8 Hz, 2H), 6.95 (d, J= 8.8 Hz, 2H), 5.97 - 5.82 (m, 4H), 5.67 (d, J= 8.0 Hz, 1H), 5.46 - 5.39 (m, 1H), 5.36 - 5.32 (m, 1H), 5.30 (ddd, J= 1.6, 3.2, 4.8 Hz, 2H), 5.28 - 5.21 (m, 5H), 5.18 - 5.04 (m, 3H), 4.81 (d, J= 10.0 Hz, 1H), 4.71 - 4.58 (m, 7H), 4.56 (br d, J= 5.6 Hz, 1H), 4.44 (d, J= 5.6 Hz, 2H).
Step I. Preparation of Int 45i
Figure imgf000391_0001
To a solution of tert-butyl ((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)carbamate (1.00 g, 2.68 mmol, 1.00 eq) and 2-bromoacetic acid (558 mg, 4.02 mmol, 289 μL, 1.50 eq) in dimethylformamide (10.0 mL) was added cesium carbonate (2.62 g, 8.03 mmol, 3.0 eq), the mixture was stirred at 25 °C for 12 h. The mixture was filtered to give filtrate. The filtrate was purified by reversed-phase column (column: spherical Cl 8, 20-45 um, 100A, SW 40, mobile phase: [water (0.1% Formic Acid) - acetonitrile) and lyophilized to afford 2-(3-(5-(((tert- butoxycarbonyl)amino)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l-yl)acetic acid Int 45i (1.50 g, 3.48 mmol, 65% yield) as a yellow solid. ' l l NMR (400 MHz, DMSO-ds) 8 = 13.25 - 12.68 (m, 1H), 7.70 (d, J= 7.6 Hz, 1H), 7.51 (br t, J= 5.6 Hz, 1H), 7.46 (s, 1H), 7.39 (br d, J=
8.0 Hz, 1H), 5.27 (dd, J = 52, 13.2 Hz, 1H), 4.54 - 4.46 (m, 1H), 4.44 - 4.18 (m, 5H), 3.19 - 3.04 (m, 1H), 2.98 - 2.80 (m, 1H), 2.44 - 2.31 (m, 1H), 2.15 - 2.06 (m, 1H), 1.40 (s, 9H). MS (ESI) m/z 432.2 [M+H]+
Step J. Preparation of Int 45j
Figure imgf000391_0002
A mixture of 2-(3-(5-(((terLbutoxycarbonyl)amino)methyl)-l-oxoisoindolin-2-yl)-2,6- dioxopiperidin-l-yl)acetic acid Int 45i (500 mg, 1.16 mmol, 1.0 eq), [azido(phenoxy)phosphoryl]oxybenzene (478 mg, 1.74 mmol, 375 μL, 1 50 eq) and triethylamine (235 mg, 2.32 mmol, 323 μL, 2.00 eq) in dioxane (2.00 mL) was stirred at 25°C for 1 h, then (E)-prop-l-en-l-yl (25,35,45,5A,65)-3,4,5-tris(((allyloxy)carbonyl)oxy)-6-(4- (hydroxymethyl) phenoxy )tetrahydro-277-pyran-2-carboxylate Int 45h (687 mg, 1.16 mmol, 1.00 e<?)was added, the mixture was stirred at 80 °C for 3 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed- phase column (column: spherical C1 8, 20-45 um, 100A, SW 40, mobile phase: [water (0.1% Formic Acid) - acetonitrile) and lyophilized to afford (£)-prop-l-en-l-yl (2S,35,45,5A,6S)-3,4,5- tris(((allyloxy)carbonyl)oxy)-6-(4-(((((3-(5-(((tert-butoxycarbonyl)amino)methyl)-l- oxoisoindolin-2-yl)-2,6-dioxopiperidin-l-yl)methyl)carbamoyl)oxy)methyl)phenoxy)tetrahydro- 27/-pyran-2-carboxylate Int 45j (600 mg, 588 μmol, 17% yield) as a white solid. (1H NMR from the pilot). 1H NMR (400 MHz, DMSO-dg) δ = 7.70 (d, J= 7.6 Hz, 1H), 7.50 (br t, J= 6.4 Hz, 1H), 7.45 (br s, 1H), 7.41 - 7 32 (m, 4H), 7.08 (br dd, J= 5.6, 8.0 Hz, 1H), 6.99 (br dd, J= 5.2, 8.4 Hz, 1H), 5.97 - 5.86 (m, 4H), 5.76 - 5.65 (m, 1H), 5.44 - 5.36 (m, 2H), 5.35 - 5.23 (m, 10H), 5.19 - 5 07 (m, 4H), 5.00 - 4.90 (m, 2H), 4.71 - 4.58 (m, 10H), 4.56 - 4.42 (m, 3H), 4.24 (br d, J = 6 0 Hz, 2H), 1 40 (s, 9H) MS (ESI) m/z 1021 5 [M+H]+
Step K. Preparation of Int 45k
A mixture of tert-butyl (2-(2-chloro-4- ((phenoxycarbonyl)amino)phenethoxy)ethyl)(methyl)carbamate Int Ij (73.0 mg, 162 μmol, 1.00 eq), (E)-prop-l-en-l-yl (2S,3S, 45,5/?, 65)-3, 4, 5-tris(((allyloxy)carbonyl)oxy)-6-(4-(((((3-(5- (aminomethyl)- 1 -oxoi soindolin-2-yl)-2,6-dioxopiperidin- 1 - yl)methyl)carbamoyl)oxy)methyl)phenoxy) tetrahydro-27/-pyran-2-carboxylate Int 45j (150 mg, 162 μmol, 1.00 eq) and triethylamine (49.5 mg, 488 μmol, 68.0 μL, 3.00 eq) in dimethyl formamide (2.00 mL) was stirred at 40 °C for 6 h. The reaction mixture was filtered to give a filtrate The filtrate was purified by reversed phase (0. 1% formic acid) and lyophilized afford (E)-prop-l-en-l-yl (25,35,45,5J?,65)-3,4,5-tris(((allyloxy)carbonyl)oxy)-6-(4-(((((3-(5-((3-(4-(2- (2-((ter/-butoxycarbonyl)(methyl)amino)ethoxy)ethyl)-3-chlorophenyl)ureido)methyl)-l- oxoisoindolin-2-yl)-2,6-dioxopiperidin-l-yl)methyl)carbamoyl)oxy)methyl)phenoxy)tetrahydro- 2/7-pyran-2-carboxylate Int 45k (160 mg, 125 μmol, 77% yield) as a white solid. MS (ESI) m/z 1175.3 [M- I 00+H]
Step L. Preparation of Int 451 To a solution of (A)-prop- l -en- l -yl (2A,35,45,5J?,65)-3,4,5-tris(((allyloxy)carbonyl)oxy)- 6-(4-(((((3-(5-((3-(4-(2-(2-((/erAbutoxycarbonyl)(methyl)amino)ethoxy)ethyl)-3- chlorophenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methyl)carbamoyl)oxy)methyl)phenoxy)tetrahydro-2A/-pyran-2-carboxylate Int 45k (160 mg, 125 μmol, 1.00 eq) in di chloromethane (1.50 mL) was added trifluoroacetic acid (160 μL), the mixture was stirred at 25 °C for 0.5 h. The reaction mixture was concentrated to give a residue and lyophilized to afford (£)-prop-l-en-l-yl (2S, 35,45, 5A,65)-3, 4,5- tris(((allyloxy)carbonyl)oxy)-6-(4-(((((3-(5-((3-(3-chloro-4-(2-(2- (methylamino)ethoxy)ethyl)phenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methyl)carbamoyl)oxy)methyl)phenoxy)tetrahydro-2A/-pyran-2-carboxylate Int 451 (140 mg, crude) as a white solid. MS (ESI) m/z 1175.6 [M+H]+
Step M. Preparation of Int 45m
A mixture of (E)-prop-l-en-l-yl (2S, 3S,4S,5R, 6S)-3, 4, 5-tris(((allyloxy)carbonyl)oxy)-6- (4-(((((3-(5-((3-(3-chloro-4-(2-(2-(methylamino)ethoxy)ethyl)phenyl)ureido)methyl)-l- oxoisoindolin-2-yl)-2,6-dioxopiperidin-l-yl)methyl)carbamoyl)oxy)methyl)phenoxy)tetrahydro- 2//-pyran-2-carboxylate Int 451 (60.0 mg, 51.0 μmol, 1.00 eq), (9//-fluoren-9-yl)m ethyl ((5)-l- (((b)- 1 -((4-((((4-nitrophenoxy)carbonyl)oxy)methyl)phenyl)amino)- 1 -oxopropan-2-yl)amino)- 1 - oxopropan-2-yl)carbamate Int 44b (36.6 mg, 56.2 μmol, 1.10 eq) and tri ethylamine (15.5 mg, 153 μmol, 21.3 μL, 3.00 eq) in dimethyl formamide (2.00 mL) was stirred at 25 °C for 2 h. The reaction mixture was filtered to give a filtrate. The filtrate was purified by prep-HPLC (column: Phenomenex luna C18 150*25mm*10um;mobile phase: [water(formic acid)- acetonitrile];gradient:66%-86% B over 10 min) to afford (E)-prop-l-en-l-yl (25,35,45,57?,65)-6- (4-(((((3-(5-((3-(4-(2-(2-((((4-((5)-2-((5)-2-((((9^-fluoren-9- yl)methoxy)carbonyl)amino)propanamido)propanamido)benzyl)oxy)carbonyl)(methyl)amino)et hoxy)ethyl)-3-chlorophenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methyl)carbamoyl)oxy)methyl)phenoxy)-3,4,5-tris(((allyloxy)carbonyl)oxy)tetrahydro-2Af- pyran-2-carboxylate Int 45m (50.0 mg, 29.6 μmol, 58% yield) as a white solid.
Step N. Preparation of Int 45n
To a solution of (A)-prop- 1 -en- 1 -yl (IS, 3S, 45.55, 65)-6-(4-(((((3-(5-((3-(4-(2-(2-((((4- ((5)-2-((5)-2-((((97A-fluoren-9- yl)methoxy)carbonyl)amino)propanamido)propanamido)benzyl)oxy)carbonyl)(methyl)amino) ethoxy)ethyl)-3-chlorophenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methyl) carbamoyl )oxy)methyl)phenoxy)-3, 4, 5-tris(((allyloxy)carbonyl)oxy)tetrahydro-2//- pyran-2-carboxylate Int 45m (25.0 mg, 14.8 μmol, 1.00 eq) in dimethyl formamide (2.00 mL) was added pyrrolidine (5.26 mg, 74.0 μmol, 6. 18 μL, 5.00 eq) and tetrakis(triphenylphosphine)palladium(0) (1.71 mg, 1.48 μmol, 0.100 eq), the mixture was stirred at 25 °C for 1 h. The mixture was filtered to give a filtrate. The filtrate was purified by prep-HPLC (column: Phenomenex luna Cl 8 150*25mm* 10um;mobile phase: [water(formic acid)- acetonitrile];gradient:l 1%-41% B over 10 min) and lyophilized to afford (2S,3S, 45,57?, 65)-6-(4-(((((3-(5-((3-(4-(2-(2-((((4-((5)-2-((5)-2- aminopropanamido)propanamido)benzyl)oxy)carbonyl)(methyl)amino)ethoxy) ethyl)-3- chlorophenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidin-l- yl)methyl)carbamoyl)oxy) methyl )phenoxy)-3, 4, 5-trihydroxytetrahydro-277-pyran-2-carboxylic acid Int 45n (10.0 mg, 8 51 gmol, 57 % yield) as a white solid.
Step O. Preparation of Compound IG-L-45
To a solution of 34-(3-(2,5-dioxo-2,5-dihydro-177-pyrrol-l-yl)-2-fluoro-6-(3-oxo-3- (2,3, 5,6-tetrafluorophenoxy)propyl)phenoxy)-3 ,6,9, 12, 15, 18,21 ,24,27,30-decamethyl- 4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid Int 36k (10.4 mg, 8.51 μmol, 1.00 eq) and (25,35,45,57?,65)-6-(4-(((((3-(5-((3-(4-(2-(2-((((4- ((5)-2-((5)-2-aminopropanamido)propanamido)benzyl) oxy)carbonyl)(methyl)amino)ethoxy)ethyl)-3-chlorophenyl)ureido)methyl)-l-oxoisoindolin-2- yl)-2,6-dioxopiperidin-l-yl)methyl)carbamoyl)oxy)methyl)phenoxy)-3,4,5- trihydroxytetrahydro-2Zf-pyran-2-carboxylic acid Int 45n (10.0 mg, 8.51 μmol, 1.00 eq) in dimethyl formamide (1.00 mL) was added triethylamine (2.58 mg, 25.5 μmol, 3.55 μL, 3.00 eq). The reaction was stirred at 25 °C for 2 h. The reaction was filtered. The filtrate was purified by prep-HPLC (column: Phenomenex luna C18 150*25mm* 10 um; mobile phase: [water (formic acid)- acetonitrile]; gradient: 18%-48% B over 20 min) and lyophilized to afford 34-(6-(3- (((25)-l-(((25)-l-((4-((((2-(4-(3-((2-(l-(((((4-(((25,37?,45,55,65)-6-carboxy-3,4,5- trihydroxytetrahydro-2Zf-pyran-2-yl)oxy)benzyl)oxy)carbonyl)amino)methyl)-2,6- dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)ureido)-2- chlorophenethoxy)ethyl)(methyl)carbamoyl)oxy)methyl)phenyl)amino)-l-oxopropan-2- yl)amino)- 1 -oxopropan-2-yl)amino)-3 -oxopropyl)-3 -(2, 5-dioxo-2, 5 -dihydro- 177-pyrrol- 1 -yl)-2- fluorophenoxy)-3,6,9,12,15,18,21,24,27,30-decamethyl-4,7, 10,13, 16,19,22,25,28,31-decaoxo- 3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid Compound IG-L-45 (3.69 mg, 1.60 μmol, 19% yield, 97% purity) as a white solid. 1H NMR (400 MHz, DMSO-<76) δ = 9.99 - 9.93 (m, 1H), 8.23 - 8.08 (m, 2H), 7.72 - 7.66 (m, 2H), 7.61 (br d, J= 8.0 Hz, 2H), 7.50 - 7.42 (m, 2H), 7.33 - 7.23 (m, 6H), 7.22 - 7.09 (m, 3H), 7.09 - 6.92 (m, 3H), 5.36 - 5.30 (m, 1H), 5.20 (td, J= 3.6, 7.6 Hz, 1H), 5.13 - 5.08 (m, 1H), 5.02 - 4.78 (m, 6H), 4.53 - 4.26 (m, 10H), 4.14 - 3.92 (m, 12H), 4.25 - 3.83 (m, 4H), 3.68 - 3.62 (m, 2H), 3.58 - 3.45 (m, 8H), 3.17 (s, 3H), 3 07 - 2.64 (m, 40H), 2.28 - 2.22 (m, 1H), 2.05 - 1.88 (m, 4H), 1.30 (br d, J= 7 2 Hz, 3H), 1.21 - 1.15 (m, 3H). MS (ESI) m/z 1117.4 [M/2+2H]+
The compounds in Table 19 were prepared in a manner similar to that described for Compound IG-L-45 using the appropriate compound as starting material.
Table 19
Figure imgf000396_0001
EXAMPLE L-52: Synthesis of 34-(6-(3-(((2S)-l-(((2S)-l-((4-(((5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-4-yl)oxy)methyl)-3- methoxyphenyl)amino)- 1 -oxopropan-2-yl)amino)- 1 -oxopropan-2-yl)amino)-3 -oxopropyl)-3 - (2, 5-dioxo-2,5-dihydro-lH-pyrrol-l-yl)-2-fluorophenoxy)-3, 6, 9, 12,15,18,21,24,27,30- decamethyl-4,7,10,13, 16, 19, 22, 25, 28,3 l-decaoxo-3, 6, 9, 12, 15,18,21,24,27,30- decaazatetratriacontanoic acid, IG-L-52
Figure imgf000397_0001
Figure imgf000398_0001
Step A. Preparation of 52a
To a solution of methyl 4-amino-2-methoxybenzoate (10.0 g, 55.2 mmol, 1.00 eq) in tetrahydrofuran (200 mL) was added lithium aluminum hydride (4.19 g, 110 mmol, 2.00 eq) at 0 °C. Then the mixture was stirred at 25 °C for 2 h. The mixture was quenched with water (4. 19 mL), sodium hydroxide (15%, 4. 19 mL) and water (8.40 mL) at 0 °C. Then the mixture was dried over sodium sulfate and fdtered. The filtrate was concentrated to give (4-amino-2- methoxy-phenyl)methanol Int 52a (8.00 g, crude) as yellow oil. rH NMR (400 MHz, DMSO-d6) δ = 6.92 (d, J= 8.0 Hz, 1H), 6.18 (d, J= 2.0 Hz, 1H), 6.10 (dd, J= 2 0, 8.0 Hz, 1H), 4.95 (s, 2H), 4.54 - 4.45 (m, 1H), 4.29 (d, J= 5.6 Hz, 2H), 3.66 (s, 3H).
Step B. Preparation of 52b
To a solution of (4-amino-2-methoxyphenyl)methanol (8.00 g, 52.2 mmol, 1.00 eq) and (((9/7- fluoren-9-yl)methoxy)carbonyl)-£-alanyl-£-alanine Int 52a (20.0 g, 52.2 mmol, 1.00 eq) in dichloromethane (20.0 mL) was added ethyl 2-ethoxy-2//-quinoline- l -carboxylate (38.8 g, 157 mmol, 3.00 eq). Then the mixture was stirred at 25 °C for 12 h. The mixture was concentrated to give a residue. The residue was triturated with ethyl acetate (100 mL) for twice. The filter cake was dried under reduced pressure to give (9Zf-fluoren-9-yl)m ethyl ((5)-l-(((5)-l-((4- (hydroxymethyl)-3-methoxyphenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl) carbamate Int 52b (21.0 g, crude) as a white solid. 1H NMR (400 MHz, DMSO-afc) δ = 9.87 (s, 1H), 8.09 (br d, J= 7.2 Hz, 1H), 7.89 (d, J= 7.2 Hz, 2H), 7.72 (br t, J= 8.4 Hz, 2H), 7 56 (br d, J= 7.6 Hz, 1H), 7.45 - 7.38 (m, 2H), 7.36 - 7.29 (m, 3H), 7.25 (d, J= 8.4 Hz, 1H), 7.14 (br d, J = 9.2 Hz, 1H), 4.90 (t, J= 5.6 Hz, 1H), 4.42 (d, J= 5.6 Hz, 3H), 4.30 - 4.21 (m, 3H), 4 08 (br dd, J = 12, 14.6 Hz, 1H), 3.70 (s, 3H), 1.31 (d, J= 7.2 Hz, 3H), 1.25 - 1.22 (m, 3H). LCMS (ESI) m/z 540.2 [M+Na]+
Step C. Preparation of Int 52c
To a solution of (9/7-fluoren-9-yl)methyl ((S)-l-(((S)-l-((4-(hydroxymethyl)-3- methoxyphenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl)carbamate Int 52b (1.40 g, 2.70 mmol, 1.00 eq) in tetrahydrofuran (20.0 mb) was added phosphorus tribromide (1.46 g, 5.41 mmol, 2.00 eq). Then the mixture was stirred at 25 °C for 2 h. The mixture was poured into ice water (20.0 mL) and extracted with ethyl acetate (3 x 20 mL). The organic layer was dried over sodium sulfate and filtered. The filtrate was concentrated to give (9/f-fluoren-9- yl)m ethyl ((5)- 1 -(((£)- 1 -((4-(bromomethyl)-3 -methoxyphenyl)amino)- 1 -oxopropan-2-yl)amino)- l-oxopropan-2-yl)carbamate Int 52c (1.57 g, crude) as a yellow solid.
Step D. Preparation of Int 52d
Figure imgf000399_0001
To a solution of l-(3-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy- l-oxoisoindolin-5-yl)methyl)urea Int 52c (40 0 mg, 87.6 μmol, 1.00 eq) and ('97/-fluoren-9- yl)m ethyl ((5)- 1 -(((5)- 1 -((4-(bromomethyl)-3 -methoxyphenyl)amino)- 1 -oxopropan-2-yl)amino)-
1-oxopropan-2-yl)carbamate (102 mg, 175 μmol, 2.00 eq) in dimethyl formamide (2.00 mL) was added silver oxide (101 mg, 438 μmol, 5.00 eq). Then the mixture was stirred at 25 °C for 12 h. The mixture was filtered The filtrate was purified by reversed phase (Cl 8, 330 g; condition: water/acetonitrile = 100/0 to 0/100, 0. 1% formic acid), further purified by reversed phase (C18, 80 g; condition: water/acetonitrile = 100/0 to 0/100, 0.1% formic acid) and lyophilized to afford (9//-fluoren-9-yl)methyl ((25)-l-(((25)-l-((4-(((5-((3-(3-chloro-4-methylphenyl)ureido)methyl)-
2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-4-yl)oxy)methyl)-3-methoxyphenyl)amino)-l- oxopropan-2-yl)amino)- 1 -oxopropan-2-yl)carbamate Int 52d (180 mg, 188 μmol, crude) as a yellow solid. LCMS (ESI) m/z 956.4 [M+H]+
Step E. Preparation of Int 52e
Figure imgf000400_0001
Int 52d Int 52e
(9H-fluoren-9-yl)methyl ((2S)-l-(((26)-l-((4-(((5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-4-yl)oxy)methyl)-3- methoxyphenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2-yl)carbamate Int 52d (170 mg, 178 μmol, 1.00 eq) in piperidine (0.200 mL) and dimethyl formamide (0.800 mL) was stirred at 25 °C for 0.5 h. The mixture was filtered. The filtrate was purified by reversed phase (C18, 40 g; condition: water/acetonitrile = 100/0 to 0/100, 0. 1% formic acid), further purified by prep-HPLC (column: Welch Ultimate C1 8 150 * 25 mm * 5 um; mobile phase: [water (formic acid) - acetonitrile]; gradient: 20% - 50% B over 40 min) and lyophilized to afford (25)-2- amino-/V-((2,S)-l-((4-(((5-((3-(3-chloro-4-methylphenyl)ureido) methyl)-2-(2,6-dioxopiperidin- 3-yl)-l-oxoisoindolin-4-yl)oxy)methyl)-3-methoxyphenyl)amino)-l-oxopropan-2- yl)propenamide Int 52e (15.0 mg, 20.4 prnol, 11% yield) as a white solid. rH NMR (400 MHz, DMSO-d6) d = 10.95 (s, 1H), 10.12 (s, 1H), 8.28 (s, 2H), 7.67 (d, J= 2.0 Hz, 1H), 7.43 (s, 1H), 7.35 (dd, J= 2.0, 8.4 Hz, 1H), 7. 19 (br d, J= 8.8 Hz, 2H), 7.13 - 7.04 (m, 3H), 6.99 (br d, J= 15.6 Hz, 1H), 5.08 (dd, J= 4.8, 13.2 Hz, 1H), 4.47 (br d, J= 5.6 Hz, 5H), 4.36 - 4.12 (m, 3H), 3.77 (s, 3H), 2.90 (br s, 1H), 2.64 - 2.55 (m, 1H), 2.40 - 2.31 (m, 1H), 2.24 (s, 3H), 2.03 - 1.95 (m, 1H), 1.31 (d, J= 7.2 Hz, 3H), 1.20 (d, J= 6.8 Hz, 3H). LCMS (ESI) m/z 734.3 [M+H]+
Step F. Preparation of Compound IG-L-52
To a solution of ((2S)-2-amino-/V-((25)-l-((4-(((5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-4-yl)oxy) methyl)-3- methoxyphenyl)amino)- 1 -oxopropan-2-yl) propenamide Int 52e (14.0 mg, 19.1 umol, 1.00 eq) and 34-(3-(2,5-dioxo-2,5-dihydro-l//-pyrrol-l-yl)-2-fluoro-6-(3-oxo-3-(2,3,5,6- tetrafluorophenoxy)propyl)phenoxy)-3,6,9, 12, 15, 18,21,24,27,30-decamethyl-4,7, 10, 13, 16, 19,22,25,28,31-decaoxo-3,6,9, 12,15,18,21,24,27,30-decaazatetratriacontanoic acid Int 36k (23.3 mg, 19.1 μmol, 1.00 eq) in dimethyl formamide (1.00 mL) was added triethylamine (3.86 mg, 38. 1 μmol, 5.31 μL, 2.00 eq). Then the mixture was stirred at 25 °C for 0.5 h. The mixture was filtered The filtrate was purified by Prep-HPLC (column: UniSil 3 - 100 C1 8 Ultra (150 * 25 mm * 3 um); mobile phase: [water (formic acid) - acetonitrile]; gradient: 20% - 50% B over 40 min) and lyophilized to afford 34-(6-(3-(((2S)-l-(((25)-l-((4-(((5-((3-(3-chloro-4- methylphenyl)ureido) methyl)-2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-4-yl)oxy) methyl)-3- methoxyphenyl)amino)- 1 -oxopropan-2-yl)amino)- 1 -oxopropan-2-yl)amino)-3 -oxopropyl)-3 - (2, 5-dioxo-2,5-dihydro-l/7-pyrrol-l-yl)-2-fluorophenoxy)-3, 6, 9, 12,15,18,21,24,27,30- decamethyl-4,7,10,13, 16, 19,22,25,28, 31-decaoxo-3,6,9,12,15,18,21,24,27,30- decaazatetratriacontanoic acid, Compound IG-L-52 (11.79 mg, 6.51 μmol, 34% yield, 99% purity) as a white solid. 1HNMR (400 MHz, DMSO-J6) δ = 10.98 (s, 1H), 10.00 - 9.86 (m, 1H), 8.85 - 8 70 (m, 1H), 8.21 - 8.04 (m, 2H), 7.64 (d, J= 2.0 Hz, 1H), 7.44 (s, 1H), 7.36 - 7.31 (m, 1H), 7.27 - 7.15 (m, 6H), 7.14 - 6.99 (m, 3H), 5.09 (dd, J= 5.2, 13.1 Hz, 1H), 4.51 (br d, J= 4.4 Hz, 3H), 4.42 - 4.14 (m, 15H), 4.13 - 3.89 (m, 13H), 3.75 (s, 3H), 3.04 - 2.69 (m, 36H), 2.57 (br d, J= 2.0 Hz, 1H), 2.38 (br d, J= 4.0 Hz, 1H), 2.24 (s, 3H), 2.08 - 1.88 (m, 3H), 1.30 (d, J= 7.2 Hz, 3H), 1.19 (br d, J= 6.8 Hz, 3H). LCMS (ESI) m/z 896.9 [M/2+2H]+
EXAMPLE L-53: Synthesis of 34-(6-(3-(((2S)-l-(((2S)-l-((4-((((2-(3-(5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidine-l- carbonyl)benzyl)(methyl)carbamoyl)oxy)methyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l- oxopropan-2-yl)amino)-3 -oxopropyl)-3 -(2,5 -dioxo-2, 5 -dihydro- 1 H-pyrrol- 1 -yl)-2- fluorophenoxy)-3,6,9,12,15,18,21,24,27,30-decamethyl-4,7, 10,13, 16,19,22,25,28,31-decaoxo- 3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid (Compound IG-L-53)
Figure imgf000401_0001
Figure imgf000402_0001
Figure imgf000403_0001
Compound IG-L-53
Step A. Preparation of Int-53a
Figure imgf000403_0002
Int 10p
Int 53a To a solution of tert-butyl ((S)-l-(((ri)-l-((4-((((4- nitrophenoxy)carbonyl)oxy)methyl)phenyl)amino)- 1 -oxopropan-2-yl)amino)- 1 -oxopropan-2- yl)carbamate Int lOp (1.31 g, 2.47 mmol, 1 00 eq) and 2 methylglycine (264 mg, 2.96 mmol, 1.20 eq) in dimethyl formimade (10.0 mL) was added triethylamine (750 mg, 7.41 mmol, 1.03 mL, 3.00 eq). Then the mixture was stirred at 25 °C for 1 h. The mixture was filtered. The filtrate was purified by reversed phase chromatography (Cl 8, 120 g, condition: water/acetonitrile = 100/0 to 0/100, 0.1% formic acid) and lyophilized to afford JV-(((4-((S)-2- ((S)-2-((tert-butoxycarbonyl)amino)propanamido) propanamido)benzyl)oxy)carbonyl)-JV- methylglycine Int 53a (1 10 g, 2 29 mmol, 92% yield) as a white solid 1H \MR (400 MHz, DMSO-d6 ) 3 = 10.02 (br d, J= 7.2 Hz, 1H), 8.21 - 8.10 (m, 2H), 8.04 (d, J= 7.2 Hz, 1H), 7.33 (d, ./~ 8.6 Hz, 1H), 6.95 (d, ./~ 9.2 Hz, 2H), 5.02 (d, J= 14.1 Hz, 2H), 4.48 - 4.34 (m, 1H), 4.01 (br t, J= 7.2 Hz, 1H), 3.95 (d, J= 5.9 Hz, 2H), 2.90 (d, J= 10.3 Hz, 3H), 1.40 (s, 9H), 1.32 (d, J
= 7.1 Hz, 3H), 1.20 (br d, J= 7.1 Hz, 3H).
Step B. Preparation of Int 53b
Figure imgf000404_0001
To a solution of N-(((4-((5)-2-((5)-2-((tert- butoxycarbonyl)amino)propanamido)propanamido)benzyl)oxy) carbonyl )-Ariri ethyl glycine Int 53a (1.10 g, 2.29 mmol, 1.00 eq) and 2-hydroxyisoindoline- 1,3 -dione (411 mg, 2.52 mmol, 1.10 eq) in dichloromethane (40.0 mL) was added 3-(ethyliminomethylideneamino)propyl- dimethylazanium;chloride (571 mg, 2.98 mmol, 1.30 eq) at 25 °C for 12 h. The mixture was fdtered. The filtrate was purified by reversed phase chromatography (C1 8, 120 g; condition: water/acetonitrile = 100/0 to 0/100, 0.1% formic acid) and lyophilized to afford 1,3- dioxoisoindolin-2-yl JV-(((4-((S)-2-((S)-2-((tert- butoxycarbonyl)amino)propanamido)propanamido)benzyl)oxy)carbonyl)-/V-methylglycinate Int 53b (1 .35 g, 2. 16 mmol, 94% yield) as a white solid. 1H NMR (400 MHz, DMSOvL) 3 = 9.99 (br s, 1H), 8.04 - 7.90 (m, 4H), 7.57 (br d, 7.6 Hz, 2H), 7.37 - 7.27 (m, 2H), 6.97 (br d, J = 6.8 Hz, 1H), 5.05 (d, J= 10.6 Hz, 2H), 4.61 (d, J= 13.0 Hz, 1H), 4.46 - 4.31 (m, 2H), 3 98 (br t, J= 7.0 Hz, 1H), 3.02 - 2.91 (m, 3H), 1.36 (s, 9H), 1.29 (br d, J= 6 8 Hz, 3H), 1.17 (br d, J= 6.8 Hz, 3H). LCMS (ESI) m/z 648. 1 [M+Na] Step C. Preparation of Int 53c
To a solution of tert-butyl ((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)methyl)carbamate (5.00 g, 13.4 mmol, 1.00 eq) in dichloromethane (100 mb) were added triethylamine (4.06 g, 40.2 mmol, 5.59 mL, 3.00 eq), dimethylaminopyridine (164 mg, 1.34 mmol, 0.100 eq) and 2-bromobenzoyl chloride (5.88 g, 26.8 mmol, 3.50 mL, 2.00 eq) at 25 °C. Then the mixture was stirred at 25 °C for 12 h. The mixture was concentrated to give a residue. The residue was purified by reversed phase chromatography (Cl 8, 330 g; condition: water/acetonitrile = 100/0 to 0/100, 0.1% formic acid) and lyophilized to afford tert-butyl ((2-(l- (2-bromobenzoyl)-2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)carbamate Int 53c (5.00 g, 8.99 mmol, 67% yield) as a yellow solid. LCMS (ESI) m/z 556.1, 558.1 [M+H]+ Step D. Preparatioh of Int 53d
To a solution of terLbutyl ((2-(l-(2-bromobenzoyl)-2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl)carbamate Int 53c (3.00 g, 5.39 mmol, 1.00 eq) in dichloromethane (45.0 mL) was added trifluoroacetic acid (15.0 mL). Then the mixture was stirred at 25 °C for 1 h. The mixture was quenched with ice water (400 mL) and extracted with ethyl acetate (3 x 100 mL). The organic layer was dried over sodium sulfate and filtered. The filtrate was concentrated to give a residue. The residue was purified by reversed phase chromatography (C18, 330 g; condition: water/acetonitrile = 100/0 to 0/100, 0 1% formic acid) and lyophilized to afford 3-(5-(aminomethyl)-l-oxoisoindolin-2-yl)-l-(2-bromobenzoyl)piperidine-2, 6-dione Int 53d (2.20 g, 4.82 mmol, 89% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) δ = 8.07 - 8.01 (m, 1H), 7.89 - 7.76 (m, 2H), 7.68 (s, 1H), 7.62 - 7.53 (m, 3H), 5.50 (dd, J= 5.2, 13.2 Hz, 1H), 4.61 - 4.34 (m, 2H), 4. 16 (s, 2H), 3.21 (br d, J= 5.2 Hz, 1H), 2.97 - 2.82 (m, 1H), 2.71 - 2.61 (m, 1H), 2.22 - 2.13 (m, 1H). LCMS (ESI) m/z 456.0, 458.0 [M+Na]+
Step E. Preparation of Int 53e
To a solution of 3-(5-(aminomethyl)-l-oxoisoindolin-2-yl)-l-(2- bromobenzoyl)piperidine-2, 6-dione Int 53d (2.20 g, 4.82 mmol, 1.00 eq) and phenyl (3-chloro- 4-methylphenyl)carbamate (1.89 g, 7.23 mmol, 1.50 eq) in dimethyl formamide (1.00 mL) and acetonitrile (5.00 mL) was added trimethylamine (1.46 g, 14.5 mmol, 2.01 mL, 3.00 eq) at 0 °C. Then the mixture was stirred at 0 °C for 0.5 h. The mixture was diluted with ice water (200 mL) and extracted with ethyl acetate (3 x 100 mL) The organic layer was washed with brine (3 x 100 mL), dried over sodium sulfate and filtered. The filtrate was concentrated to give a residue. The residue was purified by reversed phase chromatography (Cl 8, 330 g; condition: water/acetonitrile = 100/0 to 0/100, 0.1% formic acid) and lyophilized to afford l-((2-(l-(2- bromobenzoyl)-2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)-3-(3-chl oro-4- methylphenyl)urea Int 53e (0.90 g, 1.44 mmol, 29% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6 ) δ = 8.74 (s, 1H), 8.10 - 7.99 (tn, 1H), 7.91 - 7.81 (m, 1H), 7.71 - 7.63 (m, 2H), 7.57 (td, J= 2.4, 4.6 Hz, 2H), 7.52 (s, 1H), 7.43 (br d, J= 7.6 Hz, 1H), 7.22 - 7.09 (m, 2H), 6.78 (br t, J= 6.0 Hz, 1H), 5.48 (dd, J = 52, 13.2 Hz, 1H), 4.55 - 4.37 (m, 4H), 3.25 - 3.18 (m, 1H), 2.86 (br d, J= 18.8 Hz, 1H), 2.64 (br dd, J = 4.4, 13.4 Hz, 1H), 2.22 (s, 3H), 2.19 - 2.10 (m, 1H). LCMS (ESI) m/z 623.1, 625.1 [M+H]+
Step F. Preparation of Int 53f
To a solution of l-((2-(l-(2-bromobenzoyl)-2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5- yl)methyl)-3-(3-chloro-4-methylphenyl)urea Int 53e (400 mg, 641 μmol, 1.00 eq) and (1,3- dioxoisoindolin-2-yl N-(((4-((S)-2-((S)-2-((tert- butoxycarbonyl)amino)propanamido)propanamido)benzyl)oxy)carbonyl)-jV-methylglycinate Int 53b (441 mg, 705 ptnol, 1.10 eq) in dimethylacetamide (10.0 mb) were added dichloronickel; 2- (2-pyridyl)pyridine;dihydrate (38.9 mg, 64.1 μmol, 0.10 eq), zinc powder (380 mg, 5 81 mmol, 9.06 eq) and trimethylchlorosilane (209 mg, 1.92 mmol, 244 μL, 3.00 eq) at 25 °C. Then the mixture was stirred at 25 °C for 2 h. The mixture was filtered. The filtrate was diluted with water (100 mb) and extracted with ethyl acetate (3 x 200 mL). The organic layer was concentrated to give a residue. The residue was purified by reversed phase chromatography (C18, 40 g; condition: water/acetonitrile = 100/0 to 0/100, 0.1% formic acid) and lyophilized to afford 4-((S)-2-((1S)-2-((ter/-butoxycarbonyl)amino)propanamido)propanamido)benzyl (2-(3-(5- ((3-(3 -chi oro-4-methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)--2d,6o-dioixopiperidine- 1- carbonyl) benzyl)(methyl)carbamate Int 53f (150 mg, 153 μmol, 23% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6 ) δ = 10.08 - 9.87 (m, 1H), 8.75 (s, 1H), 8.11 - 7.93 (m, 2H), 7.73 - 7.57 (m, 4H), 7.54 - 7.41 (m, 4H), 7.39 - 7.22 (m, 2H), 7.20 - 7.08 (m, 3H), 7.00 - 6.92 (m, 1H), 6.79 (t, J= 5.6 Hz, 1H), 5.50 (br dd, J= 5.2, 13.6 Hz, 1H), 5.12 - 4.95 (m, 2H), 4.91 - 4.79 (m, 1H), 4.78 - 4.68 (m, 1H), 4.57 - 4.33 (m, 5H), 4.04 - 3.94 (m, 1H), 2.93 - 2.82 (m, 4H), 2.67 - 2.60 (m, 1H), 2.47 - 2.38 (m, 1H), 2.23 (s, 3H), 2.20 - 2.13 (m, 1H), 1.43 - 1.13 (m, 15H). LCMS (ESI) m/z 879.5 [M+H-100]+
Step G. Preparation of Int 53g
To a solution of 4-((S)-2-((5)-2-((tert- butoxycarbonyl)amino)propanamido)propanamido)benzyl(2-(3-(5-((3-(3-chl oro-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidine-l-carbonyl)benzyl) (methyl)carbamate (150 mg, 153 μmol, 1.00 eq) in dichloromethane (0.900 mL) was added trifluoroacetic acid (0.300 mL). Then the mixture was stirred at 25 °C for 0.5 h. The mixture was filtered. The filtrate was purified by reversed phase chromatography (Cl 8, 80 g; condition: water/acetonitrile = 100/0 to 0/100, 0.1% formic acid) and /wp-HPLC (column: Phenomenex luna C1 8 150 * 25 mm * 10 um; mobile phase: [water (formic acid) - acetonitrile]; gradient: 20% - 50% B over 15 min) and lyophilized to afford 4-((5)-2-((5)-2- aminopropanamido)propanamido)benzyl(2-(3-(5-((3-(3-chloro-4-methylphenyl)ureido)methyl) - l-oxoisoindolin-2-yl)-2,6-dioxopiperidine-l-carbonyl)benzyl)(methyl)carbamate (30.0 mg, 34.1 μmol, 22% yield) as a white solid. LCMS (ESI) m/z 879.5 [M+H]+
Step H. Preparation of Compound IG-L-53
To a solution of 4-((S)-2-((1S)-2-aminopropanamido)propanamido)benzyl(2-(3-(5-((3-(3- chloro-4-methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidine-l- carbonyl)benzyl)(methyl) carbamate Int 53g (20.0 mg, 22.7 μmol, 1.00 eq) and 34-(3-(2,5- dioxo-2,5-dihydro-177-pyrrol-l-yl)-2-fluoro-6-(3-oxo-3-(2,3,5,6- tetrafluorophenoxy)propyl)phenoxy)-3,6,9, 12, 15, 18,21,24,27,30-decamethyl- 4,7,10,13,16,19,22,25,28,31-decaoxo-3,6,9,12,15,18,21,24,27,30-decaazatetratriacontanoic acid Int 36k (27.8 mg, 22.7 μmol, 1.00 eq) in dimethyl formamid (1.00 mL) was added tri ethylamine (4.60 mg, 45.5 μmol, 6.33 μL, 2.00 eq). Then the mixture was stirred at 25 °C for 0.5 h. The mixture was filtered. The filtrate was purified by p/vp-HPLC (column: Welch Xtimate Cl 8 150 * 25 mm * 5 um; mobile phase: [water (formic acid) - acetonitrile]; gradient: 30% - 60% B over 35 min) and lyophilized to afford 34-(6-(3-(((2S)-l-(((25)-l-((4-((((2-(3-(5-((3-(3-chloro-4- methylphenyl)ureido)methyl)-l-oxoisoindolin-2-yl)-2,6-dioxopiperidine-l-carbonyl)benzyl) (methyl) carbamoyl)oxy)methyl)phenyl)amino)-l-oxopropan-2-yl)amino)-l-oxopropan-2- yl)amino)-3 -oxopropyl)-3-(2, 5 -dioxo-2, 5 -dihydro- 1 H-pyrrol - 1 -yl)-2-fluorophenoxy)-
3.6.9.12.15.18.21.24.27.30-decamethyl-4,7,10,13, 16,19,22,25,28,31-decaoxo-
3.6.9.12.15.18.21.24.27.30-decaazatetratriacontanoic acid, Compound IG-L-53 (9.00 mg, 4.60 μmol, 20% yield, 96% purity) as a white solid. 1H NMR (400 MHz, DMSO-d6) δ = 9.99 - 9.89 (m, 1H), 9.03 - 8.79 (m, 1H), 8.24 - 8.10 (m, 2H), 8.07 (br d, J= 7.6 Hz, 1H), 7.72 - 7.61 (m, 4H), 7.53 - 7.45 (m, 3H), 7.43 (br d, 8.0 Hz, 1H), 7.37 - 7.32 (m, 1H), 7.28 - 7.22 (m, 3H),
7.19 - 7 10 (m, 4H), 7.04 (br t, J= 7.6 Hz, 1H), 6.93 (ddd, J= 5.2, 8.4, 11.2 Hz, 1H), 5.56 - 5.45 (m, 1H), 5.10 - 4.97 (m, 2H), 4.91 - 4.81 (m, 1H), 4.78 - 4.68 (m, 1H), 4.58 - 4.48 (m, 1H), 4.40 - 4.28 (m, 10H), 4.25 - 4.16 (m, 5H), 4.10 - 3.89 (m, 13H), 2.95 - 2.68 (m, 40H), 2.22 (s, 3H),
2.20 - 2 11 (m, 2H), 1.96 - 1.88 (m, 2H), 1.32 - 1.27 (m, 3H), 1.18 (br s, 3H). LCMS (ESI) m/z 1938.1 [M+2H]+
EXAMPLE L-63: Synthesis of l-(3-chloro-5-(2,5-dioxo-2,5-dihydro-lH-pyrrol-l-yl)-4- methylphenyl)-3 -((2-(2,6-dioxopiperi din-3 -yl)-l-oxoisoindolin-5-yl)m ethyl )urea, IG-L-63
Figure imgf000408_0001
Int 63a
To a solution of 2-chloro-l-methyl-4-nitrobenzene (5.00 g, 29.1 mmol, 6.02 mL, 1.00 eq) in sulfuric acid (20.0 mL) and heptane (20.0 mL) was added 7V-bromosuccinimide (6.22 g, 34.9 mmol, 1.20 eq) in batches at 50 °C. The mixture was stirred at 50 °C for 2 h. The mixture was dropwised into ice water (60 mL) and extracted with ethyl acetate (3* 60 mL). The combined organic layers were dried over sodium sulfate and filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by reversed- phase column (Cl 8, 120 g; condition: water/ acetonitrile = 1/0 -0/1, 0.1%formic acid) and lyophilized to afford l-bromo-3-chloro-2-methyl-5-nitrobenzene Int 63a (1.80 g, 7.19 mmol, 24% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) 8 = 8.39 (d, J= 2.4 Hz, 1H), 8.31 (d, J= 2.4 Hz, 1H), 2.56 (s, 3H).
Step B. Preparation of Int 63b
Figure imgf000408_0002
To a solution of l-bromo-3-chloro-2-methyl-5-nitrobenzene Int 63a (1.00 g, 3.99 mmol, 1.00 eq) and tert-butyl carbamate (468 mg, 3.99 mmol, 1.00 eq) in toluene (10.0 mL) was added cesium carbonate (3.90 g, 12.0 mmol, 3.00 eq), 2-(dicyclohexylphosphino)-2,4,6-tri-i-propyl- 1 „ 1 -biphenyl (381 mg, 798 μmol, 0.200 eq) and tris(dibenzylideneacetone)dipalladiuin(0) (366 mg, 399 μmol, 0. 100 eq). The mixture was stirred at 100 °C for 1 h under nitrogen atmosphere. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (C18, 120 g; condition: water/ acetonitrile = 1/0 - 0/1, 0.1% formic acid) and lyophilized to afford tert-butyl (3-chloro-2-methyl-5-nitrophenyl)carbamate Int 63b (420 mg, 1.17 mmol, 29% yield, 80% purity) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) δ = 9.23 (s, 1H), 8.32 - 8.30 (m, 1H), 8.05 - 8.03 (m, 1H), 2.34 (s, 3H), 1.49 (s, 9H).
Step C. Preparation of Int 63c
Figure imgf000409_0001
Int 63b Int 63c
To a solution of tert-butyl (3-chloro-2-methyl-5-nitrophenyl)carbamate Int 63b (420 mg, 1.17 mmol, 1.00 eq) in methanol (20.0 mL) was added saturated ammonium chloride (188 mg, 3.52 mmol, 3.00 eq) in water (2.00 mL). Iron powder (327 mg, 5.86 mmol, 5.00 eq) was added to the mixture at 80 °C. The mixture was stirred at 80 °C for 1 h The mixture was filtered to give a filtrate and concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (C18, 80 g; condition: water/ acetonitrile = 1/0 - 0/1, 0.1% formic acid) and lyophilized to afford tert-butyl (5-amino-3-chloro-2-methylphenyl)carbamate Int 63c (53.0 mg, 206 μmol, 17% yield) as a white solid. 1H NMR (400 MHz, DMSO-<sfc) δ = 8.47 (s, 1H), 6.53 (d, 2.0 Hz, 1H), 6.44 (d, J= 2.0 Hz, 1H), 5.15 (s, 2H), 2.02 (s, 3H), 1.44
(s, 9H).
Step D. Preparation of Int 63d
Figure imgf000409_0002
To a solution of tert-butyl (5-amino-3-chloro-2-methylphenyl)carbamate Int 63c (53.0 mg, 206 μmol, 1.00 eq) in acetonitrile (1.00 mL) was added phenyl carbonochloridate (32.3 mg, 206 μmol, 25.9 μL, 1.00 eq) and pyridine (32.7 mg, 413 μmol, 33 3 μL, 2.00 eq). The mixture was stirred at 25 °C for 0.5 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (Cl 8, 12 g; condition: water/acetonitrile = 1/0 - 0/1, 0.1% formic acid) and lyophilized to afford tert-butyl phenyl (5- chloro-4-methyl-l,3-phenylene)dicarbamate Int 63d (55.0 mg, 144 μmol, 70% yield, 99% purity) as a white solid. MS (ESI) m/z 399.2 [M+Na]+
Step E. Preparation of Int 63e
Figure imgf000410_0001
To a solution of 3-(5-(aminomethyl)-l-oxoisoindolin-2-yl)piperidine-2, 6-dione Int 63d (42.9 mg, 146 μmol, 1.00 eq) in/V,7V-dimethylformamide (1.00 mL) was added triethylamine (73.8 mg, 729 μmol, 102 μL, 5.00 eq) and tert-butyl phenyl (5-chloro-4-methyl-l,3- phenylene)dicarbamate (55.0 mg, 146 μmol, 1.00 eq). The mixture was stirred at 50 °C for 1 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (C18, 40 g; condition: water/ acetonitrile = 1/0 - 0/1, 0.1% formic acid) and lyophilized to afford tert-butyl (3-chloro-5-(3-((2-(2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl)ureido)-2-methylphenyl)carbamate Int 63e (45.0 mg, 80.9 μmol, 55% yield) as a white solid. ’H NMR (400 MHz, DMSO-cZ6) δ = 10.97 (s, 1H), 8.81 (s, 1H), 8.71 - 8.68 (m, 1H), 7.69 (d, J= 8.0 Hz, 1H), 7.52 - 7.50 (m, 2H), 7.43 (d, J= 8.4 Hz, 1H), 7.26 (d, J - 2.0 Hz, 1H), 6.73 (t, J - 6.0 Hz, 1H), 5.10 (dd, J= 5.2, 13.2 Hz, 1H), 4.49 - 4.28 (m, 4H), 2.97 - 2.85 (m, 1H), 2.57 (br s, 1H), 2.44 - 2.35 (m, 1H), 2.12 - 2.11 (m, 3H), 2.04 - 1.94 (m, 1H), 1.45 (s, 9H). MS (ESI) m/z 500.2 [M-56+H]+
Step F. Preparation of Int 63f
Figure imgf000411_0001
To a solution of tert-butyl (3-chloro-5-(3-((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin- 5-yl)methyl)ureido)-2-methylphenyl)carbamate Int 63e (45.0 mg, 80.9 μmol, 1.00 eq) in dichloromethane (1.00 mL) was added trifluoroacetic acid (307 mg, 2.69 mmol, 0.200 mL, 33.3 eq). The mixture was stirred at 25 °C for 1 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (Cl 8, 40 g; condition: water/ acetonitrile = 1/0 - 0/1, 0.1% formic acid) and lyophilized to afford l-(3- amino-5-chloro-4-m ethylphenyl)-3-((2-(2,6-dioxopiperi din-3 -yl)-l-oxoisoindolin-5- yl)methyl)urea Int 63f (27.0 mg, 56.3 μmol, 69% yield, 95% purity) as a white solid MS (ESI) m/z 456.1 [M+H]+
Step G. Preparation of Compound IG-L-63
Figure imgf000411_0002
To a solution of l-(3-amino-5-chloro-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-l- oxoisoindolin-5-yl)methyl)urea Int 63f (17.0 mg, 37.3 μmol, 1.00 eq) in acetic acid (1.00 mL) was added furan-2,5-dione (3.66 mg, 37.3 μmol, 1.00 eq). The mixture was stirred at 60 °C for 12 h. The mixture was concentrated under reduced pressure to give a residue. The residue was purified by reversed-phase column (C18, 40 g; condition: water/acetonitrile = 1/0 -0/1, 0.1%formic acid) and lyophilized to afford l-(3-chloro-5-(2,5-dioxo-2,5-dihydro-l#-pyrrol-l- yl)-4-methylphenyl)-3-((2-(2,6-dioxopiperidin-3-yl)-l-oxoisoindolin-5-yl)methyl)urea, Compound IG-L-63 (3.82 mg, 7.06 μmol, 19% yield, 99% purity) as a white solid.
Figure imgf000411_0003
NMR (400 MHz, DMSO-ofc) δ = 10.97 (br s, 1H), 9.15 - 8.97 (m, 1H), 7.75 - 7.64 (m, 2H), 7 51 (s, 1H), 7.43 (d, J= 8.0 Hz, 1H), 7.25 (d, J= 2.0 Hz, 1H), 7.21 (s, 2H), 7.03 (br d, J= 4.8 Hz, 1H), 5.10 (dd, J= 5.2, 13.3 Hz, 1H), 4.47 - 4.28 (m, 4H), 2.97 - 2.83 (m, 1H), 2.63 - 2.56 (m, 1H), 2.44 - 2 35 (m, 1H), 1.99 (s, 4H). MS (ESI) m/z 536.3 [M+H]+
The compounds in Table 20 were prepared in a manner similar to that described for Compound IG-L-63 using the appropriate compound as starting material
Table 20
Figure imgf000413_0001
EXAMPLE L-67: Synthesis of l-(5-(2-(2-(2,5-dioxo-2,5-dihydro-lH-pyrrol-l- yl)ethoxy)ethyl)naphthalen-l-yl)-3-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5- yl)methyl)urea, IG-L-67
Figure imgf000414_0001
To a solution of 3-(5-(aminomethyl)-4-methoxy-l-oxoisoindolin-2-yl)piperidme-2,6- dione (200 mg, 659 μmol, 1.00 eq) in dichloromethane (5.00 mL) was added boron tribromide (3.30 g, 13.2 mmol, 1.27 mL, 20.0 eq) dropwise at 0 °C. The mixture was stirred at 25 °C for 12 h. The reaction mixture was quenched with water (10 mL), filtered and the filtrate was concentrated under reduced pressure to give a crude product. The crude product was purified by reversed phase (0.1% formic acid condition) and lyophilized to afford 3-(5-(aminomethyl)-4- hydroxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione Int 67a (150 mg, 519 μmol, 79% yield) as a brown solid. 1H NMR (400 MHz, DMSO-d6) δ - 11.00 (s, 1H), 10 36 (br s, 1H), 8.08 (br s, 2H), 7.48 (d, J= 7.6 Hz, 1H), 7.28 (d, J= 7.6 Hz, 1H), 5.11 (dd, J= 4.8, 13.2 Hz, 1H), 4.43 - 4.24
(m, 2H), 4.15 - 4.07 (m, 2H), 3.00 - 2.87 (m, 1H), 2.61 (br d, J= 17 6 Hz, 1H), 2.36 (br dd, J = 4.4, 13.2 Hz, 1H), 2.08 - 1.98 (m, 1H).
Step B. Preparation of Int 67b
Figure imgf000414_0002
TTMSS, Na2CO3 Int 67b
DME, blue LED lamp, 25 °C, 14 h A mixture of tert-butyl (2-(2-bromoethoxy)ethyl)carbamate (157 mg, 585 μmol, 1.30 eq), 5-bromonaphthalen-l-amine (100 mg, 450 μmol, 1.00 eq), (4,4-di-te/7-butyl-2,2-bipyridine) bis(3,5-difluoro-2-(5-trifluoromethyl-2-pyridinyl-kappa)phenyl-kappa) iridium(III) hexafluorophosphate (5.05 mg, 4.50 μmol, 0 0100 eq), bis(trimethylsilyl)silyl-trimethyl-silane (112 mg, 450 μmol, 139 μL, 1.00 eq) and sodium carbonate (95.5 mg, 901 μmol, 2.00 eq) in dimethyl ether (10.0 mb) was degassed and purged with nitrogen atmosphere. The mixture was stirred at 25 °C for 14 h inradiated with a 455 nm blue LED. The mixture was filtered and concentrated to afford a residue. The residue was purified by reversed phase (0.1% formic acid condition) and lyophilized to afford tert-butyl (2-(2-(5-aminonaphthalen-l- yl)ethoxy)ethyl)carbamate Int 67b (800 mg, 2.42 mmol, 67% yield) as brown oil. rH NMR (400 MHz, DMSO-d6) δ = 7.96 - 7.91 (m, 1H), 7.36 - 7.22 (m, 3H), 6.75 (br d, J= 6.8 Hz, 2H), 3.72 - 3.65 (m, 2H), 3.59 - 3.54 (m, 1H), 3.46 - 3.40 (m, 4H), 3.20 (br t, J= 7.2 Hz, 2H), 3.10 - 3.05 (m, 2H), 1.37 (s, 9H).
Step C. Preparation of Int 67c
Figure imgf000415_0001
Int 67b Int 67c
To a solution of tert-butyl (2-(2-(5-aminonaphthalen-l-yl)ethoxy)ethyl)carbamate Int 67b (800 mg, 2.42 mmol, 1.00 eq) and pyridine (383 mg, 4.84 mmol, 391 μL, 2.00 eq) in acetonitrile (10.0 mL) was added phenyl carbonochloridate (758 mg, 4.84 mmol, 607 μL, 2.00 eq) dropwise at 0 °C. The mixture was stirred at 0 °C for 1 h. The mixture was concentrated to afford a residue. The residue was purified by reversed phase (0.1% formic acid condition) and lyophilized to afford tert-butyl (2-(2-(5-((phenoxycarbonyl)amino)naphthalen-l- yl)ethoxy)ethyl)carbamate Int 67c (660 mg, 1.46 mmol, 61% yield) as a yellow solid. H NMR (400 MHz, DMSO-cL) δ = 10.08 (br s, 1H), 8.06 (d, J= 8.4 Hz, 1H), 7.99 (br d, J= 8.4 Hz, 1H), 7.66 (d, J= 7.2 Hz, 1H), 7.56 (d, J= 7.6 Hz, 1H), 7.49 (d, J= 8.4 Hz, 1H), 7.47 - 7.43 (m, 3H), 7.26 (br d, J= 12 Hz, 3H), 6.75 (br t, J= 52 Hz, 1H), 3.71 (t, J= 12 Hz, 2H), 3.45 - 3.40 (m, 2H), 3.31 (br s, 2H), 3.08 (s, 2H), 1.38 (s, 9H).
Step D. Preparation of Int 67d
Figure imgf000416_0001
To a solution of tert-butyl (2-(2-(5-((phenoxycarbonyl)amino)naphthalen-l- yl)ethoxy)ethyl)carbamate Int 67c (150 mg, 333 μmol, 1.00 eq) and 3-(5-(aminomethyl)-4- hydroxy-l-oxoisoindolin-2-yl)piperidine-2, 6-dione (125 mg, 433 μmol, 1.30 eq) m N,N- dimethylformamide (1.00 mL) was added jV,A^-diisopropylethylamine (129 mg, 999 μmol, 174 μL, 3.00 eq). The mixture was stirred at 25 °C for 2 h. The mixture was filtered. The filtrate was purified by reversed phase (0. 1% formic acid condition) and lyophilized to afford tert-butyl (2-(2-(5-(3-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5- yl)methyl)ureido)naphthalen-l-yl)ethoxy) ethyl)carbamate Int 67d (160 mg, 248 μmol, 74% yield) as a yellow solid. 1H NMR (400 MHz, DMSO-76) d = 10.97 (s, 1H), 10.25 (br d, ./ ~ 1.6 Hz, 1H), 8.75 (s, 1H), 7.95 (br d, J= 8.0 Hz, 1H), 7.88 (d, J= 7.6 Hz, 1H), 7.80 (br d, J= 8.8 Hz, 1H), 7.50 - 7.40 (m, 4H), 7.22 (d, J= 7.6 Hz, 1H), 7.16 (br t, J= 5.6 Hz, 1H), 6.77 - 6.71 (m, 1H), 5.09 (dd, 5.2, 13.2 Hz, 1H), 4.42 - 4.37 (m, 2H), 4.35 - 4.20 (m, 211), 3 69 (br t, .7 - 6.8 Hz, 2H), 3.43 - 3.40 (m, 3H), 3.10 - 3.05 (m, 2H), 2.95 - 2.87 (m, 1H), 2.60 (br d, J= 18.0 Hz, 2H), 2.38 (br dd, 7= 4 0, 13.2 Hz, 1H), 2.05 - 1.98 (m, 1H), 1.37 (s, 9H).
Step E. Preparation of Int 67 e
Figure imgf000417_0001
Int 67e
A mixture of tert-butyl (2-(2-(5-(3-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l- oxoisoindolin-5-yl)methyl) ureido)naphthalen-l-yl)ethoxy)ethyl)carbamate Int 67d (80 0 mg, 124 μmol, 1.00 eq) in hydrochloric acid/di oxane (2.00 mL) was stirred at 25 °C for 2 h. The mixture was concentrated to afford a residue. The residue was purified by reversed phase (0.1% hydrochloric acid condition) and lyophilized to afford l-(5-(2-(2-aminoethoxy)ethyl)naphthalen- l-yl)-3-((2-(2,6-dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5-yl) methyl)urea Int 67e (70.0 mg, 120 μmol, 97% yield) as a yellow solid. 1H \MR (400 MHz, DMSO-d6) δ = 10.98 (s, 1H), 10.24 (s, 1H), 8.93 (s, 1H), 8.10 - 7.97 (m, 1H), 7.93 - 7.85 (m, 3H), 7.80 (d, J= 8.4 Hz, 1H), 7.52 - 7 37 (m, 5H), 7.22 (d, J= 7.6 Hz, 1H), 5.09 (dd, J= 4.8, 13.2 Hz, 1H), 4.43 - 4.37 (m,
2H), 4.36 - 4.21 (m, 2H), 3.76 (t, J= 7.2 Hz, 2H), 3.63 (t, J= 5.4 Hz, 2H), 3.52 - 3.44 (m, 2H), 3.02 - 2 94 (m, 2H), 2.93 - 2.86 (m, 1H), 2.64 - 2.56 (m, 1H), 2.42 - 2.28 (m, 1H), 2.04 - 1.97 (m, 1H).
Step F. Preparation of Compound IG-L-67
Figure imgf000418_0001
Compound IG-L-67
To a solution of l-(5-(2-(2-aminoethoxy)ethyl)naphthalen-l-yl)-3-((2-(2,6- dioxopiperidin-3-yl)-4-hydroxy-l-oxoisoindolin-5-yl)methyl)urea Int 67e (70.0 mg, 120 μmol, 1.00 eq) in tetrahydrofuran (2.00 mL) and water (1.00 mL) was added a solution of methyl 2,5- dioxo-2,5-dihydro-177-pyrrole-l-carboxylate (37.3 mg, 240 μmol, 37.3 μL, 2.00 eq) in tetrahydrofuran (2.00 mL). Then sodium bicarbonate (30.3 mg, 361 μmol, 14.0 μL, 3.00 eq) was added and it was stirred at 25 °C for 2 h. The mixture was quenched by water (30 mL), extracted with ethyl acetate (3 x30 mL). The combined organic phases were washed with brine (2 x 30 mL), dried over anhydrous sodium sulfate, filtered and concentrated under reduced pressure to give a crude product. The crude product was purified by /vc/i-HPLC (column: Phenomenex luna Cl 8 150 * 25 mm * 10 um; mobile phase: [water (formic acid) - acetonitrile]; gradient: 25% - 55% B over 1 min), /vc/i-HPLC (column: Phenomenex luna C18 150 * 25 mm * 10 um; mobile phase: [water (hydrochloric acid) - acetonitrile]; gradient: 23% - 53% B over 10 min), reversed phase (0.1% formic acid condition) and lyophilized to afford l-(5-(2-(2-(2,5- dioxo-2,5-dihydro-17f-pyrrol-l-yl)ethoxy)ethyl)naphthalen-l-yl)-3-((2-(2,6-dioxopiperi din-3- yl)-4-hydroxy-l-oxoisoindolin-5-yl)methyl)urea Compound IG-L-67 (11.49 mg, 17.3 μmol, 14% yield, 94% purity, formate) as a white solid. rH NMR (400 MHz, DMSO-t4,) r) = 10.96 (s, 1H), 10.23 (br s, 1H), 8.75 (s, 1H), 8.15 (s, 1H), 7.95 (d, J = 8.8 Hz, 1H), 7.87 (d, J= 7.6 Hz, 1H), 7.76 (d, J = 8.4 Hz, 1H), 7.48 - 7.39 (m, 3H), 7.36 - 7.33 (m, 1H), 7.22 (d, J = 7.6 Hz, 1H), 7.19 - 7 15 (m, 1H), 7.02 - 6.98 (m, 2H), 5.13 - 5.05 (m, 1H), 4.42 - 4.38 (m, 2H), 4.35 - 4.22 (m, 2H), 3.70 - 3.68 (m, 2H), 3.56 (br d, J= 4.4 Hz, 4H), 3.21 (br d, J= 7.2 Hz, 2H), 2.93 (br dd, J = 1 6, 8.8 Hz, 1H), 2.63 - 2.63 (m, 1H), 2.40 (br d, J= 4.4 Hz, 1H), 2.04 - 2.00 (m, 1H). MS (ESI) m/z 626.2 [M+H]+ The compounds in Table 21 were prepared in a manner similar to that described for Compound IG-L-67 using the appropriate compound as starting material.
Table 21
Figure imgf000419_0001
Example 101 Generation of Isoindolinone-Glutarimide Antibody Conjugates (IGAC) through Reduction of Native Disulfide Bonds of Non-Engineered Antibodies
A targeting moiety (e.g., a mAb at 3-8 mg/mL in PBS) is exchanged into HEPES (100 mM, pH 7.0, 1 mM DTP A) via molecular weight cut-off centrifugal filtration (Millipore, 30 kDa). The resultant solution is transferred to a tared 50 mb conical tube. The protein concentration is determined to be 3-8 mg/mL by A280. To the protein solution is added TCEP (2.0-10.0 equivalents, 1 mM stock) at room temperature and the resultant mixture is incubated at 37 °C for 30-90 minutes, with gentle shaking. Upon being cooled to room temperature, a stir bar is added to the reaction tube. Next, the compound of Structure (I) (5.0-10.0 equivalents, 10 mM DMSO) is added dropwise The resultant reaction mixture is allowed to stir at ambient temperature for 30-60 minutes, at which point N-ethyl maleimide (3.0 equivalents, 100 mM DMA) is added. After an additional 15 minutes of stirring, N-acetylcysteine (6.0-11.0 equivalents, 50 mM HEPES) is added. The crude antibody conjugate is then exchanged into PBS and purified by preparative SEC (e.g. HiLoad 26/600, Superdex 200 pg) using PBS as the mobile phase. The pure fractions are concentrated via molecular weight cut-off centrifugal filtration (Millipore, 30 kDa), sterile filtered, and transferred to 15 mL conical tubes. The concentration was determined by UV-Vis and BCA, the monomer purity was determined by aSEC-HPLC and the final DAR was determined by HIC-HPLC and reduced LC-MS. The level of endotoxin determined by MCS analysis and free drug % was determined by RP-HPLC.
Example 102 In vitro cell proliferation assay One day prior to treatment with compounds or IGAC, cells were plated in white 96-well plates (SKBR: 3000 cells/well; CAL-51 : 4000 cells/well). Compounds or ADCs were added in a serial-dilution manner reaching the indicated concentrations. Plates were incubated at 37 degrees for 96h (ADCs) or 72h (compounds) whereafter a 1 : 10 dilution of C6ll Titer Glow was used to measure relative cell numbers after lOmin of incubation at room temperature.
On the day of treatment, 10,000 suspension cells/well were plated in white 96-well plates. Compounds or ADCs were added in a serial-dilution manner reaching the indicated concentrations. Plates were incubated at 37 degrees for 72h whereafter a 1 : 10 dilution of C6ll Titer Glow was used to measure relative cell numbers after lOmin of incubation at room temperature.
Example 103 Degradation assay evaluated by immunofluorescence staining
One day prior to treatment with compounds, black 96well plates were coated with fibronectin (0.2pg/ml in PBS) for 45 min at room temperature and subsequently washed with PBS. CAL-51 or SKBR3 cells were seeded at 30K cells/well (lOOpl) and incubated overnight at 37°C whereafter compounds were added reaching indicated concentrations. 6h after treatment the medium was removed, cells were washed with PBS and fixed with 10% formalin for 20 mins at room temperature. Following two PBS washes (150pl), cells were permeabilized in 0. 1% Triton X-100 in PBS for 8 mins at room temperature and subsequently washed again twice with PBS. C6lls were blocked thereafter with 1% BSA in PBS for 45 mins. Primary antibody was diluted in blocking buffer and incubated with the cells overnight at 4°C. After three washes with PBS, cells were incubated with secondary antibody for Ih at RT, washed and subsequently images were taken on an Operetta High-Content Imager.
For the determination of the DC50, a custom algorithm implemented in the PerkinElmer image analysis software Harmony-Acapella® was used.
Example 104 Degradation assay evaluated with JESS (western blot)
One day prior to treatment cells were seeded in 6 or 12well plates at a confluency of 70% Compounds or IGAC were added in the indicated concentrations and cells incubated at 37°C for indicated duration (6h, 16h, 24h). After washing the cells with ice cold PBS, RIPA lysis buffer containing protease and phosphatase inhibitors was added and cells were scraped off the plates. After vigorous vortexing, lysates were incubated on ice for lOmin and subsequently centrifuged at 12000 rpm for 12min at 4°C. Supernatants were transferred to a new tube and used for analysis on the JESS machine. Example 105 Treatment of HER2+ MDA-MB-453 syngeneic tumor bearing NOD SCID mice with an anti-Her2-Isoindolinone Glutarimide conjugate
MDA-MB-453 cells were maintained in vitro in L-15 medium supplemented with 10% fetal bovine serum and 1% Antibiotic-Antimycotic at 37 °C in an atmosphere with 5% CO2 in air. 5* 10s C6lls resuspended in 0.2 mL of PBS mixed with Matrigel (50:50) were inoculated subcutaneously into the flank of female NOD SCID mice and allowed to grow to 150 mm3. Mice were dosed intravenously with the vehicle, isotype ADC control, or a representative compound of the disclosure (single IV injection, 3 and lOmg/kg). Compound dosing solution was prepared on day of dosing by dilution in its formulation buffer Tumor volumes were measured twice weekly over a period of 28 days.
Example 106 Treatment of CD22+ WSU-DLCL2 syngeneic tumor bearing CB 17 SCID mice with anti-CD22-Isoindolinone Glutarimide conjugates
The objective of the study was to evaluate the in vivo anti-tumor efficacy of pinatuzumab, IGAC-59 and IGAC-62 in the WSU-DLCL2 lymphoma xenograft model grown in female CB17 SCID mice
The WSU-DLCL2 tumor cells were maintained in vitro in RPMI-1640 medium supplemented with 10% FBS and 1% antibiotic-antimycotic at 37°C in an atmosphere with 5% CO2 in air. WSU-DLCL2 tumor cells are a diffuse large B-cell lymphoma (DLBCL) cell line, expressing the CD22 antigen, which is a protein found on the surface of B cells. CD22 is a well- validated tumor target for the treatment of B-cell leukemia and lymphoma. The tumor cells were routinely sub-cultured twice weekly. The cells growing in exponential growth phase were harvested and counted for tumor inoculation. The mice were inoculated subcutaneously in the right flank with WSU-DLCL2 tumor cells (10* 106) in 0.1 ml of PBS and allowed to grow to 200 mm3. The mice were grouped (n=9 mice per group) and treatments were started on day 21 after cell inoculation when the average tumor volume reached 198 mm3. Mice were dosed intravenously with the vehicle, pinatuzumab, or a representative compound of the disclosure, including IGAC-59 and IGAC-62 (single IV injection, 3, 10 and 20 mg/kg). Compound dosing solution was prepared on day of dosing by dilution in its formulation buffer (20 mM histidine, 7% sucrose, pH 5.5). Tumor size was measured twice weekly over a period of 28 days in two dimensions using a caliper, and the volume was expressed in mm3 using the formula: V = 0.5 a x b2 where a and b are the long and short diameters of the tumor, respectively. Body weight was measured twice a week and animals would be euthanized if they lost over 20% of body weight from the weight at day 1 . Tumor growth inhibition (TGI) was calculated for each group using the formula: TGI (%) = [l-(Ti-TO)/ (Vi -V0)] xlOO; Ti is the average tumor volume of a treatment group on D21 post dosing, TO is the average tumor volume of the treatment group on the day of treatment start, Vi is the average tumor volume of the vehicle control group on the same day with Ti, and VO is the average tumor volume of the vehicle group on the day of treatment start.
The anti -turn or efficacy of pinatuzumab, IGAC-59 and IGAC-62 on WSU-DLCL2 xenografts grown in female CB17 SCID mice was evaluated. The tumor growth inhibition curves are shown in Figure 1. Tumor growth inhibition analysis is provided in Table 22.
Figure 1 shows a graph of in vivo tumor volume over time in the treatment of CD22+ WSU-DLCL2 syngeneic tumor bearing CB17 SCID mice with pinatuzumab, and anti-CD22 conjugates IGAC-59 and IGAC-62 (Table 3).
Table 22 Tumor Growth Inhibition Analysis: The inhibition rates of pinatuzumab, IGAC- 59 and IGAC-62 on WSU-DLCL2 tumors are calculated with tumor size data on D21 post dosing
Figure imgf000422_0001
Naked antibody pinatuzumab at 20 mg/kg did not show any activity in WSU-DLCL2 tumors, whereas conjugate IGAC-59 and IGAC-62 (Table 3) treated groups showed significant tumor growth delay compared to vehicle group. At the end of the study, IGAC-59 20 mg/kg and IGAC-62 20 mg/kg treated groups reached tumor regression demonstrating the efficacy of antibody conjugate compositions in treating cancer.
Mean body weight remained within +/- 5% of initial body weight (BW) for all groups. Food supplement was given to 3 mice across groups 5 and 7 due to a BW loss greater than 10%. Mice treated with conjugates IGAC-59 and IGAC-62 recovered and/or stabilized their body weight upon addition of food supplement demonstrating the safety of antibody conjugate compositions.
Example 107 Treatment of CD22+ WSU-DLCL2 syngeneic tumor bearing CB17 SCID mice with anti-CD22-Isoindolinone Glutarimide conjugates The objective of the study was to evaluate the in vivo anti -turn or efficacy of Pinatuzumab, IGAC-53, IGAC-60 and IGAC-62 in the WSU-DLCL2 lymphoma xenograft model grown in female CB17 SCID mice
The WSU-DLCL2 tumor cells were maintained in vitro in RPMI-1640 medium supplemented with 10% FBS and 1% antibiotic-antimycotic at 37°C in an atmosphere with 5% CO2 in air. The tumor cells were routinely sub-cultured twice weekly. The cells growing in exponential growth phase were harvested and counted for tumor inoculation. The mice were inoculated subcutaneously in the right flank with WSU-DLCL2 tumor cells (10*106) in 0.1 ml of PBS and allowed to grow to 200 mm3 The mice were grouped (n=9 mice per group) and treatments were started on day 21 after cell inoculation when the average tumor volume reached 186 mm3. Mice were dosed intravenously with the vehicle, pinatuzumab, or a representative compound of the disclosure (single IV injection, 3, 10 and 20mg/kg). Compound dosing solution was prepared on day of dosing by dilution in its formulation buffer (20 mM histidine, 7% sucrose, pH 5.5). Tumor size was measured twice weekly over a period of 28 days in two dimensions using a caliper, and the volume was expressed in mm3 using the formula: V = 0.5 a x b2 where a and b are the long and short diameters of the tumor, respectively. Body weight was measured twice a week and animals would be euthanized if they lost over 20% of body weight from the weight at day 1 Tumor growth inhibition (TGI) was calculated for each group using the formula: TGI (%) = [l-(Ti-TO)/ (Vi -V0)] xlOO; Ti is the average tumor volume of a treatment group on D24 post dosing, TO is the average tumor volume of the treatment group on the day of treatment start, Vi is the average tumor volume of the vehicle control group on the same day with Ti, and V0 is the average tumor volume of the vehicle group on the day of treatment start.
In this study, the anti-tumor efficacy of Pinatuzumab, IGAC-53, IGAC-60 and IGAC-62 on WSU-DLCL2 xenografts grown in female CB17 SCID mice was evaluated. The body weight change curves and tumor growth curves are shown in Figure 2, tumor growth inhibition data is shown in Table 23.
Figure 2 shows a graph of in vivo tumor volume over time in the treatment of CD22+ WSU-DLCL2 syngeneic tumor bearing CB17 SCID mice with pinatuzumab, and anti-CD22 conjugates IGAC-53, IGAC-60 and IGAC-62 (Table 3).
Table 23 Tumor Growth Inhibition Analysis: The inhibition rates of pinatuzumab, IGAC- 53 and IGAC-60 and IGAC-62 on WSU-DLCL2 tumors are calculated with tumor size data on D24 post dosing.
Figure imgf000423_0001
Figure imgf000424_0001
Naked antibody pinatuzumab at 5 mg/kg did not show any activity in WSU-DLCL2 tumors. In contrast, all ADC treated groups showed significant tumor growth delay compared to that of vehicle and pinatuzumab and in a dose dependent manner. At the end of the study, IGAC-62 20 mg/kg treated group reached tumor stasis. Mean body weight remained within +/- 5% of initial BW for all groups. Food supplement was given to 7 mice across group 2, 4, 5, 7, 8 due to a BW loss greater than 10%. Mice recovered and/or stabilized their body weight upon addition of food supplement. Overall, the tested DACs were well tolerated.
Example 108 Treatment of HER2+ NCI-N87 gastric tumor xenograft bearing female B ALB/c nude mice with anti-HER2-Isoindolinone Glutarimide conjugates
The objective of the study was to evaluate the in vivo anti-tumor efficacy of IGAC-58 and IGAC-61 in NCI-N87 gastric tumor xenograft model grown in female BALB/c nude mice.
The NCI-N87 tumor cells were maintained in vitro in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic at 37°C in an atmosphere with 5% CO? in air. NCI-N87 is a HER2 -positive adenocarcinoma, gastric cancer xenograft model utilized in studying pre-clinical monotherapies and combination therapies The tumor cells were routinely sub-cultured twice weekly. The cells growing in exponential growth phase were harvested and counted for tumor inoculation. The mice were inoculated subcutaneously in the right flank with NCI-N87 tumor cells (10*106) in 0.2 mL of PBS mixed with Matrigel (50:50). The treatments were started on day 5 after cell inoculation when the average tumor volume reached 200 mm3. Mice were dosed intravenously with the vehicle, isotype ADC control, or a representative compound of the disclosure (single IV injection, 5 and 20 mg/kg). Compound dosing solution was prepared on day of dosing by dilution in its formulation buffer (20 mM histidine, 7% sucrose, pH 5.5). The main efficacy endpoint was to see impact of compounds on tumor growth Tumor size was measured twice weekly over a period of 28 days in two dimensions using a caliper, and the volume was expressed in mm3 using the formula: V = 0.5 a x b2 where a and b are the long and short diameters of the tumor, respectively. Body weight was measured twice a week and animals would be euthanized if they lost over 20% of body weight from the weight at day 1 .
Figure 3 shows a graph of in vivo tumor volume over time in the treatment of HER2+ NCI-N87 gastric tumor xenograft bearing female BALB/c nude mice with anti-HER2 conjugates IGAC-58 and IGAC-61 (Table 3).
Results summary and discussion: IGAC-61 showed a dose dependent response at 5 vs 20 mg/kg. At the 5mg/kg dose IGAC-61 led to regression over the first 10 days post dosing, then showed tumor regrowth from D14. At the 20 mg/kg doses, both IGAC-61 and IGAC-58 led to regression over the first 10 days, and tumor regression was maintained throughout the 28 days post dosing. (Fig. 3), demonstrating efficacy in treating HER2 positive cancer.
In this study, all treatments were well-tolerated and mice slightly gained body weight over the course of the study No clinically relevant body weight loss or other clinical signs due to the treatment were observed, demonstrating the safety of the anti-HER2 conjugates.
Example 109 Treatment of HER2+ NCI-N87 gastric tumor xenograft bearing female
BALB/c nude mice with anti-HER2-Isoindolinone Glutarimide conjugates
The objective of the study was to evaluate the in vivo anti-tumor efficacy of IGAC-54, IGAC-55, IGAC-56 and IGAC-57 in NCI-N87 gastric tumor xenograft model grown in female BALB/c nude mice.
The NCI-N87 tumor cells were maintained in vitro in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic at 37°C in an atmosphere with 5% CO? in air. The tumor cells were routinely sub-cultured twice weekly. The cells growing in exponential growth phase were harvested and counted for tumor inoculation. The mice were inoculated subcutaneously in the right flank with NCI-N87 tumor cells (10* 106) in 0.2 mL of PBS mixed with Matrigel (50:50). The treatments were started on day 5 after cell inoculation when the average tumor volume reached 200 mm3. Mice were dosed intravenously with the vehicle, isotype ADC control, or a representative compound of the disclosure (single IV injection, 3 and 10 mg/kg). Compound dosing solution was prepared on day of dosing by dilution in its formulation buffer (20 mM histidine, 7% sucrose, pH 5.5). The main efficacy endpoint was to see impact of compounds on tumor growth. Tumor size was measured twice weekly over a period of 21 days in two dimensions using a caliper, and the volume was expressed in mm3 using the formula: V = 0.5 a x b2 where a and b are the long and short diameters of the tumor, respectively. Body weight was measured twice a week and animals would be euthanized if they lost over 20% of body weight from the weight at day 1. Figure 4 shows a graph of in vivo tumor volume over time in the treatment of HER2+ NCI-N87 gastric tumor xenograft bearing female BALB/c nude mice with anti-HER2 conjugates IGAC-54, IGAC-55, IGAC-56 and IGAC-57 (Table 3).
Results summary and discussion: IGAC-57 showed a dose dependent response at 3 vs 10 mg/kg. At the 3mg/kg dose IGAC-57 and IGAC-56 at the 10 mg/kg dose led to regression over the first 14 days post dosing, then showed tumor stasis at D21. At the 10 mg/kg doses, IGAC-57, IGAC-54 and IGAC-55 led to regression over the first 10 days, and tumor regression was maintained throughout the 21 days post dosing (Figure 4).
In this study, all treatments were well-tolerated and mice slightly gained body weight over the course of the study No clinically relevant body weight loss or other clinical signs due to the treatment were observed, demonstrating safety of the anti-HER2 conjugates.
All references, including publications, patent applications, and patents, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.

Claims

WHAT IS CLAIMED:
1 An antibody conjugate composition comprising an isoindolinone-glutarimide moiety covalently attached to an antibody by an antibody linker, wherein the antibody binds to a tumor-associated antigen or cell-surface receptor.
2 The antibody conjugate composition of claim 1 having Formula I:
Ab-[L-IG]P I or a pharmaceutically acceptable salt thereof, wherein:
Ab is the antibody;
L is the antibody linker;
IG is the isoindolinone-glutarimide moiety; and p is an integer from 1 to 12.
3 The antibody conjugate composition of claim 2 wherein a phenolic oxygen of the isoindolinone-glutarimide moiety is attached to the antibody linker.
4 The antibody conjugate composition of claim 2 wherein the nitrogen of the glutarimide group of the isoindolinone-glutarimide moiety is attached to the antibody linker.
5 The antibody conjugate composition of claim 2 wherein a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), C1-C40 heteroalkyl, and a glycoside, or combinations thereof is attached to: (1) a phenolic oxygen, or (2) the nitrogen of the glutarimide group of the isoindolinone-glutarimide moiety.
6 The antibody conjugate composition of claim 5 wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
7 The antibody conjugate composition of claim 2 selected from Formulae la and lb:
Figure imgf000427_0001
Pla
Figure imgf000428_0001
or a pharmaceutically acceptable salt, stereoisomer, mixture of stereoisomers, tautomer, or isotopic analog thereof, wherein: m is 0, 1 or 2;
X1 is selected from the group consisting of CH2, C(=O) and N=N;
X2 is independently selected from the group consisting of F, Cl, Br, I, -CN, C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), (C1-C6 alkyl diyl)-(C6-C20 aryl), -(C1-C6 alkyl diyl)-NRaRb, -(C1-C6 alkyldiyl)-ORa, (C1-C6 alkyldiyl)-(C3-C20 carbocyclyl), (C1-C6 alkyldiyl)-(C2-C20 heterocyclyl), (C1-C6 alkyldiyl)-(C1-C20 heteroaryl), C6-C20 aryl, C3-C20 carbocyclyl, C2-C20 heterocyclyl, C1-C20 heteroaryl, -C(=NH)NH(OH), -C(=NH)NH2, -C(=0)NRaRb,
C(~O)NRa NRaRh, -C(=0)NH(C1-C6 alkyldiyl) NRaRb, C(=O)ORa, NRaRb, NO2, ORa, -OC(=O)Ra, -SRa, -S(O)Ra, -S(O)2Ra, -S(O)2NRa, and -S(O)3H;
Ra is independently selected from H, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl;
Rb is independently selected from H, -OH, -O-(C1-C6 alkyl), C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl; n is 0, 1, 2, 3, or 4;
X3 is selected from the group consisting of a bond, O, C1-C12 alkyldiyl, C2-C12 alkenyldiyl, C2-C12 alkynyldiyl, C1-C12 heteroalkyldiyl, -(C1-C5 alkyldiyl)-(C6-C20 aryldiyl)-, -(C1-C6 alkyl diyl)NRa-, -(C1-C6 alkyldiyl)O-, -(C1-C6 alkyldiyl)-(C3-C20 carbocyclyldiyl)-, -(C1-C6 alkyl diyl)-(C2-C20 heterocyclyldiyl)-, -(C1-C6 alkyldiyl)-(C1-C20 heteroaryldiyl)- -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl)-, C6-C20 aryldiyl, C3-C20 carb ocyclyl diyl, C2-C20 heterocyclyldiyl, and C1-C20 heteroaryl diyl;
X4 is selected from the group consisting of H, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), and -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl);
X5 is selected from the group consisting of a bond, C1-C12 alkyldiyl, C2-C12 alkenyldiyl, C2-C12 alkynyldiyl, C1-C12 heteroalkyldiyl, -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl), -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl)-0-(C2-C20 heterocyclyl), -(C1-C6 alkyldiyl)NRa- -(C1-C6 alkyldiyl)O-, -(C1-C6 alkyldiyl)-(C3-C20 carb ocyclyl diyl), -C1-C6 alkyl diyl)-(C2-C20 heterocyclyldiyl), -(C1-C6 alkyldiyl)-( C1-C20 heteroaryldiyl), -(C1-C12 heteroalkyldiyl)-(Cg-C20 aryldiyl), -(C1-C12 heteroalkyl diyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl), C6-C20 aryldiyl, C3-C20 carbocyclyldiyl, C2-C20 heterocyclyldiyl, and C1-C20 heteroaryldiyl; and
L is the antibody linker; wherein each alkyl, alkyldiyl, alkenyl, alkenyldiyl, alkynyl, alkynyldiyl, heteroalkyl, heteroalkyl diyl, aryl, aryldiyl, carbocyclyl, carbocyclyldiyl, heterocyclyl, heterocyclyldiyl, heteroaryl, and heteroaryl diyl is independently and optionally substituted with one or more groups selected from F, Cl, Br, I, -CN, -CH3, -CH2CH3, -CH=CH2, -CO, -C=CCH3, - CH2CH2CH3, -CH(CH3)2, -CH2CH(CH3)2, -CH2OH, -CH2OCH3, -CH2CH2OH, -C(CH3)2OH, -CH(OH)CH(CH3)2, -C(CH3)2CH2OH, -CH2CH2SO2CH3, -CH2OP(O)(OH)2, -CH2F, -CHF2, -CF3J -CH2CF3, -CH2CHF2, -CH(CH3)CN, -C(CH3)2CN, CH2CN, -CH2NH2, - CH2NHSO2CH3, -CH2NHCH3, -CH2N(CH3)2, -CO2H, -COCH3, -CO2CH3, -CO2C(CH3)3, - COCH(OH)CH3, -C0NH2, -CONHCH3, -CON(CH3)2, -C(CH3)2CONH2, -NH2, -NHCH3, - N(CH3)2, -NHCOCH3, -N(CH3)COCH3, -NHS(O)2CH3, -N(CH3)C(CH3)2CONH2, - N(CH3)CH2CH2S(O)2CH3, -NHC(=NH)H, -NHC(=NH)CH3, -NHC(=NH)NH2, - NHC(=O)NH2, -NO2, =0, -OH, -OCH3, -OCH2CH3, -OCH2CH2OCH3, -OCH2CH2OH, - OCH2CH2N(CH3)2, -0CH2F, -0CHF2, -0CF3, -0P(0)(0H)2, -S(O)2N(CH3)2, -SCH3, - S(O)2CH3, and -S(0)3H.
8 The antibody conjugate composition of any one of claims 1 to 7, wherein the antibody linker is covalently attached to a cysteine amino acid of the antibody.
9 The antibody conjugate composition of claim 8, wherein the antibody is a cysteine-engineered antibody.
10. The antibody conjugate composition of claim 7 wherein m is 0.
11. The antibody conjugate composition of claim 7 wherein m is 1.
12. The antibody conjugate composition of claim 7 wherein m is 2.
13. The antibody conjugate composition of claim 7 wherein X1 is CH2.
14. The antibody conjugate composition of claim 7 wherein X1 is C(=O).
15. The antibody conjugate composition of claim 7 wherein X1 is N=N.
16. The antibody conjugate composition of claim 7 wherein X2 comprises a -
NHC(=0)NH- group.
17. The antibody conjugate composition of claim 7 wherein X2 is selected from the group consisting of C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl )-(C6-C20 aryl), and -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-( C1-C12 heteroalkyl).
18. The antibody conjugate composition of claim 7 wherein X2 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl).
19. The antibody conjugate composition of claim 17 wherein X2 is -CH2NHC(=0)NH-(C6-C20 aryl).
20. The antibody conjugate composition of claim 18 wherein X2 is:
Figure imgf000430_0001
wherein:
** indicates the point of attachment to the isoindolinone-glutarimide moiety.
21. The antibody conjugate composition of claim 7 wherein X3 is O.
22. The antibody conjugate composition of claim 7 wherein X3 comprises a - NHC(=0)NH- group.
23. The antibody conjugate composition of claim 7 wherein X3 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl).
24 The antibody conjugate composition of claim 23 wherein X3 is -CH2NHC(=0)NH-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl).
25. The antibody conjugate composition of claim 7 wherein X3 of Formula la is selected from -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-O-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-N(Ra)-, and -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl diyl).
26. The antibody conjugate composition of claim 25 wherein X3 is -CH2CH2CH2NHC(=O)NH-(C6-C20 aryldiyl)-O-
27. The antibody conjugate composition of claim 25 wherein X3 is selected from the structures:
Figure imgf000431_0001
and wherein:
* indicates the point of attachment to L;
** indicates the point of attachment to the phenyl glutarimide moiety,
R6 is independently selected from F, Cl, Br, I, -CN, OH, -O-(C1-C12 alkyl), C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, C1-C12 heteroalkyl, C6-C20 aryl, C3-C20 carbocyclyl, C2-C20 heterocyclyl, and C1-C20 heteroaryl; nl is 1, 2, 3, or 4;
Y1 is selected from CF2 and NH; and
Y2 is selected from NH, O, and CH2.
28. The antibody conjugate composition of claim 7 wherein X3 is selected from:
Figure imgf000432_0001
wherein:
* indicates the point of attachment to L; indicates the point of attachment to the isoindolinone-glutarimide moiety;
R4 is selected from H and C1-C12 alkyl;
R6 is independently selected from F, Cl, Br, I, -CN, OH, C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, and C1-C12 heteroalkyl; and q is selected from 0, 1, 2, 3, and 4.
29. The antibody conjugate composition of claim 7 wherein X3 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl).
30. The antibody conjugate composition of claim 29 wherein X3 is selected from:
Figure imgf000432_0002
wherein:
* indicates the point of attachment to L;
** indicates the point of attachment to the isoindolinone-glutarimide moiety;
R6 is independently selected from F, Cl, Br, I, -CN, OH, C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, and C1-C12 heteroalkyl; and q is selected from 0, 1, 2, 3, and 4.
31. The antibody conjugate composition of claim 7 of Formula la:
Figure imgf000432_0003
la.
32. The antibody conjugate composition of claim 31 wherein X2 is -OH and n is 1 .
33. The antibody conjugate composition of claim 31 selected from the structures:
Figure imgf000433_0001
Figure imgf000434_0001
34. The antibody conjugate composition of claim 31 wherein X4 is H.
35. The antibody conjugate composition of claim 31 wherein X4 is selected from the group consisting of C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), and -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-O-(C2-C20 heterocyclyl).
36. The antibody conjugate composition of claim 35 wherein X4 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-0-(C2-C20 heterocyclyl), and C2-C20 heterocyclyl is a glucuronide.
37. The antibody conjugate composition of claim 31 wherein X4 of formula la is selected from the formulae:
Figure imgf000434_0002
wherein R is selected from H, C1-C6 alkyl, and O-(C1-C6 alkyl); and * indicates the point of attachment to IG.
38. The antibody conjugate composition of claim 7 of Formula lb:
Figure imgf000435_0001
39. The antibody conjugate composition of claim 38 wherein n is 2, 3 or 4 and one of
X2 is -OH.
40. The antibody conjugate composition of claim 38 selected from the structures:
Figure imgf000435_0002
41. The antibody conjugate composition of claim 38 of Formula lb wherein X3 is selected from -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl) and -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl).
42. The antibody conjugate composition of claim 38 selected from the Formulae Ic-g:
Figure imgf000435_0003
Figure imgf000436_0001
where R is independently selected from H, C1-C6 alkyl, and O-(C1-C6 alkyl); na is an integer from 1 to 5; and Y is CH2 or O.
43. The antibody conjugate composition of claim 42 wherein R is -CH3 and na is 1.
44. The antibody conjugate composition of claim 42 wherein n is 2, 3 or 4 and one of X2 is -OH.
45. The antibody conjugate composition of claim 38 selected from the Formulae Ih and li:
Figure imgf000437_0001
wherein R is selected from H, C1-C6 alkyl, and O-(C1-C6 alkyl); and X5a is -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl)-0-(C2-C20 heterocyclyl).
46. The antibody conjugate composition of claim 45 wherein C2-C20 heterocyclyl of X5a is a glucuronide.
47. The antibody conjugate composition of claim 46 wherein X5a is:
Figure imgf000437_0002
wherein * indicates the point of attachment.
48. The antibody conjugate composition of claim 45 wherein L has the structure:
Figure imgf000438_0001
wherein:
L1 is independently selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyldiyl;
Lla is independently selected from an amino acid, amino, hydroxyl, halide, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof; o is 0, 1, or 2;
L2 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl;
* indicates the point of attachment to a cysteine thiol of Ab; and
** indicates the point of attachment to the isoindolinone-glutarimide moiety.
49. The antibody conjugate composition of claim 48 selected from the Formulae Ij- m:
Figure imgf000438_0002
Figure imgf000439_0001
Figure imgf000440_0001
where t is selected from 0, 1, 2, 3, and 4.
50. The antibody conjugate composition of claim 49 wherein L1 is a bond and Lla is
F
51. The antibody conjugate composition of claim 2 wherein the antibody linker comprises an immolating group.
52. The antibody conjugate composition of claim 2 wherein the antibody linker comprises a peptide unit.
53. The antibody conjugate composition of claim 2 wherein L has the formula:
-Str-(PEP)n-(IM)m- wherein:
Str is a stretcher unit covalently attached to the antibody;
PEP is a protease-cleavable, peptide unit covalently attached to Str and IM or IG;
IM is an immolative unit covalently attached to IG; n is 0 or 1 ; and m is 0 or 1 .
54. The antibody conjugate composition of claim 53 wherein IG is attached to L by Str.
55. The antibody conjugate composition of claim 53 wherein IG is attached to L by
PEP.
56. The antibody conjugate composition of claim 53 wherein IG is attached to L by
IM.
57. The antibody conjugate composition of claim 53 wherein L is a branched linker and Str is covalently attached to: (i) the antibody; and (ii) a solubilizing unit comprising a group selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), and a glycoside, or combinations thereof, wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
58 The antibody conjugate composition of claim 57 wherein the solubilizing unit and the terminus of the solubilizing unit covalently attached to Str are selected from the structures:
Figure imgf000441_0001
Figure imgf000442_0001
wherein * indicates the point of attachment to Str.
59. The antibody conjugate composition of claim 57 wherein L is a branched linker and PEP is covalently attached to: (i) Str and IM or IG; and (ii) a solubilizing unit comprises a group selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), and a glycoside, or combinations thereof, wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof.
60. The antibody conjugate composition of claim 57 wherein L is a branched linker and IM is covalently attached to: (i) IG; and (ii) a solubilizing unit comprises a group selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), and a glycoside, or combinations thereof, wherein the terminus of the solubilizing unit is a group selected from an amino acid, amino, hydroxyl, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof
61. The antibody conjugate composition of claim 53 wherein Str has the structure:
Figure imgf000443_0001
wherein:
* indicates the point of attachment to a cysteine thiol of Ab;
** indicates the point of attachment to PEP or to the isoindolinone-glutarimide moiety;
R1 is selected from the group consisting of C1-C12 alkyldiyl, C1-C12 alkyldiyl-C(=O), C1- C12 alkyldiyl-NH, (CH2CH2O)r, (CH2CH2O)r-C(=O), (CH2CH2O)r-CH2, C6-C20 aryldiyl, (C6- C20 aryldiyl)-(C1-C12 alkyldiyl), and (C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl); r is an integer ranging from 1 to 10; and alkyldiyl, heteroalkyldiyl, and aryldiyl are independently and optionally substituted with one or more groups selected from F, Cl, -CN, -NHz, -CH2NH2, -OH, -OCH3, -OCH2CH3, - OCH2CH2OCH3, -OCH2CH2OH, -OCH2CH2N(CH3)2, -0CH2F, -OCHF2, -OCF3, - OP(O)(OH)2, -S(O)2N(CH3)2, -SCH3, -S(O)2CH3, -S(O)3H, and a solubilizing unit.
62. The antibody conjugate composition of claim 61 wherein R1 is selected from - (CH2)5-, and -CH2CH2-
63. The antibody conjugate composition of claim 61 wherein R1 is selected from C6- C20 aryldiyl, (C6-C20 aryldiyl)-(C1-C12 alkyldiyl), and (C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl).
64. The antibody conjugate composition of claim 61 wherein Str is selected from the structure:
Figure imgf000444_0001
wherein: one of Y1, Y2, Y3, Y4 and Y5 is C-L'-R1, another one of Y1, Y2, Y3, Y4 and Y5 is C-L2- R2, and the remaining three of Y1, Y2, Y3, Y4 and Y5 are each independently N, C-R3, or C-L3- R3a;
R1, R2, and R3a each independently comprise one or more moieties selected from an amino acid element, a charged element, a heteroalkylene element, a hydrophilic element, a trigger element, an immolative unit, a polar cap, a isoindolinone-glutarimide moiety, and combinations thereof; provided that at least one of R1 and R2 comprises the isoindolinone-glutarimide moiety; each occurrence of R3 is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, aminyl, amidyl, aldehyde, hydroxyl, cyano, nitro, thiol, carboxy, carboxyalkyl, alkyl-S(O)3H, alkyl-O-P(O)3H, alkyl- P(0)3H, -O-carboxy alkyl, -O-alkyl-S(O)3H, -O-alkyl-O-P(O)3H, -O-alkyl-P(O)3H, -S(O)3H, - OP(O)3H, -P(O)3H, alkyl-O-P(O)3-alkyl, alkyl-P(O)3-alkyl, -O-alkyl-S(O)3-alkyl, -O-alkyl-O- P(O)3-alkyl, -O-alkyl-P(O)3-alkyl, -S(O)3-alkyl, -OP(O)3-alkyl, -P(O)3-alkyl, sulfamide, sulfmimide, and a carbohydrate,
L1, L2, and L3 are each independently a linker comprising an optionally substituted alkylene, an optionally substituted alkenylene, an optionally substituted alkynylene, an optionally substituted heteroalkylene, an optionally substituted heteroalkenylene, an optionally substituted heteroalkynylene, a heteroatomic linker, an optionally substituted cycloalkylene, an optionally substituted arylene, an optionally substituted heterocyclylene, an optionally substituted heteroarylene, or combinations thereof; and
* indicates the point of attachment to a cysteine thiol of Ab
65. The antibody conjugate composition of claim 64 wherein Str is selected from the structure:
Figure imgf000445_0001
wherein:
L1 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl;
Lla is selected from an amino acid, amino, hydroxyl, halide, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof; o is 0, 1, or 2;
L2 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl;
* indicates the point of attachment to a cysteine thiol of Ab; and
** indicates the point of attachment to PEP or to the isoindolinone-glutarimide moiety.
66. The antibody conjugate composition of claim 65 wherein L1 or L2 comprise a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), and a glycoside, or combinations thereof.
67. The antibody conjugate composition of claim 66 wherein L1 or L2 comprises glucuronic acid having the structure:
Figure imgf000445_0002
68. The antibody conjugate composition of claim 65 wherein L1 or L2 is selected from (N(CH3)CH2C(=O))q, (N(CH3)CH2CH2C(=O))q, N(CH3)CH2CH2OCH2CH2C(=O))q, (CTLCTLOjq, (CEhCEhOjq- C(=O), and (CEhCTLOjq-CEh, where q is an integer from 2 to 20.
69. The antibody conjugate composition of claim 53 selected from formulas:
Figure imgf000446_0001
wherein * indicates the point of attachment to a cysteine thiol of Ab and indicates the point of attachment to IG.
70. The antibody conjugate composition of claim 53 wherein n is 1, m is 1, and PEP- IM has the formula:
Figure imgf000446_0002
wherein * indicates the point of attachment to Str and ** indicates the point of attachment to IG;
AA is independently selected from a natural or unnatural amino acid side chain, or one or more of AA, and an adjacent nitrogen atom form a 5 -membered ring proline amino acid, and the wavy line indicates a point of attachment;
Cyc is selected from C6-C20 aryldiyl and C1-C20 heteroaryldiyl, optionally substituted with one or more groups selected from F, Cl, NO2, -OH, -OCH3, and glucuronic acid having the structure:
Figure imgf000447_0001
R7 is selected from the group consisting of -CH(R8)O-, -CH2-, -CH2N(R8)CH(R8)-, - CH(R8)OC(=O)-, -CH(R8)OC(=O)N(R8)CH(R8)-, -CH(R8)OP(=O)2OCH(R8)-, and - CH(R8)OC(=O)N(R8)-(C1-C6 alkyldiyl)-N(R8)C(=O)OCH(R8)-;
R8 is selected from H, C1-C6 alkyl, C(=O)- C1-C6 alkyl, and -C(=O)N(R9)2,
R9 is independently selected from the group consisting of H, C1-C12 alkyl, and - (CH2CH2O)„- (CH2)m— OH, where m is an integer from 1 to 5, and n is an integer from 2 to 50, or two R9 groups together form a 5- or 6-membered heterocyclyl ring; y is an integer from 2 to 12; and z is 0 or 1.
71. The antibody conjugate composition of claim 70 wherein AA is independently selected from the side chain of a naturally occurring amino acid.
72. The antibody conjugate composition of claim 71 wherein AA is independently selected from H, -CH3, -CH(CH3)2, -CH2(C6H5), -CH2C(O)NH2, -CH2CH2CO2H, -CH2CO2H, -CH2CH2CH2CH2NH2, -CH2CH2CH2NHC(NH)NH2, -CH2CH(CH3)2, -CH2SO3H, and -CH2CH2CH2NHC(O)NH2; or two AA form a 5-membered ring proline amino acid.
73. The antibody conjugate composition of claim 70 wherein PEP-IM comprises at least one natural or unnatural amino acid side chain AA substituted with C1-C40 heteroalkyl
74. The antibody conjugate composition of claim 73 wherein C1-C40 heteroalkyl comprises a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), and a glycoside, or combinations thereof.
75. The antibody conjugate composition of claim 74 wherein the solubilizing unit is selected from (N(CH3)CH2C(=O))q, (N(CH3)CH2CH2C(=O))q, N(CH3)CH2CH2OCH2CH2C(=O))q, (CH2CH2O)q, (CH2CH2O)q-C(=O), and (CH2CH2O)q-CH2, where q is an integer from 2 to 20.
76. The antibody conjugate composition of claim 70 wherein y is 2, PEP is a dipeptide, and PEP-IM has the formula:
Figure imgf000448_0001
wherein AA1 and AA2 are independently selected from a side chain of a naturally- occurring amino acid.
77. The antibody conjugate composition of claim 76 wherein the dipeptide is selected from ala-ala, val-cit, and phe-ala.
78. The antibody conjugate composition of claim 76 wherein AA1 is -CH(CH3)2, and AA2 is -CH2CH2CH2NHC(O)NH2.
79. The antibody conjugate composition of claim 76 wherein AA1 and AA2 are each -CH3
80. The antibody conjugate composition of claim 70 wherein y is 3, PEP is a tripeptide, and PEP-IM has the formula:
Figure imgf000448_0003
81. The antibody conjugate composition of claim 70 wherein y is 4, PEP is a tetrapeptide PEP-IM, and has the formula:
Figure imgf000448_0002
82. The antibody conjugate composition of claim 70 where z is 1 and IM has the formula:
*-Cyc-R7-** wherein:
* indicates the point of attachment to PEP; and
** indicates the point of attachment to IG.
83. The antibody conjugate composition of claim 82 where R7 has the formula:
*-CH2OC(=O)NHCH(R8)-** wherein:
R8 is selected from H and C1-C6 alkyl;
* indicates the point of attachment to PEP; and ** indicates the point of attachment to IG.
84. The antibody conjugate composition of claim 83 where R8 is H.
85. The antibody conjugate composition of claim 83 where R8 is -CH3.
86. The antibody conjugate composition of claim 82 wherein IM is selected from the formulae:
Figure imgf000449_0001
wherein:
* indicates the point of attachment to PEP; and
** indicates the point of attachment to IG.
87. The antibody conjugate composition of claim 82 where IM is selected from the formulae:
Figure imgf000450_0001
wherein:
* indicates the point of attachment to PEP; and ** indicates the point of attachment to IG.
88. An isoindolinone-glutarimide linker compound selected from Formulae Ila and lib:
Figure imgf000450_0002
or a pharmaceutically acceptable salt, stereoisomer, mixture of stereoisomers, tautomer, or isotopic analog thereof, wherein: m is 0, 1 or 2;
X1 is selected from the group consisting of CH2, C(=O) and N=N;
X2 is independently selected from the group consisting of F, Cl, Br, I, -CN, C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), (C1-C6 alkyl diyl)-(C6-C20 aryl), -(C1-C6 alkyl diyl)-NRaRb, -(C1-C6 alkyldiyl)-ORa, (C1-C6 alkyldiyl)-(C3-C20 carbocyclyl), (C1-C6 alkyldiyl)-(C2-C20 heterocyclyl), (C1-C6 alkyldiyl)-(C1-C20 heteroaryl), C6-C20 aryl, C3-C20 carbocyclyl, C2-C20 heterocyclyl, C1-C20 heteroaryl, -C(=NH)NH(OH), -C(=NH)NH2, -C(=0)NRaRb, -C(=O)NRa-NRaRb, -C(=O)NH(C1-C6 alkyldiyl)-NRaRb, -C(=O)ORa, -NRaRb, -NO2, -ORa, -OC(=O)Ra, -SRa, -S(O)Ra, -S(O)2Ra, -S(O)2NRa, and -S(O)3H;
Ra is independently selected from H, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl;
Rb is independently selected from H, OH, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl; n is 0, 1, 2, 3, or 4;
X3 is selected from the group consisting of a bond, O, C1-C12 alkyldiyl, C2-C12 alkenyldiyl, C2-C12 alkynyldiyl, C1-C12 heteroalkyldiyl, -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl)-, -(C1-C6 alkyl diyl)NRa- -(C1-C6 alkyldiyl)O- -(C1-C6 alkyldiyl)-(C3-C20 carbocyclyldiyl)-, -(C1-C6 alkyl diyl)-(C2-C20 heterocyclyldiyl)-, -(C1-C6 alkyldiyl)-(C1-C20 heteroaryldiyl)- -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl)-, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl)-, C6-C20 aryldiyl, C3-C20 carbocyclyldiyl, C2-C20 heterocyclyldiyl, and C1-C20 heteroaryl diyl;
X4 is selected from the group consisting of H, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aiyldiyl)-(C1-C12 heteroalkyl);
X5 is selected from the group consisting of a bond, C1-C12 alkyldiyl, C2-C12 alkenyldiyl, C2-C12 alkynyldiyl, C1-C12 heteroalkyldiyl, -(C1-C6 alkyldiyl)-(C6-C20 aryldiyl), -(C1-C6 alkyldiyl)— (C6— C20 aryldiyl)-0-(C2-C20 heterocyclyl), -(C1-C6 alkyldiyl)NRa- -(C1-C6 alkyldiyl)O- -(C1-C6 alkyldiyl)-(C3-C20 carb ocyclyl diyl), -C1-C6 alkyl diyl)-(C2-C20 heterocyclyldiyl), -(C1-C6 alkyldiyl)-(C1-C20 heteroaryldiyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl), -(C1-C12 heteroalkyl diyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl), C6-C20 aryldiyl, C3-C20 carbocyclyldiyl, C2-C20 heterocyclyldiyl, and C1-C20 heteroaryldiyl,
L is the antibody linker; and
Z is:
Figure imgf000452_0001
where the wavy line is the attachment to L; wherein each alkyl, alkyldiyl, alkenyl, alkenyldiyl, alkynyl, alkynyldiyl, heteroalkyl, heteroalkyl diyl, aryl, aryldiyl, carbocyclyl, carbocyclyldiyl, heterocyclyl, heterocyclyldiyl, heteroaryl, and heteroaryl diyl is independently and optionally substituted with one or more groups selected from F, Cl, Br, I, -CN, -CH3, -CH2CH3, -CH=CH2, -C=CH, -C=CCH3, - CH2CH2CH3, CH(CH3)2, CH2CH(CH3)2, CH2OH, CH2OCH3, CH2CH2OH, C(CH3)2OH, -CH(OH)CH(CH3)2, -C(CH3)2CH2OH, -CH2CH2SO2CH3, -CH2OP(O)(OH)2, -CH2F, -CHF2, -CF3, -CH2CF3, -CH2CHF2, -CH(CH3)CN, -C(CH3)2CN, -CH2CN, -CH2NH2, - CH2NHSO2CH3, -CH2NHCH3, -CH2N(CH3)2, -CO2H, -COCH3, -CO2CH3, -CO2C(CH3)3, - COCH(OH)CH3, -CONH2J -CONHCH3, -CON(CH3)2, -C(CH3)2CONH2, -NH2, -NHCH3, - N(CH3)2, NHCOCH3, N(CH3)COCH3, NHS(O)2CH3, N(CH3)C(CH3)2CONH2, N(CH3)CH2CH2S(O)2CH3, -NHC(=NH)H, -NHC(=NH)CH3, -NHC(=NH)NH2, - NHC(=O)NH2, -NO2, =0, -OH, -0CH3, -OCH2CH3, -OCH2CH2OCH3, -OCH2CH2OH, - OCH2CH2N(CH3)2, -OCH2F, -OCHF2, -OCF3, -OP(O)(OH)2, -S(O)2N(CH3)2, -SCH3, - S(O)2CH3, and -S(0)3H.
89. The isoindolinone-glutarimide linker compound of claim 88 wherein
L has the formula:
-Str'-(PEP)„-(IM)m- wherein:
Str1 is a stretcher unit covalently attached to Z;
PEP is a protease-cleavable, peptide unit covalently attached to Str1 and IM; IM is an immolative unit covalently attached the isoindolinone-glutarimide moiety; n is 0 or 1 ; and m is 0 or 1 .
90. The isoindolinone-glutarimide linker compound of claim 89 wherein PEP-IM is selected from the structures:
Figure imgf000453_0001
wherein ** indicates the point of attachment to the isoindolinone-glutarimide moiety.
91. The isoindolinone-glutarimide linker compound of claim 89 wherein Z-Str1 has the structure:
Figure imgf000453_0002
wherein:
** indicates the point of attachment to PEP or the isoindolinone-glutarimide moiety;
R1 is selected from the group consisting of C1-C12 alkyldiyl, C1-C12 alkyldiyl-C(=O), C1-C12 alkyldiyl-NH, (CH2CH2OX (CH2CH2O)r-C(=O), (CJECILOX-CTE, C6-C20 aryldiyl, (C6- C20 aryldiyl)-(C1-C12 alkyldiyl), and (C6-C20 aryldiyl)-(C1-C12 heteroalkyldiyl); r is an integer ranging from 1 to 10; and alkyldiyl, heteroalkyldiyl, and aryldiyl are independently and optionally substituted with one or more groups selected from F, Cl, -CN, -NH2, -CH2NH2, -OH, -OCH3, -OCH2CH3, - OCH2CH2OCH3, -OCH2CH2OH, -OCH2CH2N(CH3)2, -OCH2F, -OCHF2, -OCF3, - OP(O)(OH)2, -S(O)2N(CH3)2, -SCH3, -S(O)2CH3, -S(O)3H, and a solubilizing unit.
92. The isoindolinone-glutarimide linker compound of claim 91 wherein R1 is selected from -(CH2)5- and -CH2CH2-.
93. The isoindolinone-glutarimide linker compound of claim 91 wherein R1 is selected from C6-C20 aryldiyl, (C6-C20 aryldiyl)-(C1-C12 alkyldiyl), and (C6-C20 aryldiyl)-(C1- C12 heteroalkyl diyl).
94. The isoindolinone-glutarimide linker compound of claim 89 wherein Z-Str1 is selected from the structure:
Figure imgf000454_0001
wherein: one of Y1, Y2, Y3, Y4 and Y5 is C-L'-R1, another one of Y1, Y2, Y3, Y4 and Y5 is C-L2- R2, and the remaining three of Y1, Y2, Y3, Y4 and Y5 are each independently N, C-R3, or C-L3- R3a;
R1, R2, and R3a each independently comprise one or more moieties selected from an amino acid element, a charged element, a heteroalkylene element, a hydrophilic element, a trigger element, an immolative unit, a polar cap, an isoindolinone-glutarimide moiety, and combinations thereof; provided that at least one of R1 and R2 comprises the isoindolinone-glutarimide moiety; each occurrence of R3 is independently selected from the group consisting of hydrogen, deuterium, alkyl, haloalkyl, halo, alkoxy, haloalkoxy, amino, aminyl, amidyl, aldehyde, hydroxyl, cyano, nitro, thiol, carboxy, carboxyalkyl, alkyl-S(O)3H, alkyl-O-P(O)3H, alkyl- P(0)3H, -O-carboxyalkyl, -O-alkyl-S(O)3H, -O-alkyl-O-P(O)3H, -O-alkyl-P(O)3H, -S(O)3H, - OP(O)3H, -P(O)3H, alkyl-O-P(O)3-alkyl, alkyl-P(O)3-alkyl, -O-alkyl-S(O)3-alkyl, -O-alkyl-O- P(O)3-alkyl, -O-alkyl-P(O)3-alkyl, -S(O)3-alkyl, -OP(O)3-alkyl, -P(O)3-alkyl, sulfamide, sulfinimide, and a carbohydrate,
L1, L2, and L3 are each independently a linker comprising an optionally substituted alkylene, an optionally substituted alkenylene, an optionally substituted alkynylene, an optionally substituted heteroalkylene, an optionally substituted heteroalkenylene, an optionally substituted heteroalkynylene, a heteroatomic linker, an optionally substituted cycloalkylene, an optionally substituted arylene, an optionally substituted heterocyclylene, an optionally substituted heteroarylene, or combinations thereof; and
* indicates the point of attachment to a cysteine thiol of Ab
95. The isoindolinone-glutarimide linker compound of claim 89 wherein Z-Str1 has the structure:
Figure imgf000455_0001
wherein:
L1 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl;
Lla is selected from an amino acid, amino, hydroxyl, halide, hydrogen, carboxylic acid, glycerol, or a sugar such as pentaerythritol, maltitol, sorbitol, xylitol, erythritol, isomalt, or combinations thereof; o is 0, 1, or 2;
L2 is selected from a bond, C1-C12 alkyldiyl, and C1-C40 heteroalkyl diyl; and
** indicates the point of attachment to PEP or to the isoindolinone-glutarimide moiety.
96. The isoindolinone-glutarimide linker compound of claim 95 wherein L1 or L2 comprise a solubilizing unit selected from polyglycine, polysarcosine, polyethyleneoxy (PEG), and a glycoside, or combinations thereof.
97. The isoindolinone-glutarimide linker compound of claim 95 wherein L1 or L2 is selected from (N(CH3)CH2C(=O))q, (N(CH3)CH2CH2C(=O))q, N(CH3)CH2CH2OCH2CH2C(=O))q, (CH2CH2O)q, (CH2CH2O)q-C(=O), and (CH2CH2O)q-CH2, where q is an integer from 2 to 20.
98. An isoindolinone-glutarimide compound selected from Formula III:
Figure imgf000455_0002
or a pharmaceutically acceptable salt, stereoisomer, mixture of stereoisomers, tautomer, or isotopic analog thereof, wherein: m is 0, 1 or 2; X1 is selected from the group consisting of CH2, C(=O) and N=N;
X2 is independently selected from the group consisting of F, Cl, Br, I, -CN, C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl )-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), (C1-C6 alkyl diyl)-(C6-C20 aryl), -(C1-C6 alkyl diyl)-NRaRb, -(C1-C6 alkyldiyl)-ORa, (C1-C6 alkyldiyl)-(C3-C20 carbocyclyl), (C1-Cs alkyldiyl)-(C2-C20 heterocyclyl), (C1-C6 alkyldiyl)-(C1-C20 heteroaryl), C6-C20 aryl, C3-C20 carbocyclyl, C2-C20 heterocyclyl, C1-C20 heteroaryl, -C(=NH)NH(OH), -C(=NH)NH2, -C(=O)NRaRb, -C(=O)NRb-NRaRh, -C(=O)NH(C1-C6 alkyldiyl)-NRaRb, -C(=O)ORa, -NRaRb, -NO2, -ORa, -OC(=O)Ra, -SRa, -S(O)Ra, -S(O)2Ra, -S(O)2NRa, and -S(O)3H;
Ra is independently selected from H, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl;
Rb is independently selected from H, OH, C1-C6 alkyl, phenyl, and benzyl, wherein phenyl and benzyl are optionally substituted with one or more groups independently selected from the group consisting of F, Cl, -CN, C1-C12 alkyl, C2-C12 alkenyl, and C2-C12 alkynyl; n is 0, 1, 2, 3, or 4; and
X4 is selected from the group consisting of H, C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl); wherein each alkyl, alkyldiyl, alkenyl, alkenyldiyl, alkynyl, alkynyldiyl, heteroalkyl, heteroalkyl diyl, aryl, aryldiyl, carbocyclyl, carbocyclyldiyl, heterocyclyl, heterocyclyldiyl, heteroaryl, and heteroaryl diyl is independently and optionally substituted with one or more groups selected from F, Cl, Br, I, -CN, -CH3, -CH2CH3, -CH=CH2, -C=CH, -C=CCH3, - CH2CH2CH3, -CH(CH3)2, -CH2CH(CH3)2, -CH2OH, -CH2OCH3, -CH2CH2OH, -C(CH3)2OH, -CH(OH)CH(CH3)2, -C(CH3)2CH2OH, -CH2CH2SO2CH3, -CH2OP(O)(OH)2, -CH2F, -CHF2, -CF3, -CH2CF3, -CH2CHF2, -CH(CH3)CN, -C(CH3)2CN, -CH2CN, -CH2NH2, - CH2NHSO2CH3, -CH2NHCH3, -CH2N(CH3)2, -CO2H, -COCH3, -CO2CH3, -CO2C(CH3)3, - COCH(OH)CH3, -CONH2, -CONHCH3, -CON(CH3)2, -C(CH3)2CONH2, -NH2, -NHCH3, - N(CH3)2, NHCOCH3, -N(CH3)COCH3, -NHS(O)2CH3, -N(CH3)C(CH3)2CONH2, - N(CH3)CH2CH2S(O)2CH3, -NHC(=NH)H, -NHC(=NH)CH3, -NHC(=NH)NH2, - NHC(=0)NH2, -NO2, =0, -OH, -0CH3, -OCH2CH3, -OCH2CH2OCH3, -OCH2CH2OH, - OCH2CH2N(CH3)2, -OCH2F, -OCHF2, -OCF3, -OP(O)(OH)2, -S(O)2N(CH3)2, -SCH3, - S(O)2CH3, and -S(O)3H.
99. The isoindolinone-glutarimide compound of claim 98 wherein m is 0.
100. The isoindolinone-glutarimide compound of claim 98 wherein m is 1.
101. The isoindolinone-glutarimide compound of claim 98 wherein m is 2.
102. The isoindolinone-glutarimide compound of claim 98 wherein X1 is CH2.
103. The isoindolinone-glutarimide compound of claim 98 wherein X1 is C(=O).
104. The isoindolinone-glutarimide compound of claim 98 wherein X1 is N=N.
105. The isoindolinone-glutarimide compound of claim 98 wherein X2 comprises a -
NHC(=O)NH- group.
106. The isoindolinone-glutarimide compound of claim 98 wherein X2 is selected from the group consisting of C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl )-(C6-C20 aryl), and -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl)
107. The isoindolinone-glutarimide compound of claim 98 wherein X2 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl).
108. The isoindolinone-glutarimide compound of claim 107 wherein X2 is CH2NHC(-O)NH (C6 C20 aryl).
109. The isoindolinone-glutarimide compound of claim 106 wherein X2 is:
Figure imgf000457_0001
where ** indicates the point of attachment.
110. The isoindolinone-glutarimide compound of claim 98 wherein X4 is H.
111. The isoindolinone-glutarimide compound of claim 98 wherein X4 is selected from the group consisting of C1-C12 heteroalkyl, -(C1-C12 heteroalkyldiyl)-(C6-C20 aryl), -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-(C1-C12 heteroalkyl), and -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-O-(C2-C20 heterocyclyl).
112. The isoindolinone-glutarimide compound of claim 111 wherein X4 is -(C1-C12 heteroalkyldiyl)-(C6-C20 aryldiyl)-0-(C2-C20 heterocyclyl), and C2-C20 heterocyclyl is a glucuronide.
113. The isoindolinone-glutarimide compound of claim 112 wherein X4 of formula la is selected from the formulae:
Figure imgf000458_0001
wherein R is selected from H, C1-C6 alkyl, and O-(C1-C6 alkyl); and * indicates the point of attachment.
114. The isoindolinone-glutarimide compound of claim 98 selected from Table la.
115. An antibody conjugate composition prepared by conjugation of a cysteine amino acid of an antibody with an isoindolinone-glutarimide linker compound of claim 88
116. An antibody conjugate composition prepared by conjugation of a cysteine amino acid of an antibody with an isoindolinone-glutarimide linker compound selected from Table 2.
117. A process for preparing an antibody conjugate composition comprising reacting a cysteine amino acid of an antibody with an isoindolinone-glutarimide linker compound of claim 86 whereby an antibody conjugate composition is formed.
118. A pharmaceutical composition comprising a therapeutically effective amount of the antibody conjugate composition of any one of claims 1 to 87, and one or more pharmaceutically acceptable diluent, vehicle, carrier or excipient
119. A method for treating cancer comprising administering a therapeutically effective amount of the pharmaceutical composition of claim 118, to a patient in need thereof, wherein the cancer is selected from hematological and solid tumors.
120. The method of claim 119 wherein the cancer is selected from breast cancer, triple negative breast cancer, lung cancer, non-small cell lung cancer, small cell lung cancer, colorectal cancer, and lymphoma, diffuse large B-cell lymphoma (DLBCL), follicular cancer, leukemia, and acute myelogenous leukemia (AML).
121. The method of claim 119 wherein the cancer is GSPT1 -dependent.
122. The method of claim 119 wherein the antibody conjugate composition modulates the level of GSPT-1 in the patient.
123. Use of an antibody conjugate composition of any one of claims 1 to 87 in the manufacture of a medicament for the treatment of cancer in a mammal.
124. An antibody conjugate composition of any one of claims 1 to 87 for use in a method for treating cancer.
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