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WO2025184565A1 - Targeted protein modification - Google Patents

Targeted protein modification

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Publication number
WO2025184565A1
WO2025184565A1 PCT/US2025/017935 US2025017935W WO2025184565A1 WO 2025184565 A1 WO2025184565 A1 WO 2025184565A1 US 2025017935 W US2025017935 W US 2025017935W WO 2025184565 A1 WO2025184565 A1 WO 2025184565A1
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WO
WIPO (PCT)
Prior art keywords
alkyl
substituted
compound
cancer
halo
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
PCT/US2025/017935
Other languages
French (fr)
Inventor
III Armand B. COGNETTA
Corentine M. C. LAURIN
Veronika M. SHOBA
Rodrigo A. RODRIGUEZ
Minh L. N. TRAN
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Weatherwax Biotechnologies Corp
Original Assignee
Weatherwax Biotechnologies Corp
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Filing date
Publication date
Application filed by Weatherwax Biotechnologies Corp filed Critical Weatherwax Biotechnologies Corp
Publication of WO2025184565A1 publication Critical patent/WO2025184565A1/en
Pending legal-status Critical Current
Anticipated expiration legal-status Critical

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/14—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing three or more hetero rings
    • 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
    • A61K47/54—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 organic compound
    • A61K47/55—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 organic compound the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug, i.e. a dimer, oligomer or polymer of pharmacologically or therapeutically active compounds

Definitions

  • a modifier protein targeting chimeric (OmniTAC) compound which targets the transcription factor p53, comprising a targeting ligand, a recruiting ligand, and a linker, wherein the targeting ligand is attached to the recruiting ligand via the linker; wherein the targeting ligand is configured to bind to target protein, wherein the target protein is a wild-type (WT) or a mutant p53, and the recruiting ligand is configured to bind to a modifier protein such that the modifier protein induces a change to the WT or mutant p53; and wherein the modifier protein comprises a non-degradative protein that activates, stabilizes, and/or corrects misfolding of the target protein.
  • WT wild-type
  • the recruiting ligand is configured to bind to a modifier protein such that the modifier protein induces a change to the WT or mutant p53
  • the modifier protein comprises a non-degradative protein that activates, stabilizes, and/or corrects misfolding of the target protein
  • R 1 is the targeting ligand with a structure of Formula (II):
  • R 2 is a recruiting ligand
  • L is a linker with the following structure: -(AP) m -L 1A -L 1B -(AP) m -;
  • AP is PEG, ether, amide, sulfonamide, sulfone, sulfoxide, sulfonate, phosphonate, ester, urea, carbamate, substituted phosphine oxide, optionally substituted C1-6 alkyl, optionally substituted C3-12 cycloalkyl, optionally substituted 3- to 12- membered heterocycloalkyl, optionally substituted 3- to 12- membered heteroaryl, or optionally substituted Ce-12 aryl;
  • L 1A and L 1B are each independently polyethylene glycol (PEG), C1-50 alkylene-PEG, C2-50 alkenylene-PEG, C2-50 alkynylene-PEG, C1-50 alkylene, C2-50 alkenylene, C2-50 alkynylene, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, C6-12 aryl, 3- to 12- membered heteroaryl, 3- to 12- membered heterocycloalkyl-C1-10 alkylene, 3- to 12- membered heterocycloalkyl-PEG, or PEG-3- to 12- membered heterocycloalkyl-PEG, spirocyclic cores, or a combination thereof, each of which may be substituted with one or more halogen, deuterium, methyl, deuterated methyl, trifluoromethyl, amide, sulfonamide, sulfone, ester, urea, carbamate, C3-12 cycloal
  • R A is C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl or 3- to 12- membered heteroaryl;
  • Y 1 , Y 2 , Y 3 , Y 4 , Y 5 , and Y 6 are each independently CH, C, NH, N, NO, S, SO, or absent, wherein at least two of Y 1 , Y 2 , Y 3 and Y 4 is CH, C, NH, N, NO, S, or SO, and wherein at least one of Y 5 and Y 6 is CH, C, NH, N, NO, S, or SO;
  • Y 7 and Y 8 are each independently C or N;
  • R 1A is a cysteine reactive group, C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, -SOR 1A1 , or -COR 1A1 , wherein the C1-6 alkyl and C3 -12 cycloalkyl is optionally substituted with -CN, halogen, or C1-6 alkylamines;
  • R 1B is deuterium, halogen, -CN, -OH, -OC1-6 alkyl, -OC1-6 haloalkyl, -NH2, NHC1-6 alkyl, -N(C1-6 alkyl) 2 , -NHCOMe, -OCOMe, -OCONR 1BA R 1BB , C1-6 alkyl, -COOR 1BB , -CONR 1BA R 1BB , - NR1BACOR1BB, _ N02 , _ NR IB SO25 -SO 2 (C1-6alkyl), -SO 2 NR 1BA R 1BB , -SO 2 NH-heteroaryl, or two R 1G taken together form an aryl or heteroaryl ring;
  • R 1BA is hydrogen or C1-6 alkyl
  • R 1BB is hydrogen, -COC1-6 alkyl, C1-6alkyl, C6-12 aryl, 3- to 12- membered heteroaryl
  • R 1C is deuterium, halogen, -OH, -OC1-6 alkyl, -OC1-6 haloalkyl, -NH2, NHC1-6 alkyl, - N(C1-6 alkyl) 2 , -NO 2 , -NHCOMe, or -OCOMe;
  • R 1D is hydrogen or C1-6 alkyl
  • R 1E is C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, or 3- to 12- membered heteroaryl, wherein the C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, C6-12 aryl, and 3- to 12- membered heteroaryl are optionally substituted with halogen, C1-6 alkyl, C1-6 alkoxy, C1-6 carboxylic acid, -NH 2 , or -N(C1-6alkyl)2; or R 1D and R 1E combine with the carbon to which is attached to form a cyclic structure, wherein the cyclic structure is C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, C6-12 aryl, and 3- to 12- membered heteroaryl, wherein the cyclic structure is optionally substituted with one or more R 1DE ;
  • R 1DE is deuterium, halogen, -CN, -OH, -NH2, -NH(C1-6 alkyl), -NH(C1-6 haloalkyl), - N(C1-6 alkyl ) 2 , -OC1-6 alkyl, -OC1-6 haloalkyl, C1-6 alkyl, C1-6 alkoxy, C1-6 haloalkyl, C1-6 haloalkoxy, -NHCO(C 1-6 haloalkyl), -CO2(C 1-6 alkyl), -CONH(C 1-6 alkyl), -SO2NH(C1-6 alkyl), - SO 2 N(C1-6 alkyl) 2 , -SO 2 (C1-6 alkyl), or -SO 2 NMe(C1-6 alkyl);
  • R 1F is hydrogen or C1-6 alkyl; m is 0 or 1; n is 0 to 5; o is 0 or 1; and wherein an atom on one of R 1B , R 1DE , or R 1E or the cyclic structure of R 1D and R 1E is covalently linked to L.
  • the compound of Formula (I) has the structure of Formula (II- A): wherein:
  • R B is 3- to 12- membered heterocycloalkyl
  • R 1DE is deuterium, halogen, -OH, -OMe, -OCF3, -NH2, -NH(C1-6alkyl), or -N(C1-6alkyl)2; and p is 0 to 5.
  • the compound of Formula (II- A) has the structure of Formula (II-B): wherein:
  • X 1 , X 2 , X 3 , and X 4 are each independently C, CH, NH, N, NO, S, SO or absent, wherein at least two of X 1 , X 2 , X 3 , and X 4 are C, CH, NH, N, NO, S, or SO; and p is 1 to 3.
  • the compound of Formula (II- A) has the structure of Formula
  • the compound of Formula (III- A) or Formula (III-B) has the structure of Formula (III-A1) or Formula (III-B1):
  • B is a absent, -NH-, -0-, CO, amide, C1-6 alkylene, C2-6 alkenylene, or C2-6 alkynylene, wherein the C1-6 alkylene, C2-6 alkenylene, and C2-6 alkynylene is optionally substituted with deuterium, halogen, or C1-3 alkoxy;
  • W 1 and W 2 are each independently NH, N, O, or S;
  • R c and R D are each independently optionally substituted C3-12 cycloalkyl, optionally substituted 3- to 12- membered heterocycloalkyl, optionally substituted C6-12 aryl or optionally substituted 3- to 12- membered heteroaryl;
  • R 1H and R 11 are each independently hydrogen or C1-6 alkyl, wherein the C1-6 alkyl is optionally substituted with deuterium or halogen.
  • the compound of Formula (III-A1) or Formula (III-B1) has the structure of Formula (III-A2) or Formula (III-B2):
  • X 1 , X 2 , X 3 , and X 4 are each independently C, CH, NH, N, NO, S, SO or absent, and wherein at least two of X 1 , X 2 , X 3 , and X 4 is C, CH, NH, N, NO, S, SO.
  • the compound of Formula (III-A1) or Formula (III-B1) has the structure of Formula (IV-A), Formula (IV-B), Formula (IV-C), or Formula (IV-D):
  • Formula (IV-C), or Formula (IV-D) has the structure of Formula (IV-A1), Formula (IV-B1), Formula (IV- Cl), or Formula (IV-D1):
  • X 1 , X 2 , X 3 , and X 4 are each independently CH, N, NO, S, SO or absent, and wherein at least two of X 1 , X 2 , X 3 , and X 4 is CH, N, NO, S, SO;
  • R 1B , R 1C , and R 1L are each independently halogen, -OH, -NH2, -NH(C1-6 alkyl), -NH(C1-6 alkyl) 2 , -OC1-6 alkyl, -OCH3, -OCF3, -NO 2 , -NHAc, or -OAc;
  • R 1DE is halogen, deuterium, hydroxyl, trifluoromethoxy, or amine; or wherein when R 1DE is in (R 1DE ) p -i, then R 1DE is deuterium, halogen, -CN, -OH, -NH2, - NH(C 1-6 alkyl), -NH(C1-6haloalkyl), -OC1-6 alkyl, -OC1-6 haloalkyl, C1-6 alkyl, C1-6 haloalkyl, - NHCO(C1-6 haloalkyl), -CO 2 (C1-6 alkyl), -CONH(C1-6 alkyl), -SO 2 NH(C1-6 alkyl), -SO 2 N(C1-6 alkyl) 2 , -SO2(C 1-6 alkyl), or -SO2NMe(C1-6 alkyl); and q is 0 to 5.
  • the compound of Formula (III- A) or Formula (III-B) has the structure of Formula (IV-A2) or Formula (IV-C2):
  • the modifier protein targeting chimeric (OmniTAC) compound has the structure of Formula V:
  • R 1 is one of the following:
  • R 2 , R 3 , R 4 and independently hydrogen or C1-4 alkyl
  • Y 1 is one of the following:
  • L is a bivalent, saturated or unsaturated, straight or branched Ci-60 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -S-, - N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O) 2 -, -N(H)S(O) 2 -, -N(C1-6 alkyl)S(O) 2 -, -S(O) 2 N(H)-, -S(O) 2 N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, - C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6
  • the modifier protein targeting chimeric (OmniTAC) compound has the structure of Formula VI:
  • R 1 is -(phenyl substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-N(R 2 )-(C 2 -4alkynylene)-(indolyl substituted with C1-4haloalkyl and -N(R 3 )-(3-6 membered saturated heterocyclyl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclyl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
  • Y 1 is one of the following:
  • L is a bivalent, saturated or unsaturated, straight or branched Ci-60 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -S-, - N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O) 2 -, -N(H)S(O) 2 -, -N(C1-6 alkyl)S(O) 2 -, -S(O) 2 N(H)-, -S(O) 2 N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, - C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6
  • FIG. 1 illustrates a non-limiting list of modifier proteins and associated ligands that can be used to design recruiting ligands, organized by mechanism of action.
  • FIG. 2 illustrates a non-limiting list of modifier proteins and references for associated ligands that can be used to design recruiting ligands, organized by mechanism of action.
  • FIG. 3 illustrates effects of OmniTAC treatment on the viability of NUGC3 and NUGC3 p53 Y220C KO cells.
  • FIG. 4 illustrates ternary complex formation between the target protein, p53 Y220C, and the modifier protein, in lysate.
  • FIG. 5 illustrates ternary complex formation between the target protein, p53 Y220C, and the modifier protein, in live cells.
  • a platform which may be useful for modifying a target protein. Modifying the target protein can include activating or reactivating a target protein.
  • the platform may include compounds such as modifier protein targeting chimeric (OmniTAC) compounds, methods of their preparation, and methods of using them.
  • TP53 is the most frequently mutated gene in cancer, with mutations identified in at least half of all human cancers. Widely known as the “Guardian of the Genome”, TP53 is a crucial tumor suppressor. One might expect mutations in the TP53 gene to result in loss of WTp53 function, as seen with other tumor suppressor genes. Strikingly, most of the cancer- associated TP53 mutations lead to the production of full-length p53 protein with only a single amino acid change. This mutant accumulates in tumor cells at levels much higher than in normal cells, contrary to the common loss of function modality. Despite 40 years of research on this gene and over 130,000 studies, there has been no clinical success against this pivotal target.
  • Accumulated mutant p53 is only present in cancer cells, representing a unique therapeutic opportunity to develop a first-in-class, selective therapy against a target that is present in half of all cancers.
  • Compounds of the present disclosure can provide this precise selectivity using a targeted protein modification approach.
  • Compounds of the present disclosure are capable of providing selective, targeted protein modifications.
  • Current drug approaches to therapeutics generally involve using small molecules, biologies, and/or genetic therapies to modify a biological target of interest, e.g., a protein target.
  • Such approaches are limited in that small molecules generally have a small range of method of action and may not be catalytic; and biologic or genetic therapies may have poor oral bioavailability and cell permeability, making targeting of intracellular proteins challenging.
  • the compounds of the present disclosure advantageously bring a target protein in proximity with a modifier protein, which provides a modification to the target protein to exert a therapeutic effect. This approach leverages the protein modification capabilities of existing modifier proteins and desired properties of small molecules to induce changes in disease-associated target proteins in vivo, enabling the development of highly specific and potent drugs.
  • a compound described herein comprises a targeting ligand, a linker, and a recruiting ligand.
  • a compound described herein comprises a targeting ligand, a linker, and a recruiting ligand, connected via attachment points.
  • the compound may comprise or consist of a modifier protein targeting chimeric (OmniTAC) compound.
  • the OmniTAC compound may comprise a heterobifunctional compound (BFM).
  • the OmniTAC compound may include a targeting ligand.
  • the OmniTAC compound may include a recruiting ligand.
  • the OmniTAC compound may include a linker.
  • the linker may attach the targeting ligand to the recruiting ligand.
  • the linker may attach the targeting ligand to the recruiting ligand via an attachment point.
  • Some embodiments include a modifier protein targeting chimeric (OmniTAC) compound comprising a targeting ligand, a recruiting ligand, and a linker; wherein the targeting ligand is attached to the recruiting ligand via the linker.
  • Some embodiments include a modifier protein targeting chimeric (OmniTAC) compound comprising a targeting ligand, a recruiting ligand, and a linker; wherein the targeting ligand is attached to the recruiting ligand via the linker through an attachment point.
  • a modifier protein targeting chimeric (OmniTAC) compound comprising a targeting ligand, a recruiting ligand, and a linker; wherein the targeting ligand is attached to the recruiting ligand via the linker through an attachment point.
  • the compound has a structure of Formula I: wherein R 1 is the targeting ligand; L is the linker; and R 2 is the recruiting ligand.
  • R 1 is the targeting ligand
  • L is the linker
  • R 2 is the recruiting ligand.
  • the compound has a structure of Formula IA1 :
  • R 1 — L— R 2 (IA1) wherein R 1 is ligand that binds a target protein; L is the linker; and R 2 is a ligand that binds an effector protein.
  • R J (p53)— L— R 2 (BRD) (IA2) wherein R ⁇ p53) is ligand that binds WT, mutant, truncated or full length p53; L is the linker; and R 2 (BRD) is a ligand that binds to a bromodomain.
  • the compound includes some aspect of a natural or organic compound.
  • the compound is synthetic.
  • the compound is engineered.
  • the compound may be purified.
  • the compound is substantially pure.
  • substantially pure means that the compound is substantially separated or isolated from contaminants or impurities.
  • a substantially pure compound comprises less than 10%, less than 5%, less than 2%, less than 1%, less than 0.5%, or less than 0.1% by weight of impurities.
  • the compound comprises or consists of a small molecule.
  • a small molecule includes an organic compound having a molecular weight of less than 900 daltons.
  • the compound may have a molecular weight below 2500 daltons, below 2250 daltons, below 2000 daltons, below 1750 daltons, below 1500 daltons, or below 1250 daltons.
  • the compound may have a molecular weight below 1000 daltons, below 900 daltons, below 800 daltons, below 700 daltons, below 600 daltons, or below 500 daltons.
  • the targeting ligand may include a ligand of a protein such as a target protein.
  • the targeting ligand may be configured to bind to a target protein.
  • the targeting ligand may bind the target protein.
  • the targeting ligand may include a moiety that binds the target protein.
  • the targeting ligand may be a part of a heterobifunctional compound such as an OmniTAC compound.
  • the targeting ligand may connect to a linker or recruiting ligand.
  • the targeting ligand is incorporated into an in vivo engineered protein.
  • the targeting ligand may include a small molecule.
  • the targeting ligand comprises a small molecule moiety.
  • the targeting ligand has a molecular weight of 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, or 2500 daltons, or a range defined by any two of the aforementioned numbers of daltons.
  • the targeting ligand may bind directly to the target protein.
  • the binding between the targeting ligand and the target protein is covalent.
  • the covalent binding may be with a cysteine, lysine, or methionine, or any other reactive residue of the target protein.
  • the binding between the targeting ligand and the target protein is non- covalent.
  • N-acyl-N-alkyl N-acyl-N-alkyl a-substituted ⁇ -substituted Oxaziridine for sulfonamide for sulfonamide for acrylamides acrylamides methionine lysine lysine for cysteine for cysteine X N or O
  • Non-limiting, exemplary cysteine reactive groups that can be attached to the RL or the TL are shown below:
  • the binding between the target protein and the targeting ligand comprises a binding affinity with an equilibrium dissociation constant (Kd) below 100 ⁇ M, a Kd below 90 ⁇ M, a Kd below 80 ⁇ M, a Kd below 70 ⁇ M, a Kd below 60 ⁇ M, a Kd below 50 ⁇ M, a Kd below 45 ⁇ M, a Kd below 40 ⁇ M, a Kd below 35 ⁇ M, a Kd below 30 ⁇ M, a Kd below 25 ⁇ M, a Kd below 20 ⁇ M, a Kd below 15 ⁇ M, a Kd below 14 ⁇ M, a Kd below 13 ⁇ M, a Kd below 12 ⁇ M, a Kd below 11 ⁇ M, a Kd below 10 ⁇ M, a Kd below 9 ⁇ M, a Kd below 8 ⁇ M, a Kd below 7 ⁇ M, a Kd below 6 ⁇ M, a
  • Kd equilibrium dissociation
  • the binding between the target protein and the targeting ligand comprises a binding affinity with an equilibrium dissociation constant (Kd) of at least 100 ⁇ M, a Kd of at least 90 ⁇ M, a Kd of at least 80 ⁇ M, a Kd of at least 70 ⁇ M, a Kd of at least 60 ⁇ M, a Kd of at least 50 ⁇ M, a Kd of at least 45 ⁇ M, a Kd of at least 40 ⁇ M, a Kd of at least 35 ⁇ M, a Kd of at least 30 ⁇ M, a Kd of at least 25 ⁇ M, a Kd of at least 20 ⁇ M, a Kd of at least 15 ⁇ M, a Kd of at least 14 ⁇ M, a Kd of at least 13 ⁇ M, a Kd of at least 12 ⁇ M, a Kd of at least 11 ⁇ M, a Kd of at least 10 ⁇ M, a Kd of at least 9 ⁇
  • Kd
  • a Kd of at least 6 ⁇ M a Kd of at least 5 ⁇ M, a Kd of at least 4 ⁇ M, a Kd of at least 3 ⁇ M, a Kd of at least 2 ⁇ M, or a Kd of at least 1 pM.
  • a target protein may include a protein intended to be modified, e.g. by a modifier protein.
  • the target protein may be an enzymatic interacting partner for the modifier protein.
  • the target protein may be modified by the modifier protein.
  • the target protein may be any protein upon which the modifier protein exerts its effects.
  • the modifier protein may be modified by the target protein.
  • target proteins may include, in non-limiting examples, structural proteins, signaling proteins such as receptor proteins, channel proteins, or enzymes.
  • the target protein comprises a tumor suppressor, metabolic enzyme, protein aggregate, or haploinsufficient protein.
  • the target protein may include a tumor suppressor.
  • the target protein may be a metabolic protein.
  • the target protein may include an enzyme.
  • the target protein may include an aggregate protein.
  • the target protein may include a haploinsufficient protein.
  • the target protein includes a tumor suppressor.
  • a tumor suppressor includes tumor protein P53 (P53 or p53).
  • P53 is also an example of protein that can activate DNA repair, arrest growth, or initiate apoptosis.
  • P53 is controlled by a multitude of post-translational modifications (PTMs) such as phosphorylation. Phosphorylation of P53 may dictate its activation status.
  • the target protein may include P53 or another protein that modulates DNA repair, cell growth, or apoptosis.
  • P53 is an example of a transcription factor. A mutation in p53 is observed in over 50% of all cancers. 90% of these mutations are missense and result in inactive or dominant forms of p53.
  • P53 has generally been an undruggable target. Previous approaches, mostly small molecules, have had only limited success in rescuing wild-type p53 function. Compared to existing pharmacochaperones, BFMs that recruit proteins capable of modulating p53 activity have a better chance of effectively re-activating p53.
  • the linker may be further attached to a recruiting ligand, for example, via click or amide coupling.
  • the compound provided herein targets p53 for modification by a modifier protein described herein.
  • the modification comprises a post -translation modification of p53. Further modifications are provided herein.
  • the p53 may include any detail as described at uniprot.org under accession number P04637 (as last accessed Nov. 10, 2022).
  • p53 may include a polypeptide having the following amino acid sequence: MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPH HERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVWPYEPPEVGSDCTTIHYNYM CNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHH ELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDA
  • the p53 of SEQ ID NO: 1 is wild-type p53.
  • the p53 may include a mutant form of p53.
  • the mutant form may be with regard to SEQ ID NO: 1.
  • the mutant form may include a functional fragment or SEQ ID NO: 1.
  • a functional fragment of SEQ ID NO: 1 has at least some of the function of wild type p53.
  • the mutant form of p53 may include an amino acid sequence at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, or at least 99% identical, to SEQ ID NO: 1.
  • the mutant form of p53 may in some instances include an amino acid sequence less than 75% identical, less than 80% identical, less than 85% identical, less than 90% identical, less than 91% identical, less than 92% identical, less than 93% identical, less than 94% identical, less than 95% identical, less than 96% identical, less than 97% identical, less than 98% identical, less than 99% identical, or less than 100% identical, to SEQ ID NO: 1.
  • the p53 may comprise a mutant p53.
  • the targeting ligand may bind the p53 mutant.
  • Some aspects relate to a heterobifunctional compound comprising: a p53 binding moiety attached to a recruiting ligand that binds a modifier protein, wherein the p53 binding moiety binds to one of a plurality of mutant forms of p53.
  • Some aspects relate to a heterobifunctional compound comprising: a p53 binding moiety attached to a recruiting ligand that binds a modifier protein, wherein the p53 binding moiety binds a mutant form of p53.
  • the mutant form of p53 is the p53 Y220C mutant, wherein the tyrosine at amino acid position 220 of p53 is substituted with a cysteine.
  • Some aspects include a method of activating ap53 mutant protein, comprising contacting the p53 mutant protein with a compound disclosed herein.
  • p53 binding ligands can bind to p53’s DNA binding domain (amino acids 92-312) of wild-type (WT) or mutant p53. In some embodiments, p53 binding ligands can bind to a cleft in C-terminus of p53 WT or mutant. In some embodiments, p53 binding ligands can bind p53 (WT or mutant) at the edge of DNA binding domain (site of CDB3 binding). In some embodiments, p53 binding ligands can interact with Asp268 of p53 WT or mutant.
  • the p53 mutant is the Y220C mutant.
  • the p53 binding ligands may interact with Cys220, Asp228, Thrl50, Ser227, and Leul45.
  • the p53 binding ligands may interact with Cys220, Asp228, Thrl50, Ser227, or Leul45 of the p52 Y220C mutant.
  • the p53 binding ligands may interact with any combination of Cys220, Asp228, Thrl50, Ser227, and Leul45 of the p53 Y220C mutant.
  • the interaction may comprise a covalent binding.
  • the p53 binding ligand may interact with Cys220.
  • the p53 binding ligand may interact with Asp228.
  • the binding ligand may interact with Cysl24, Cysl82, Cys220 (in p53 Y220C mutant), Cys 229, or Cys277.
  • the binding ligands may interact with Cys220 of the p53 Y220C mutant.
  • Some aspects include a heterobifunctional compound (BFM) comprising: a p53 binding moiety attached to a recruiting ligand that binds a modifier protein, wherein the p53 binding moiety binds to one of a plurality of mutant forms of p53.
  • Some aspects include a heterobifunctional compound comprising: a p53 binding moiety attached to a recruiting ligand that binds a modifier protein.
  • the p53 binding moiety may bind to a mutant form of p53, such as a mutant form of p53 selected from a mutant form described herein.
  • the mutant form may include a substitution such as a Y220C mutation.
  • the modifier protein comprises BRIM.
  • Some aspects include a method of activating a p53 mutant protein, comprising contacting the p53 mutant protein with a compound disclosed herein.
  • a target protein comprises a protein associated with a disease state.
  • the target protein may be present, upregulated, or downregulated in the disease state, or a mutation in the target protein may contribute to the disease state.
  • the target protein may play a role in the disease state, such as a deleterious role or a protective role with regard to the disease state.
  • a target protein comprises a protein with a modification status associated with a disease state.
  • the compound provided herein targets the target protein for modification by a modifier protein described herein such that the target protein is no longer associated with the disease state.
  • the phosphorylation status of the target protein may be associated with the disease state. Examples of disease states may include cancer.
  • the disease state includes cancer.
  • the target protein may be in a subject.
  • the target protein may be in a cell.
  • the target protein may be intrinsic to the cell.
  • the target protein may be endogenous to the cell.
  • the target protein is extrinsic to the cell.
  • the target protein is exogenous to the cell.
  • the cell may be a cell of the subject.
  • the target protein undergoes a change because of contact or proximity with the modifier protein.
  • the target protein may undergo a modification.
  • the modification may be an enzymatic modification.
  • the modification may include a post- translational modification.
  • Some examples of modifications may include phosphorylation, palmitoylation, methylation, glycosylation, ligation, sulfonation, ubiquitylation, SUMOylation, fucosylation, sialylation, tyrosylation, acylation, acetylation, or tetradecanoylation.
  • the modification may be added to the target protein or may be removed from the target protein.
  • the modification may include phosphorylation, dephosphorylation, methylation, demethylation, deacylation, deacetylation, glycosylation, deglycosylation, ubiquitylation, or deubiquitylation.
  • the modification may be covalent.
  • the modification may be non-covalent.
  • the target protein may undergo a structural change. Examples of structural changes may include protein folding or misfolding.
  • the structural change may include cleavage.
  • the modification may include changes in cellular localization.
  • the structural change may include changes in oligomerization state.
  • the modification may include the change in stability of target protein, its half-life, or concentration in certain subcellular compartments.
  • the structural change may include the ability of protein to interact with other proteins.
  • the target protein may be more active as a result of the change.
  • the target protein may be less active as a result of the change.
  • the enzymatic activity of the target protein may be affected as a result of the change.
  • the target protein activity is increased or decreased by about 1.5 -fold, 2-fold, 3 -fold, 4-fold, 5 -fold, 10-fold, 20-fold, 50-fold, 100-fold as a result of the change.
  • R 1 is a targeting ligand with a structure of Formula (II): Formula (II), wherein:
  • R A is C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl or 3- to 12- membered heteroaryl;
  • Y 1 , Y 2 , Y 3 , Y 4 , Y 5 , and Y 6 are each independently CH, C, NH, N, NO, S, SO, or absent, wherein at least two of Y 1 , Y 2 , Y 3 and Y 4 is CH, C, NH, N, NO, S, or SO, and wherein at least one of Y 5 and Y 6 is CH, C, NH, N, NO, S, or SO;
  • Y 7 and Y 8 are each independently C or N;
  • R 1A is a cysteine reactive group, C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, -SOR 1A1 , or -COR 1A1 , wherein the C1-6 alkyl and C3 -12 cycloalkyl is optionally substituted with -CN, halogen, or C1-6 alkylamines;
  • R 1B is deuterium, halogen, -CN, -OH, -OC1-6 alkyl, -OC1-6 haloalkyl, -NH2, NHC1-6 alkyl, -N(C1-6 alkyl) 2 , -NHCOMe, -OCOMe, -OCONR 1BA R 1BB , C1-6 alkyl, -COOR 1BB , -CONR 1BA R 1BB , - NR 1BA COR 1BB , -NO 2 , -NR 1B SO 2 , -SO 2 (C1-6alkyl), -SO 2 NR 1BA R 1BB , -SO 2 NH-heteroaryl, or two R 1G taken together form an aryl or heteroaryl ring;
  • R 1BA is hydrogen or C1-6 alkyl
  • R 1BB is hydrogen, -COC1-6 alkyl, Ci-ealkyl, Ce-12 aryl, 3- to 12- membered heteroaryl;
  • R 1C is deuterium, halogen, -OH, -OC1-6 alkyl, -OC1-6 haloalkyl, -NH2, NHC1-6 alkyl, - N(C1-6 alkyl) 2 , -NO 2 , -NHCOMe, or -OCOMe;
  • R 1E is C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, or 3- to 12- membered heteroaryl, wherein the C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, and 3- to 12- membered heteroaryl are optionally substituted with halogen, C1-6 alkyl, C1-6 alkoxy, C1-6 carboxylic acid, -NH2, or -N(Ci-ealkyl)2; or R 1D and R 1E combine with the carbon to which is attached to form a cyclic structure, wherein the cyclic structure is C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, and 3- to 12- membered heteroaryl, wherein the cyclic structure is optionally substituted with one or more R 1DE ;
  • R 1DE is deuterium, halogen, -CN, -OH, -NH2, -NH(C1-6 alkyl), -NH(C1-6 haloalkyl), - N(C1-6 alkyl)2, -OC1-6 alkyl, -OC1-6 haloalkyl, C1-6 alkyl, C1-6 alkoxy, C1-6 haloalkyl, C1-6 haloalkoxy, -NHCO(C 1-6 haloalkyl), -CO2(C 1-6 alkyl), -CONH(C 1-6 alkyl), -SO2NH(C1-6 alkyl), - SO 2 N(C1-6 alkyl) 2 , -SO 2 (C1-6 alkyl), or -SO 2 NMe(C1-6 alkyl);
  • R 1F is hydrogen or C1-6 alkyl; n is 0 to 5; o is 0 or 1; and
  • R 1B , R 1DE , or R 1E or the cyclic structure of R 1D and R 1E is covalently linked to L.
  • R 1D and R 1E combine to form a cyclic structure, wherein the cyclic structure is 3- to 7- membered heterocycloalkyl.
  • the cyclic structure is pyridinyl.
  • R 1 is a targeting ligand with a structure of Formula (II- A): wherein:
  • R B is 3- to 12- membered heterocycloalkyl
  • R 1DE is deuterium, halogen, -OH, -OMe, -OCF3, -NH2, -NH(C1-6alkyl), or -N(C1-6alkyl)2; and p is 0 to 5.
  • R 1 is a targeting ligand with a structure of Formula (II-B): wherein:
  • X 1 , X 2 , X 3 , and X 4 are each independently C, CH, NH, N, NO, S, SO or absent, wherein at least two of X 1 , X 2 , X 3 , and X 4 are C, CH, NH, N, NO, S, or SO; and p is 1 to 3.
  • the recruiting ligand may be configured to bind to a modifier protein.
  • the recruiting ligand may include a moiety that binds the modifier protein.
  • the recruiting ligand may bind the modifier protein.
  • the recruiting ligand may bind the protein or other macromolecule that interacts with a modifier protein.
  • the modifier may induce a change in the target protein.
  • the recruiting ligand is configured to bind to a modifier protein such that the modifier protein induces a change to the target protein.
  • the recruiting ligand may be a part of a heterobifunctional compound (BFM) such as an OmniTAC compound.
  • BFM heterobifunctional compound
  • the recruiting ligand may connect to a linker or targeting ligand.
  • the recruiting ligand is incorporated into an in vivo engineered protein.
  • the recruiting ligand may include a small molecule.
  • the recruiting ligand comprises a small molecule moiety.
  • the recruiting ligand has a molecular weight of 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, or 2500 daltons, or a range defined by any two of the aforementioned numbers of daltons.
  • the recruiting ligand may bind directly to the modifier protein.
  • the binding between the recruiting ligand and the modifier protein is covalent.
  • the covalent binding may be with a cysteine, lysine, methionine, or any other reactive residue of the modifier protein.
  • the binding between the recruiting ligand and the modifier protein is non-covalent.
  • R 2 comprises a recruiting ligand (RL) that binds to modifier proteins.
  • the recruiting ligands can be synthesized from parent ligands.
  • Parent ligands are small molecule binders for modifier proteins; these binders can be activators, inhibitors or have no effect on the modifier protein.
  • recruiting ligands comprise parent ligands with a chemical handle to attach to L or R 1 directly through appropriate chemical transformation. In some cases, the parent ligand may already contain a suitable chemical handle that can be utilized without affecting the binding ability of the ligand.
  • the recruiting ligand is the parent ligand.
  • the recruiting ligand is a truncated analogue of the parent ligand.
  • the recruiting ligand is an analogue of the parent ligand where a functional group or ring has been replaced by an appropriate bioisostere.
  • R 2 is designed as an analogue of the parent ligand by attaching a chemical handle that (1) is solvent exposed and (2) does not impair the binding to the modifier protein.
  • the exit vector is defined as the orientation and area projected by attachment of a linker to a parent ligand.
  • One parent ligand can lead to several R 2 designs with varied exit vector and/or chemical handles. The attachment point should have a minimal impact on the binding mode and affinity of the parent ligand. To do so, the following guidelines can be followed:
  • the binding mode is analyzed to identify solvent exposed regions of the ligand.
  • SAR structure activity relationship
  • the chemical handle can be: carboxylic acid, alkyne, amine, azide, isocyanide, sulfonyl chloride, sulfonyl fluoride, alkyl bromide, alkyl chloride, alkyl iodide, alkyl mesylate, aldehydes, ketone.
  • the chemical handle should be chosen such that it is compatible with other functional groups within the parent ligand.
  • the parent ligand is selected from the compounds listed in FIG. 1 or FIG. 2. In some embodiments, the parent ligand is selected from the compounds listed in FIG. 1. In some embodiments, the parent ligand is selected from the compounds listed in FIG. 2.
  • the linker may be a part of a heterobifunctional compound such as an OmniTAC compound.
  • the linker may connect a targeting ligand to a recruiting ligand.
  • the linker may directly connect to both the targeting ligand and the recruiting ligand.
  • the linker may include a ligand of a protein such as a target protein.
  • the linker comprises a carboxylate. In some embodiments, the linker comprises an anhydride. In some embodiments, the linker comprises a polypeptide. In some embodiments, the linker comprises piperazine. In some embodiments, the linker comprises piperidyl. In some embodiments, the linker comprises triazole. In some embodiments, the linker comprises enamines. [0062] In some embodiments, the linker comprises a chain length of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 carbon atoms, or a range defined by any two of the aforementioned numbers of atoms. In some embodiments, the linker comprises a chain length of between 2 to 24 atoms. In some embodiments, the linker comprises a chain length of between 2 to 18 atoms.
  • the linker comprises: (a) a structure selected from the nonlimiting group consisting of polyethylene glycol, an aromatic group, an alkyl, an alkenyl, an alkyl phosphate, an alkyl siloxane, an epoxy, a glycidyl, a carboxylate, an anhydride, a piperazine, a piperidyl, a triazole, or a combination thereof; or (b) a polypeptide of natural or synthetic source having a chain length of between 2 to 24 amino acids.
  • the linker comprises one or more covalently connected structural units of A (e.g., -Ai . . . A q ⁇ ), wherein Ai is a group coupled to at least one of a recruiting ligand, a targeting ligand, or a combination thereof.
  • Ai links a recruiting ligand, a targeting ligand, or a combination thereof directly to another recruiting ligand, targeting ligand, or combination thereof.
  • Ai links a recruiting ligand, a targeting ligand, or a combination thereof indirectly to another recruiting ligand, targeting ligand, or combination thereof through A q .
  • R j or R 1 ' 2 groups Cri-nheterocyclyl optionally substituted with 0-6 R L1 or R L2 groups, aryl optionally substituted with 0-6 R L1 or R L2 groups, heteroaryl optionally substituted with 0-6 R L1 or R L2 groups, where R ljl or R L2 , each independently, can be linked to other A groups to form cycloalkyl or heterocyclyl moiety which can be further substituted with 0-4 R ; ' : groups.
  • R L1 , R : 2 _ R L3 , R L4 and R L5 are, each independently, H, halo, C1-8alkyl, OC1-8alkyl, SC1-8alkyl, NHCusalkyl, N(Cj.
  • q is an integer greater than or equal to 0. In some embodiments, q is an integer greater than or equal to 1.
  • a q is a group which is connected to a recruiting ligand or recruiting ligand moiety, and Ai and A q are connected via structural units of A (number of such structural units of A: q-2).
  • a q is a group which is connected to Ai and to a recruiting ligand or recruiting ligand moiety.
  • q is 1, the structure of the linker is -Ai-, and Ai is a group which is connected to a recruiting ligand or recruiting ligand moiety and a targeting ligand moiety.
  • q is an integer from 1 to 100, 1 to 90, 1 to 80, 1 to 70, 1 to 60, 1 to 50, 1 to 40, 1 to 30, 1 to 20, or 1 to 10.
  • the linker comprises or consists of optionally substituted (poly)ethyleneglycol having about 1 to about 100 ethylene glycol units, about 1 to about 50 ethylene glycol units, about 1 to about 25 ethylene glycol units, about 1 to about 10 ethylene glycol units, about 1 to about 8 ethylene glycol units, about 1 to about 6 ethylene glycol units, about 2 to about 4 ethylene glycol units, or optionally substituted alkyl groups interdispersed with optionally substituted (), N, S, P or Si atoms.
  • the linker is substituted with an aryl, phenyl, benzyl, alkyl, alkylene, halogen, or heterocycle group.
  • the linker may be asymmetric or symmetrical.
  • the linker may be any suitable moiety' as described herein.
  • the linker is or includes a substituted or unsubstituted polyethylene glycol group ranging in size from about 1 to about 12 ethylene glycol units, from about 1 to about 10 ethylene glycol units, from about 2 to about 6 ethylene glycol units, from about 2 to 5 ethylene glycol units, and from about 2 to about 4 ethylene glycol units.
  • the linkers comprise a structure -(AP) m -L 1A -L 1B -(AP) m -.
  • AP, L 1A , and L 1B are as described in the specification and claims herein.
  • AP is PEG, ether, amide, sulfonamide, sulfone, sulfoxide, sulfonate, phosphonate, ester, urea, carbamate, substituted phosphine oxide, optionally substituted C1-6 alkyl, optionally substituted C3-12 cycloalkyl, optionally substituted 3- to 12- membered heterocycloalkyl, optionally substituted 3- to 12- membered heteroaryl, or optionally substituted C6-12 aryl.
  • L 1A and L 1B are each independently polyethylene glycol (PEG), Ci-50 alkylene-PEG, C2-50 alkenylene-PEG, C2-50 alkynylene-PEG, C1-50 alkylene, C2-50 alkenylene, C2-50 alkynylene, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-naryl, 3- to 12- membered heteroaryl, 3- to 12- membered heterocycloalkyl-Ci-10 alkylene, 3- to 12- membered heterocycloalkyl-PEG, or PEG-3- to 12- membered heterocycloalkyl-PEG, spirocyclic cores, or a combination thereof, each of which may be substituted with one or more halogen, deuterium, methyl, deuterated methyl, trifluoromethyl, amide, sulfonamide, sulfone, ester, urea, carbamate, C
  • PEG polyethylene glycol
  • the linker comprises the following structure, wherein n is any integer from I to 30:
  • L is one of the following: [0074] In certain embodiments, L is one of the following:
  • the compound is a compound of Formula (III- A) or Formula
  • the compound is a compound of Formula (III-A1) or
  • Formula (III-B1) wherein: B is a absent, -NH-, -O-, CO, amide, C1-6 alkylene, C2-6 alkenylene, or C2-6 alkynylene, wherein the C1-6 alkylene, C2-6 alkenylene, and C2-6 alkynylene is optionally substituted with deuterium, halogen, or C1-3 alkoxy;
  • W 1 and W 2 are each independently NH, N, O, or S;
  • R c and R D are each independently optionally substituted C3-12 cycloalkyl, optionally substituted 3- to 12- membered heterocycloalkyl, optionally substituted Ce-12 aryl or optionally substituted 3- to 12- membered heteroaryl;
  • R 1H and R 11 are each independently hydrogen or C1-6 alkyl, wherein the C1-6 alkyl is optionally substituted with deuterium or halogen.
  • the compound is a compound of Formula (III-A2) or Formula (III-B2): wherein:
  • X 1 , X 2 , X 3 , and X 4 are each independently C, CH, NH, N, NO, S, SO or absent, and wherein at least two of X 1 , X 2 , X 3 , and X 4 is C, CH, NH, N, NO, S, SO.
  • R 2 is: wherein:
  • X 5 , X 6 , X 7 , X 8 , and X 14 are each independently C, CH, CD, CF, NH, N, NO, S, SO or absent, and wherein at least one of X 5 and X 6 is C, CH, CD, CF, NH, N, NO, S, or SO;
  • X 9 , X 10 , X 11 , X 12 , and X 13 are each independently C, CH, CD, CF, NH, N, NO, S, SO or absent, and wherein at least two of X 9 , X 10 , X 11 , X 12 , and X 13 are C, CH, CD, CF, CCH3, CCD3, CCF 3 , N, NH, NO, S, or SO;
  • R 1J is NH2, NH(C1-6 alkyl), N(C1-6 alkyl)2 or absent;
  • the compound is a compound of Formula (IV-A), Formula (IV-B), Formula (IV-C), or Formula (IV-D):
  • the compound is a compound of Formula (IV-A1), Formula
  • R 1B , R 1C , and R 1L are each independently halogen, -OH, -NH2, -NH(C1-6 alkyl), -NH(CI-6 alkyl) 2 , -OC1-6 alkyl, -OCH3, -OCF3, -NO 2 , -NHAc, or -OAc;
  • R 1DE is halogen, deuterium, hydroxyl, trifluoromethoxy, or amine; or wherein when R 1DE is in (R 1DE ) p -i, then R 1DE is deuterium, halogen, -CN, -OH, -NH2, - NH(C 1-6 alkyl), -NH(C1-6haloalkyl), -OC1-6 alkyl, -OC1-6 haloalkyl, C1-6 alkyl, C1-6 haloalkyl, - NHCO(C1-6 haloalkyl), -CO 2 (C1-6 alkyl), -CONH(C1-6 alkyl), -SO 2 NH(C1-6 alkyl), -SO 2 N(C1-6 alkyl) 2 , -SO2(C 1-6 alkyl), or -SO2NMe(C1-6 alkyl); and q is 0 to 5. [0084] In certain embodiments, R 2 is: wherein:
  • X 21 is C, CH, or N
  • X 22 , and X 23 are each independently C, CH, CO, N, NH, CNH 2 , or CO(C1-6 alkyl);
  • the compound is a compound of Formula (IV-A2) or Formula (IV-C2):
  • R 1A is a cysteine reactive group or C1-6 alkyl, wherein the Ci- 6 alkyl is optionally substituted with halogen.
  • R 1B is -OC1-6 alkyl, -OC1-6 haloalkyl, -OCON(C1-6 alkyl)2, -SO2(C1-6 alkyl), or -SO2N(C1-6 alkyl)2.
  • R 1DE is deuterium, halogen, -OH, -OMe, or -OCF3.
  • R 1F is hydrogen or methyl.
  • R 1 is one of the following:
  • Y 1 is one of the following:
  • R 1 is -(3-6 membered saturated heterocyclylene containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R 2 )-(indolyl substituted with C1-4haloalkyl and 0 or 1 -N(R 3 )-(C2-4 alkynylene)-N(R 2 )-(phenyl substituted with 0 or 1 C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl or -S(O)2-(C1-4 alkyl)).
  • R 1 is -(3-6 membered saturated heterocyclylene containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of halo, hydroxyl, and
  • Y 1 is -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R 2 )2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
  • Y 1 is -(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R 2 )2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
  • Y 1 is -(imidazo[4,5-b]pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R 2 )2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
  • Y 1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R 4 )-(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
  • Y 1 is -(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
  • Y 1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl, and 5-membered heteroaryl)-(C1-6 alkylene substituted by 1 or 2 hydroxyl)-(phenyl or pyridinyl substituted with 0,
  • Y 1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(pyridin-2-onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
  • Y 1 is -(phenylene or pyridinylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R 4 )-(pyridin-2-onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
  • Y 1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(O)- (pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, or 5-membered heteroaryl, wherein the 5 -membered heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R 4 )-(C1-6 alkylene)-(phenyl or pyridinyl substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl).
  • Y 1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl)-(5-10 membered heteroaryl substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and 5 -membered heteroaryl, wherein the 5 -membered heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene, wherein the C1-6 alkylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of C1-4 alkyl and 6-membered heteroaryl).
  • Y 1 is one of the following:
  • L is a bivalent, saturated or unsaturated, straight or branched C5-30 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O) 2 -, - N(H)S(O) 2 -, -N(C1-6 alkyl)S(O) 2 -, -S(O) 2 N(H)-, -S(O) 2 N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, -C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(H)-, -
  • L is a bivalent, saturated or unsaturated, straight or branched C5-30 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -N(H)-, -N(C 1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O) 2 -, -N(H)S(O) 2 -, - N(C1-6 alkyl)S(O) 2 -, -S(O) 2 N(H)-, or -S(O) 2 N(C1-6 alkyl)-.
  • R 1 is -(phenyl substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-N(R 2 )-(C 2 -4alkynylene)-(indolyl substituted with C1-4haloalkyl and -N(R 3 )-(3-6 membered saturated heterocyclyl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclyl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
  • R 2 , R 3 , R 4 and independently hydrogen or C1-4 alkyl
  • Y 1 is one of the following:
  • L is a bivalent, saturated or unsaturated, straight or branched Ci-60 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -S-, - N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O) 2 -, -N(H)S(O) 2 -, -N(C1-6 alkyl)S(O) 2 -, -S(O) 2 N(H)-, -S(O) 2 N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, - C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6
  • R 1 is -(phenyl substituted with methoxy and 0 or 1 occurrences of halo, hydroxyl, or C1-4 alkyl)-N(R 2 )-(C 3 alkynylene)-(indolyl substituted with - CH 2 CF 3 and -N(R 3 )-(piperidinyl substituted by 1 or 2 substituents independently selected from the group consisting of fluoro and methyl).
  • R 1 is -(phenyl substituted with methoxy and 0 or 1 occurrences of halo, hydroxyl, or C1-4 alkyl)-N(R 2 )-(C 3 alkynylene)-(indolyl substituted with - CH 2 CF 3 and -N(R 3 )-(piperidinyl substituted by 1 or 2 substituents independently selected from the group consisting of fluoro and methyl).
  • R 1 is
  • Y 1 is -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
  • Y 1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R 4 )-(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
  • Y 1 is -(phenylene substituted by 0 or 1 substituent independently selected from the group consisting of halo and C1-4 alkyl)-(C1-4 alkylene)-N(R 4 )-(pyridinylene substituted with C1-4alkoxyl and 0 or 1 occurrences of halo or C1-4 alkyl)-(isoxazolyl substituted by 1, 2, or 3 C1-4 alkyl).
  • Y 1 is one of the following:
  • L is -S(O)2N(C1-6 alkyl)-, -S(O)2N(C1-6 alkyl)-(Co-e-alkylene)- (3-6 membered heterocyclyl containing 1 nitrogen atom)-C(O)-, -S(O)2N(C1-6 alkyl)-(C3-6- cycloalkylene)-N(H)C(O)-, or -S(O)2N(C1-6 alkyl)-(C3-6-cycloalkylene)-(C1-6-alkylene)- N(H)C(O)-.
  • L is -S(O)2N(C1-6 alkyl)-.
  • L is - S(0)2N(C1-6 alkyl)-(Co-6-alkylene)-(3-6 membered heterocyclyl containing 1 nitrogen atom)- C(O)-. In certain embodiments, L is -S(O)2N(C1-6 alkyl)-(C3-6-cycloalkylene)-N(H)C(O)-. In certain embodiments, L is -S(O)2N(C1-6 alkyl)-(C3-6-cycloalkylene)-(C1-6-alkylene)-N(H)C(O)-.
  • the compound is a compound in any of Tables 1-5 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in any of tables 1- 5. In certain embodiments, the compound is a compound in Table 1 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in Table 1. In certain embodiments, the compound is a compound in Table 2 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in Table 2. In certain embodiments, the compound is a compound in Table 3 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in Table 3.
  • the compound is a compound in Table 4 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in Table 4. In certain embodiments, the compound is a compound in Table 5 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in Table 5.
  • the pharmaceutical composition may include a compound described herein.
  • the pharmaceutical composition may include an OmniTAC compound.
  • the pharmaceutical composition comprises a heterobifunctional compound.
  • the pharmaceutical composition is sterile.
  • the pharmaceutical composition may include the compound and a pharmaceutically acceptable carrier.
  • the pharmaceutically acceptable carrier comprises a water. In some embodiments, the pharmaceutically acceptable carrier comprises a buffer. In some embodiments, the pharmaceutically acceptable carrier comprises a saline solution. In some embodiments, the pharmaceutically acceptable carrier comprises water, a buffer, or a saline solution.
  • the pharmaceutical compositions may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained- release formulation; (3) topical application, for example, as a cream, ointment, or a controlled- release patch or spray applied to the skin; (4) intravaginally or intrarectally, for example, as a pessary, cream or foam; (5) sublingually; (6) ocularly; (7) transdermally; or (8) nasally.
  • the invention provides a pharmaceutical composition comprising a compound described herein (such as a compound
  • wetting agents such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, release agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the compositions.
  • antioxidants examples include: (1) water soluble antioxidants, such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like; (2) oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol, and the like; and (3) metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.
  • water soluble antioxidants such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like
  • oil-soluble antioxidants such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), le
  • Formulations of the present invention include those suitable for oral, nasal, topical (including buccal and sublingual), rectal, vaginal and/or parenteral administration.
  • the formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy.
  • the amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, the particular mode of administration.
  • the amount of active ingredient which can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound which produces a therapeutic effect. Generally, out of one hundred percent, this amount will range from about 0.1 percent to about ninety -nine percent of active ingredient, preferably from about 5 percent to about 70 percent, most preferably from about 10 percent to about 30 percent.
  • a formulation of the present invention comprises an excipient selected from the group consisting of cyclodextrins, celluloses, liposomes, micelle forming agents, e.g., bile acids, and polymeric carriers, e.g., polyesters and polyanhydrides; and a compound of the present invention.
  • an aforementioned formulation renders orally bioavailable a compound of the present invention.
  • Methods of preparing these formulations or compositions include the step of bringing into association a compound of the present invention with the carrier and, optionally, one or more accessory ingredients.
  • the formulations are prepared by uniformly and intimately bringing into association a compound of the present invention with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product.
  • Formulations of the invention suitable for oral administration may be in the form of capsules, cachets, pills, tablets, lozenges (using a flavored basis, usually sucrose and acacia or tragacanth), powders, granules, or as a solution or a suspension in an aqueous or non-aqueous liquid, or as an oil-in-water or water-in-oil liquid emulsion, or as an elixir or syrup, or as pastilles (using an inert base, such as gelatin and glycerin, or sucrose and acacia) and/or as mouth washes and the like, each containing a predetermined amount of a compound of the present invention as an active ingredient.
  • a compound of the present invention may also be administered as a bolus, electuary or paste.
  • the active ingredient is mixed with one or more pharmaceutically-acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and/or silicic acid; (2) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose and/or acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds and surfactants, such
  • compositions may also comprise buffering agents.
  • Solid compositions of a similar type may also be employed as fillers in soft and hard-shelled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols and the like.
  • a tablet may be made by compression or molding, optionally with one or more accessory ingredients.
  • Compressed tablets may be prepared using binder (for example, gelatin or hydroxypropylmethyl cellulose), lubricant, inert diluent, preservative, disintegrant (for example, sodium starch glycolate or cross-linked sodium carboxymethyl cellulose), surface-active or dispersing agent.
  • Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.
  • the tablets, and other solid dosage forms of the pharmaceutical compositions of the present invention may optionally be scored or prepared with coatings and shells, such as enteric coatings and other coatings well known in the pharmaceutical-formulating art. They may also be formulated so as to provide slow or controlled release of the active ingredient therein using, for example, hydroxypropylmethyl cellulose in varying proportions to provide the desired release profile, other polymer matrices, liposomes and/or microspheres. They may be formulated for rapid release, e.g., freeze-dried.
  • compositions may be sterilized by, for example, filtration through a bacteria-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved in sterile water, or some other sterile injectable medium immediately before use.
  • These compositions may also optionally contain opacifying agents and may be of a composition that they release the active ingredient(s) only, or preferentially, in a certain portion of the gastrointestinal tract, optionally, in a delayed manner.
  • embedding compositions which can be used include polymeric substances and waxes.
  • the active ingredient can also be in micro-encapsulated form, if appropriate, with one or more of the above-described excipients.
  • Liquid dosage forms for oral administration of the compounds of the invention include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs.
  • the liquid dosage forms may contain inert diluents commonly used in the art, such as, for example, water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3 -butylene glycol, oils (in particular, cottonseed, groundnut, com, germ, olive, castor and sesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.
  • inert diluents commonly used in the art, such as, for example, water or other solvents, solubilizing
  • Suspensions in addition to the active compounds, may contain suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.
  • suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.
  • Formulations of the pharmaceutical compositions of the invention for rectal or vaginal administration may be presented as a suppository, which may be prepared by mixing one or more compounds of the invention with one or more suitable nonirritating excipients or carriers comprising, for example, cocoa butter, polyethylene glycol, a suppository wax or a salicylate, and which is solid at room temperature, but liquid at body temperature and, therefore, will melt in the rectum or vaginal cavity and release the active compound.
  • suitable nonirritating excipients or carriers comprising, for example, cocoa butter, polyethylene glycol, a suppository wax or a salicylate, and which is solid at room temperature, but liquid at body temperature and, therefore, will melt in the rectum or vaginal cavity and release the active compound.
  • Formulations of the present invention which are suitable for vaginal administration also include pessaries, tampons, creams, gels, pastes, foams or spray formulations containing such carriers as are known in the art to be appropriate.
  • Dosage forms for the topical or transdermal administration of a compound of this invention include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants.
  • the active compound may be mixed under sterile conditions with a pharmaceutically - acceptable carrier, and with any preservatives, buffers, or propellants which may be required.
  • the ointments, pastes, creams and gels may contain, in addition to an active compound of this invention, excipients, such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.
  • excipients such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.
  • Powders and sprays can contain, in addition to a compound of this invention, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances.
  • Sprays can additionally contain customary propellants, such as chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, such as butane and propane.
  • Transdermal patches have the added advantage of providing controlled delivery of a compound of the present invention to the body.
  • dosage forms can be made by dissolving or dispersing the compound in the proper medium.
  • Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate of such flux can be controlled by either providing a rate controlling membrane or dispersing the compound in a polymer matrix or gel.
  • Ophthalmic formulations are also contemplated as being within the scope of this invention.
  • Injectable depot forms are made by forming microencapsule matrices of the subject compounds in biodegradable polymers such as polylactide-polyglycolide. Depending on the ratio of drug to polymer, and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissue.
  • biodegradable polymers such as polylactide-polyglycolide.
  • Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissue.
  • in vivo engineered proteins include an in vivo engineered protein complex comprising a compound such as an OmniTAC compound directly bound to a target protein at one end of the compound and a modifier protein at another end of the compound.
  • a compound such as an OmniTAC compound directly bound to a target protein at one end of the compound and a modifier protein at another end of the compound.
  • Some embodiments include an in vivo engineered protein comprising: a target protein directly bound to a compound such as OmniTAC compound.
  • the compound comprises a targeting ligand.
  • the targeting ligand binds to a binding region on the target protein.
  • the binding region on the target protein comprises a particular domain or amino acid residue.
  • the target protein is directly bound to the targeting ligand by a non-covalent interaction between the target protein and the targeting ligand.
  • the binding between the target protein and the targeting ligand comprises a binding affinity described herein.
  • the compound described herein further comprises a recruiting ligand.
  • the recruiting ligand is attached to the targeting ligand via a linker such as a linker described herein.
  • the target protein may include a structural change and/or modification, as compared to the same target protein not bound to the compound, such as a modification and/or structural change resulting from association with the modifier protein.
  • Some embodiments include an in vivo engineered protein comprising a modifier protein directly bound to a compound such as an OmniTAC compound.
  • the compound comprises a recruiting ligand.
  • the recruiting ligand binds to a binding region on the modifier protein.
  • the binding region on the modifier protein comprises a particular domain or amino acid residue.
  • the modifier protein is directly bound to the recruiting ligand by a non-covalent interaction between the modifier protein and the recruiting ligand.
  • the binding between the modifier protein and the recruiting ligand comprises a binding affinity described herein.
  • the compound described herein further comprises a targeting ligand.
  • the targeting ligand is attached to the recruiting ligand via a linker such as a linker described herein.
  • the modifier protein may be any modifier protein disclosed herein.
  • the target protein may be any target protein disclosed herein.
  • the compound comprises a heterobifunctional compound.
  • the compound comprises an OmniTAC compound.
  • the compound comprises a targeting ligand, a recruiting ligand, and a linker.
  • a modified protein disclosed herein is formed in vivo upon administration of the compound or pharmaceutical composition to a subject. Some embodiments relate to a method of forming an in vivo engineered protein, comprising administering the compound or pharmaceutical composition to the subject.
  • a method may include use of an OmniTAC compound.
  • a method includes use of a heterobifunctional compound.
  • Some embodiments include a method for inducing a change in a target protein, comprising: contacting the target protein with a modifier protein via a modifier protein targeting chimeric compound (OmniTAC) such that the modifier protein induces a change to the target protein.
  • the change may be or may include a modification described herein, and/or a structural change described herein.
  • the change may include a change in activity of the target protein.
  • the change may include a change in cellular location and/or cellular sublocalization of the target protein.
  • Some embodiments include a method for inducing a change in a p53 protein, comprising contacting the p53 protein with a modifier protein via a compound described herein, e.g. OmniTAC compound, such that the modifier protein induces a change to the p53 protein.
  • Some embodiments include a method for inducing a change in a p53 protein, comprising contacting the P53 protein with a modifier protein via a modifier protein targeting chimeric compound (OmniTAC) such that the modifier protein induces a change to the p53 protein.
  • the change may include phosphorylation.
  • Some embodiments include a method of activating a p53 mutant protein. The method may comprise contacting the p53 mutant protein with a compound disclosed herein, e.g, an OmniTAC compound.
  • the change in the target protein may be or may include any change described herein.
  • the change includes phosphorylation.
  • the change includes dephosphorylation.
  • the change includes palmitoylation.
  • the change includes depalmitoylation.
  • the change includes methylation.
  • the change includes demethylation.
  • the change includes glycosylation.
  • the change includes deglycosylation.
  • the change includes ligation.
  • the change includes cleavage.
  • the change includes sulfonation.
  • the change includes desulfonation.
  • the change includes ubiquitylation. In some embodiments, the change includes deubiquitylation. In some embodiments, the change includes SUMOylation. In some embodiments, the change includes deSUMOylation. In some embodiments, the change includes fucosylation. In some embodiments, the change includes defucosylation. In some embodiments, the change includes sialylation. In some embodiments, the change includes desialylation. In some embodiments, the change includes tyrosylation. In some embodiments, the change includes detyrosylation. In some embodiments, the change includes acylation. In some embodiments, the change includes deacylation. In some embodiments, the change includes acetylation. In some embodiments, the change includes deacetylation.
  • the change includes decanoylation. In some embodiments, the change includes dedecanoylation. In some embodiments, the change includes a structural change. In some embodiments, the change includes binding or aggregation with another protein. In some embodiments, the change includes protein folding. In some embodiments, the change includes protein misfolding. In some embodiments, the change includes changes in cellular sub-localization. In some embodiments, the change includes nuclear localization. In some embodiments, the change includes mitochondrial localization.
  • the method may include measuring the change.
  • the measurement may be made after administration of the compound to a cell or subject.
  • the measurement may be made in relation to a control or baseline measurement.
  • the measurement may be made by any of a variety of methods.
  • Measuring the change may include using a detection reagent that binds to a target protein and yields a detectable signal. After use of the detection reagent that binds to the target protein and yields the detectable signal, a readout may be obtained that is indicative of the presence, absence or amount of the change in the target protein.
  • Measuring the change may include concentrating, filtering, or centrifuging a sample, e.g. comprising the target protein, the modifier protein, and/or the compound described herein.
  • Measuring the change may include using an assay method such as microscopy, spectrophotometry, mass spectrometry, chromatography, liquid chromatography, high- performance liquid chromatography, solid-phase chromatography, a lateral flow assay, an immunoassay, an enzyme-linked immunosorbent assay, a western blot, a dot blot, or immunostaining, or a combination thereof.
  • the measurement may be obtained using mass spectrometry.
  • assay methods may include using mass spectrometry, a protein chip, or a reverse-phased protein microarray.
  • a measurement may be generated using an immunoassay such as an enzyme-linked immunosorbent assay, western blot, dot blot, or immunohistochemistry.
  • the measurement may be obtained using sequencing.
  • a measurement may be obtained using flow cytometry.
  • a measurement may be obtained using chromatography, for example high performance liquid chromatography.
  • the change may be measured or assessed using an enzyme activity assay.
  • the change may be measured or assessed using histochemistry or immunohistochemistry.
  • the change may be measured or assessed using microscopy.
  • the change may be assessed using an assay such as an immunoassay, a colorimetric assay, a lateral flow assay, a fluorescence assay, a proteomics assay, or a cell-based assay.
  • the change may be measured using a reporter gene assay, e.g., a luciferase reporter gene assay.
  • the change may be measured or assessed using luminescence or fluorescence.
  • the change may be measured or assessed using microscopy.
  • the change may be measured or assessed or normalized using cell viability.
  • any compound described herein may be used in a method herein.
  • the compound comprises a targeting ligand, a recruiting ligand, and a linker.
  • the targeting ligand is configured to bind to a target protein described herein.
  • the recruiting ligand is configured to bind to a modifier protein described herein.
  • the method may be performed in a subject.
  • the method may be performed in a cell or a sample of a subject. Examples of subjects include vertebrates, animals, mammals, dogs, cats, cattle, rodents, mice, rats, primates, monkeys, and humans.
  • the subject is a mammal.
  • the subject is a human.
  • the compounds described herein are used to treat a subject.
  • the method may include administering a compound, e.g., a heterobifunctional compound described herein such as an OmniTAC compound.
  • a pharmaceutical composition described herein is administered.
  • the subject may have a disease and may be in need of treatment thereof.
  • the administration improves a symptom or parameter of the disease.
  • the disease is caused by a dysfunction and/or dysregulation of a target protein described herein, e.g., p53.
  • the disease is cancer. The symptoms may be improved as assessed by a measurement made in relation to a baseline measurement.
  • the heterobifunctional compounds described herein such as a compound of Formula I, II, III, IV, V, VI or other compounds in Section I, provide therapeutic benefits to patients suffering from cancer. Accordingly, one aspect of the invention provides a method of treating cancer. The method comprises administering to a patient in need thereof a therapeutically effective amount of a compound described herein, such as a compound of Formula I, II, III, IV, V, VI or other compounds in Section I, to treat the cancer.
  • the compound is a compound of Formula I.
  • the particular compound of Formula I is a compound defined by one of the embodiments described above.
  • the cancer is ovarian cancer, uterine cancer, endometrial cancer, cervical cancer, prostate cancer, testicular cancer, breast cancer, brain cancer, lung cancer, oral cancer, esophageal cancer, head and neck cancer, stomach cancer, colon cancer, rectal cancer, skin cancer, sebaceous gland carcinoma, bile duct and gallbladder cancers, liver cancer, pancreatic cancer, bladder cancer, urinary tract cancer, kidney cancer, eye cancer, thyroid cancer, lymphoma, or leukemia.
  • the cancer is prostate cancer.
  • the cancer is squamous cell cancer, lung cancer including small cell lung cancer, non-small cell lung cancer, vulval cancer, thyroid 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, hepatic carcinoma, anal carcinoma, penile carcinoma, and head and neck cancer.
  • lung cancer including small cell lung cancer, non-small cell lung cancer, vulval cancer, thyroid 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, glioblast
  • the cancer is at least one selected from the group consisting of ALL, T-Iineage Acute lymphoblastic Leukemia (T-ALL), T-Iineage lymphoblastic Lymphoma (T-LL), Peripheral T-cell lymphoma, Adult T-cell Leukemia, Pre-B ALL, Pre-B Lymphomas, Large B-cell Lymphoma, Burkitts Lymphoma, B-cell ALL, Philadelphia chromosome positive ALL, Philadelphia chromosome positive CML , lymphoma, leukemia, multiple myeloma myeloproliferative diseases, large B cell lymphoma, or B cell Lymphoma.
  • T-ALL T-Iineage Acute lymphoblastic Leukemia
  • T-LL T-Iineage lymphoblastic Lymphoma
  • Peripheral T-cell lymphoma Peripheral T-cell lymphoma
  • Adult T-cell Leukemia Pre-B ALL, Pre-B Lymphomas
  • the cancer is a solid tumor or leukemia.
  • the cancer is colon cancer, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, lung cancer, leukemia, bladder cancer, stomach cancer, cervical cancer, testicular cancer, skin cancer, rectal cancer, thyroid cancer, kidney cancer, uterus cancer, espophagus cancer, liver cancer, an acoustic neuroma, oligodendroglioma, meningioma, neuroblastoma, or retinoblastoma.
  • the cancer is small cell lung cancer, non-small cell lung cancer, melanoma, cancer of the central nervous system tissue, brain cancer, Hodgkin’s lymphoma, non-Hodgkin ’s lymphoma, cutaneous T-Cell lymphoma, cutaneous B-Cell lymphoma, or diffuse large B-Cell lymphoma.
  • the cancer is breast cancer, colon cancer, small -cell lung cancer, non-small cell lung cancer, prostate cancer, renal cancer, ovarian cancer, leukemia, melanoma, or cancer of the central nervous system tissue.
  • the cancer is colon cancer, small-cell lung cancer, non-small cell lung cancer, renal cancer, ovarian cancer, renal cancer, or melanoma.
  • the cancer is a fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangio endothelio sarcoma, Ewing’s tumor, leiomyosarcoma, rhabdomyosarcoma, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adeno carcinomas, cystadeno carcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms’ tumor, epithelial carcinoma, glioma, astrocytoma, medulloblastoma
  • the cancer is a neuroblastoma, meningioma, hemangiopericytoma, multiple brain metastase, glioblastoma multiforms, glioblastoma, brain stem glioma, poor prognosis malignant brain tumor, malignant glioma, anaplastic astrocytoma, anaplastic oligodendroglioma, neuroendocrine tumor, rectal adeno carcinoma, Dukes C & D colorectal cancer, unresectable colorectal carcinoma, metastatic hepatocellular carcinoma, Kaposi’s sarcoma, karotype acute myeloblastic leukemia, Hodgkin’s lymphoma, non-Hodgkin’s lymphoma, cutaneous T-Cell lymphoma, cutaneous B-Cell lymphoma, diffuse large B-Cell lymphoma, low grade follicular lymphoma, metastatic melanoma
  • the cancer is hepatocellular carcinoma, ovarian cancer, ovarian epithelial cancer, or fallopian tube cancer; papillary serous cystadeno carcinoma or uterine papillary serous carcinoma (UPSC); prostate cancer; testicular cancer; gallbladder cancer; hcpatocholangio carcinoma; soft tissue and bone synovial sarcoma; rhabdomyosarcoma; osteosarcoma; chondrosarcoma; Ewing sarcoma; anaplastic thyroid cancer; adreno corticaladenoma; pancreatic cancer; pancreatic ductal carcinoma or pancreatic adenocarcinoma; gastrointestinal/stomach (GIST) cancer; lymphoma; squamous cell carcinoma of the head and neck (SCCHN); salivary gland cancer; glioma, or brain cancer; neurofibromatosis- 1 associated malignant peripheral nerve sheath tumors (MPNST); Waldenstrom's macroglobin, or apop
  • the cancer is hepatocellular carcinoma (HCC), hepatoblastoma, colon cancer, rectal cancer, ovarian cancer, ovarian epithelial cancer, fallopian tube cancer, papillary serous cystadeno carcinoma, uterine papillary serous carcinoma (UPSC),hepatocholangio carcinoma, soft tissue and bone synovial sarcoma, rhabdomyosarcoma, osteosarcoma, anaplastic thyroid cancer, adrenocortical adenoma, pancreatic cancer, pancreatic ductal carcinoma, pancreatic adenocarcinoma, glioma, neurofibromatosis- 1 associated malignant peripheral nerve sheath tumors (MPNST), Waldenstrom's macroglobulinemia, or medulloblastoma.
  • HCC hepatocellular carcinoma
  • UPSC papillary serous cystadeno carcinoma
  • UPSC papillary serous carcinoma
  • UPSC papillary serous carcinoma
  • the cancer is a solid tumor, such as a sarcoma, carcinoma, or lymphoma.
  • the cancer is kidney cancer; hepatocellular carcinoma(HCC) or hepatoblastoma, or liver cancer; melanoma; breast cancer; colorectal carcinoma, or colorectal cancer; colon cancer; rectal cancer; anal cancer; lung cancer, such as non-small cell lung cancer (NSCLC) or small cell lung cancer (SCLC); ovarian cancer, ovarian epithelial cancer, ovarian carcinoma, or fallopian tube cancer; papillary serous cystadeno carcinoma oruterine papillary serous carcinoma (UPSC); prostate cancer; testicular cancer; gallbladder cancer; hepatochol angiocarcinoma; soft tissue and bone synovial sarcoma; rhabdomyo sarcoma; osteosarcoma; chondro sarcoma; Ewing sarcoma; anaplastic thyroid
  • the cancer is hepatocellular carcinoma (HCC), hepatoblastoma, colon cancer, rectal cancer, ovarian cancer, ovarian epithelial cancer, ovarian carcinoma, fallopian tube cancer, papillary serous cystadenocarcinoma, uterine papillary serous carcinoma (UPSC), hepatocholangio carcinoma, soft tissue and bone synovial sarcoma, rhabdomyosarcoma, osteosarcoma, anaplastic thyroid cancer, adrenocortical carcinoma, pancreatic cancer, pancreatic ductal carcinoma, pancreatic adenocarcinoma, glioma, neurofibromatosis- 1 associated malignant peripheral nerve sheath tumors (MPNST), Waldenstrom's macroglobulinemia, or medulloblastoma.
  • HCC hepatocellular carcinoma
  • hepatoblastoma colon cancer
  • rectal cancer ovarian cancer
  • ovarian cancer ovarian epitheli
  • the cancer is hepatocellular carcinoma (HCC). In some embodiments, the cancer is hepatoblastoma. Tn some embodiments, the cancer is colon cancer. In some embodiments, the cancer is rectal cancer. In some embodiments, the cancer is ovarian cancer, or ovarian carcinoma. In some embodiments, the cancer is ovarian epithelial cancer. In some embodiments, the cancer is fallopian tube cancer. In some embodiments, the cancer is papillary serous cystadenocarcinoma. In some embodiments, the cancer is uterine papillary serous carcinoma (UPSC). In some embodiments, the cancer is hepatocholangiocarcinoma.
  • HCC hepatocellular carcinoma
  • the cancer is hepatoblastoma. Tn some embodiments, the cancer is colon cancer. In some embodiments, the cancer is rectal cancer. In some embodiments, the cancer is ovarian cancer, or ovarian carcinoma. In some embodiments, the cancer is ovarian epithelial cancer. In some embodiment
  • the cancer is soft tissue and bone synovial sarcoma. In some embodiments, the cancer is rhabdomyosarcoma. In some embodiments, the cancer is osteosarcoma. In some embodiments, the cancer is anaplastic thyroid cancer. In some embodiments, the cancer isadrenocortical carcinoma. In some embodiments, the cancer is pancreatic cancer, or pancreatic ductal carcinoma. In some embodiments, the cancer is pancreatic adenocarcinoma. In some embodiments, the cancer is glioma. In some embodiments, the cancer is malignant peripheral nerve sheath tumors (MPNST). In some embodiments, the cancer is neurofibromatosis- 1 associated MPNST. In some embodiments, the cancer is Waldenstrom's macroglobulinemia. In some embodiments, the cancer is medulloblastoma.
  • MPNST peripheral nerve sheath tumors
  • the cancer is neurofibromatosis- 1 associated MPNST.
  • the cancer is Waldenstrom'
  • the cancer has a p53 mutation.
  • Another aspect of the invention provides a method of causing death of a cancer cell.
  • the method comprises contacting a cancer cell with an effective amount of a compound described herein, such as a compound of Formula I, II, III, IV, V or VI, or other compounds in Section I, to cause death of the cancer cell.
  • a compound described herein such as a compound of Formula I, II, III, IV, V or VI, or other compounds in Section I.
  • the particular compound of Formula I or II is a compound defined by one of the embodiments described above.
  • the cancer cell is selected from ovarian cancer, uterine cancer, endometrial cancer, cervical cancer, prostate cancer, testicular cancer, breast cancer, brain cancer, lung cancer, oral cancer, esophageal cancer, head and neck cancer, stomach cancer, colon cancer, rectal cancer, skin cancer, sebaceous gland carcinoma, bile duct and gallbladder cancers, liver cancer, pancreatic cancer, bladder cancer, urinary tract cancer, kidney cancer, eye cancer, thyroid cancer, lymphoma, or leukemia.
  • the cancer cell is one or more of the cancers recited in the section above entitled “Cancer.”
  • the cancer is a prostate cancer cell.
  • the compounds useful within the methods of the invention may be used in combination with one or more additional therapeutic agents useful for treating any disease contemplated herein.
  • additional therapeutic agents may comprise compounds that are commercially available or synthetically accessible to those skilled in the art. These additional therapeutic agents are known to treat, prevent, or reduce the symptoms, of a disease or disorder contemplated herein.
  • the method further comprises administering to the subject an additional therapeutic agent that treats the disease contemplated herein.
  • a synergistic effect may be calculated, for example, using suitable methods such as, for example, the Sigmoid-E m ax equation (Holford & Scheiner, 1981, Clin. Pharmacokinet. 6:429- 453), the equation of Loewe additivity (Loewe & Muischnek, 1926, Arch. Exp. Pathol Pharmacol. 114:313-326) and the median-effect equation (Chou & Talalay, 1984, Adv. Enzyme Regul. 22:27-55).
  • Each equation referred to above may be applied to experimental data to generate a corresponding graph to aid in assessing the effects of the drug combination.
  • the corresponding graphs associated with the equations referred to above are the concentration-effect curve, isobologram curve and combination index curve, respectively.
  • the compound of the invention and the therapeutic agent are coadministered to the subject. In other embodiments, the compound of the invention and the therapeutic agent are coformulated and co-administered to the subject.
  • the compound is administered in combination with a second therapeutic agent having activity against cancer.
  • the second therapeutic agent is mitomycin, tretinoin, ribomustin, gemcitabine, vincristine, etoposide, cladribine, mitobronitol, methotrexate, doxorubicin, carboquone, pentostatin, nitracrine, zinostatin, cetrorelix, letrozole, raltitrexed, daunorubicin, fadrozole, fotemustine, thymalfasin, sobuzoxane, nedaplatin, cytarabine, bicalutamide, vinorelbine, vesnarinone, aminoglutethimide, amsacrine, proglumide, elliptinium acetate, ketanserin, doxifluridine, etretinate, iso
  • the second therapeutic agent is an mTOR inhibitor, which inhibits cell proliferation, angiogenesis and glucose uptake.
  • Approved mTOR inhibitors useful in the present invention include everolimus (Afinitor®, Novartis); temsirolimus (Torisel®, Pfizer); and sirolimus (Rapamune®, Pfizer).
  • the second therapeutic agent is a Poly ADP ribose polymerase (PARP) inhibitor.
  • PARP Poly ADP ribose polymerase
  • Approved PARP inhibitors useful in the present invention include olaparib (Lynparza®, AstraZeneca); rucaparib (Rubraca®, Clovis Oncology); and niraparib (Zejula®, Tesaro).
  • Other PARP inhibitors being studied which may be used in the present invention include talazoparib (MDV3800/BMN 673/LT00673, Medivation/Pfizer/Biomarin); veliparib (ABT-888, AbbVie); and BGB-290 (BeiGene, Inc.).
  • the second therapeutic agent is a phosphatidylinositol 3 kinase (PI3K) inhibitor.
  • PI3K inhibitors useful in the present invention include idelalisib (Zydelig®, Gilead).
  • PI3K inhibitors being studied which may be used in the present invention include alpelisib (BYL719, Novartis); taselisib (GDC-0032, Genentech/Roche); pictilisib (GDC-0941, Genentech/Roche); copanlisib (BAY806946, Bayer); duvelisib (formerly IPI-145, Infinity Pharmaceuticals); PQR309 (Piqur Therapeutics, Switzerland); and TGR1202 (formerly RP5230, TG Therapeutics).
  • the second therapeutic agent is a proteasome inhibitor.
  • Approved proteasome inhibitors useful in the present invention include bortezomib (Velcade®, Takeda); carfilzomib (Kyprolis®, Amgen); and ixazomib (Ninlaro®, Takeda).
  • the second therapeutic agent is a histone deacetylase (HDAC) inhibitor.
  • HDAC inhibitors useful in the present invention include vorinostat (Zolinza®, Merck); romidepsin (Istodax®, Celgene); panobinostat (Farydak®, Novartis); and belinostat (Beleodaq®, Spectrum Pharmaceuticals).
  • Other HDAC inhibitors being studied which may be used in the present invention include entinostat (SNDX-275, Syndax Pharmaceuticals) (NCT00866333); and chidamide (Epidaza®, HBI-8000, Chipscreen Biosciences, China).
  • the second therapeutic agent is a CDK inhibitor, such as a CDK 4/6 inhibitor.
  • CDK 4/6 inhibitors useful in the present invention include palbociclib (Ibrance®, Pfizer); and ribociclib (Kisqali®, Novartis).
  • Other CDK 4/6 inhibitors being studied which may be used in the present invention include abemaciclib (Ly2835219, Eli Lilly); and trilaciclib (G1T28, G1 Therapeutics).
  • the second therapeutic agent is an indoleamine (2,3)-dioxygenase (IDO) inhibitor.
  • IDO inhibitors being studied which may be used in the present invention include epacadostat (INCB024360, Incyte); indoximod (NLG-8189, NewLink Genetics Corporation); capmanitib (INC280, Novartis); GDC-0919 (Genentech/Roche); PF-06840003 (Pfizer);
  • the second therapeutic agent is a growth factor antagonist, such as an antagonist of platelet-derived growth factor (PDGF), or epidermal growth factor (EGF) or its receptor (EGFR).
  • PDGF platelet-derived growth factor
  • EGF epidermal growth factor
  • EGFR epidermal growth factor
  • Approved PDGF antagonists which may be used in the present invention include olaratumab (Lartruvo®; Eli Lilly).
  • Approved EGFR antagonists which may be used in the present invention include cetuximab (Erbitux®, Eh Lilly); necitumumab (Portrazza®, Eh Lilly), panitumumab (Vectibix®, Amgen); and osimertinib (targeting activated EGFR, Tagrisso®, AstraZeneca).
  • the second therapeutic agent is an aromatase inhibitor.
  • Approved aromatase inhibitors which may be used in the present invention include exemestane (Aromasin®, Pfizer); anastazole (Arimidex®, AstraZeneca) and letrozole (Femara®, Novartis).
  • the second therapeutic agent is an antagonist of the hedgehog pathway.
  • Approved hedgehog pathway inhibitors which may be used in the present invention include sonidegib (Odomzo®, Sun Pharmaceuticals); and vismodegib (Erivedge®, Genentech), both for treatment of basal cell carcinoma.
  • the second therapeutic agent is a folic acid inhibitor.
  • Approved folic acid inhibitors useful in the present invention include pemetrexed (Alimta®, Eh Lilly).
  • the second therapeutic agent is a CC chemokine receptor 4 (CCR4) inhibitor.
  • CCR4 inhibitors being studied that may be useful in the present invention include mogamulizumab (Poteligeo®, Kyowa Hakko Kirin, Japan).
  • the second therapeutic agent is an isocitrate dehydrogenase (IDH) inhibitor.
  • IDH inhibitors being studied which may be used in the present invention include AG120 (Celgene; NCT02677922); AG221 (Celgene, NCT02677922; NCT02577406);
  • the second therapeutic agent is an arginase inhibitor.
  • Arginase inhibitors being studied which may be used in the present invention include AEB1102 (pegylated recombinant arginase, Aeglea Biotherapeutics), which is being studied in Phase 1 clinical trials for acute myeloid leukemia and myelodysplastic syndrome (NCT02732184) and solid tumors (NCT02561234); and CB-1158 (Calithera Biosciences).
  • the second therapeutic agent is a glutaminase inhibitor.
  • Glutaminase inhibitors being studied which may be used in the present invention include CB-839 (Calithera Biosciences).
  • the second therapeutic agent is an antibody that binds to tumor antigens, that is, proteins expressed on the cell surface of tumor cells.
  • Approved antibodies that bind to tumor antigens which may be used in the present invention include rituximab (Rituxan®, Genentech/Biogenldec); ofatumumab (anti-CD20, Arzerra®, GlaxoSmithKline); obinutuzumab (anti-CD20, Gazyva®, Genentech), ibritumomab (anti-CD20 and Yttrium-90, Zevalin®, Spectrum Pharmaceuticals); daratumumab (anti-CD38, Darzalex®, Janssen Biotech), dinutuximab (anti-glycolipid GD2, Unituxin®, United Therapeutics); trastuzumab (anti-HER2, Herceptin®, Genentech); ado-trastuzumab emtansine (anti-HER2, fuse
  • the second therapeutic agent is a topoisomerase inhibitor.
  • Approved topoisomerase inhibitors useful in the present invention include irinotecan (Onivyde®, Merrimack Pharmaceuticals); topotecan (Hycamtin®, GlaxoSmithKline).
  • Topoisomerase inhibitors being studied which may be used in the present invention include pixantrone (Pixuvri®, CTI Biopharma).
  • the second therapeutic agent is a nucleoside inhibitor, or other therapeutic that interfere with normal DNA synthesis, protein synthesis, cell replication, or will otherwise inhibit rapidly proliferating cells.
  • nucleoside inhibitors or other therapeutics include trabectedin (guanidine alkylating agent, Yondelis®, Janssen Oncology), mechlorethamine (alkylating agent, Valchlor®, Aktelion Pharmaceuticals); vincristine (Oncovin®, Eli Lilly; Vincasar®, Teva Pharmaceuticals; Marqibo®, Talon Therapeutics); temozolomide (prodrug to alkylating agent 5-(3-methyltriazen-l-yl)-imidazole-4-carboxamide (MTIC) Temodar®, Merck); cytarabine injection (ara-C, antimetabolic cytidine analog, Pfizer); lomustine (alkylating agent, CeeNU®, Bristol-Myers Squibb; Gleostine
  • the second therapeutic agent is a platinum-based therapeutic, also referred to as platins.
  • Platins cause cross-linking of DNA, such that they inhibit DNA repair and/or DNA synthesis, mostly in rapidly reproducing cells, such as cancer cells.
  • Approved platinum-based therapeutics which may be used in the present invention include cisplatin (Platinol®, Bristol-Myers Squibb); carboplatin (Paraplatin®, Bristol-Myers Squibb; also, Teva; Pfizer); oxaliplatin (Eloxitin® Sanofi-Aventis); and nedaplatin (Aqupla®, Shionogi).
  • Other platinum-based therapeutics which have undergone clinical testing and may be used in the present invention include picoplatin (Poniard Pharmaceuticals); and satraplatin (IM-216, Agennix).
  • the second therapeutic agent is a taxane compound, which causes disruption of microtubules, which are essential for cell division.
  • Approved taxane compounds which may be used in the present invention include paclitaxel (Taxol®, Bristol-Myers Squibb), docetaxel (Taxotere®, Sanofi-Aventis; Docefrez®, Sun Pharmaceutical), albumin-bound paclitaxel (Abraxane®; Abraxis/Celgene), and cabazitaxel (Jevtana®, Sanofi -Aventis).
  • Other taxane compounds which have undergone clinical testing and may be used in the present invention include SID530 (SK Chemicals, Co.) (NCT00931008).
  • the second therapeutic agent is an inhibitor of anti-apoptotic proteins, such as BCL-2.
  • Approved anti-apoptotics which may be used in the present invention include venetoclax (Venclexta®, AbbVie/Genentech); and blinatumomab (Blincyto®, Amgen).
  • Other therapeutic agents targeting apoptotic proteins which have undergone clinical testing and may be used in the present invention include navitoclax (ABT-263, Abbott), a BCL-2 inhibitor (NCT02079740).
  • the second therapeutic agent is a selective estrogen receptor modulator (SERM), which interferes with the synthesis or activity of estrogens.
  • SERMs useful in the present invention include raloxifene (Evista®, Eh Lilly).
  • the second therapeutic agent is an inhibitor of interaction between the two primary p53 suppressor proteins, MDMX and MDM2.
  • Inhibitors of p53 suppression proteins being studied which may be used in the present invention include ALRN- 6924 (Aileron), a stapled peptide that equipotently binds to and disrupts the interaction of MDMX and MDM2 with p53.
  • ALRN-6924 is currently being evaluated in clinical trials for the treatment of AML, advanced myelodysplastic syndrome (MDS) and peripheral T-cell lymphoma (PTCL) (NCT02909972; NCT02264613).
  • the second therapeutic agent is an inhibitor of transforming growth factor-beta (TGF-beta or TGF0).
  • TGF-beta transforming growth factor-beta
  • Inhibitors of TGF-beta proteins being studied which may be used in the present invention include NIS793 (Novartis), an anti-TGF-beta antibody being tested in the clinic for treatment of various cancers, including breast, lung, hepatocellular, colorectal, pancreatic, prostate and renal cancer (NCT 02947165).
  • the inhibitor of TGF-beta proteins is fresolimumab (GC1008; Sanofi-Genzyme), which is being studied for melanoma (NCT00923169); renal cell carcinoma (NCT00356460); and non-small cell lung cancer (NCT02581787).
  • the additional therapeutic agent is a TGF-beta trap, such as described in Connolly et al. (2012) Int'l J. Biological Sciences 8:964-978.
  • the second therapeutic agent is a cancer vaccine.
  • the cancer vaccine is selected from sipuleucel-T (Provenge®, Dendreon/Valeant Pharmaceuticals), which has been approved for treatment of asymptomatic, or minimally symptomatic metastatic castrate-resistant (hormone-refractory) prostate cancer; and talimogene laherparepvec (Imlygic®, BioVex/ Amgen, previously known as T-VEC), a genetically modified oncolytic viral therapy approved for treatment of unresectable cutaneous, subcutaneous and nodal lesions in melanoma.
  • the second therapeutic agent is an immune checkpoint inhibitor selected from a PD-1 antagonist, a PD-L1 antagonist, or a CTLA-4 antagonist.
  • a compound disclosed herein or a pharmaceutically acceptable salt thereof is administered in combination with nivolumab (anti -PD-1 antibody, Opdivo®, Bristol-Myers Squibb); pembrolizumab (anti -PD-1 antibody, Keytruda®, Merck); ipilimumab (anti-CTLA-4 antibody, Yervoy®, Bristol-Myers Squibb); durvalumab (anti-PD-Ll antibody, Imfinzi®, AstraZeneca); or atezolizumab (anti-PD-Ll antibody, Tecentriq®, Genentech).
  • immune checkpoint inhibitors suitable for use in the present invention include REGN2810 (Regeneron), an anti-PD-1 antibody tested in patients with basal cell carcinoma (NCT03132636); NSCLC (NCT03088540); cutaneous squamous cell carcinoma (NCT02760498); lymphoma (NCT02651662); and melanoma (NCT03002376); pidilizumab (CureTech), also known as CT- 011, an antibody that binds to PD-1, in clinical trials for diffuse large B-cell lymphoma and multiple myeloma; avelumab (Bavencio®, Pfizer/Merck KGaA), also known as MSB0010718C), a fully human IgGl anti-PD-Ll antibody, in clinical trials for non-small cell lung cancer, Merkel cell carcinoma, mesothelioma, solid tumors, renal cancer, ovarian cancer, bladder cancer, head and neck cancer, and gastric cancer; and P
  • the term “about” a number refers to that number plus or minus 15% of that number.
  • the term “about” a range refers to that range minus 15% of its lowest value and plus 15% of its greatest value.
  • the terms “comprising” (and any variant or form of comprising, such as “comprise” and “comprises”), “having” (and any variant or form of having, such as “have” and “has”), “including” (and any variant or form of including, such as “includes” and “include”) or “containing” (and any variant or form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited, elements or method steps. It is contemplated that any embodiment discussed in this specification can be implemented with respect to any compound, protein, and/or method of the present disclosure.
  • determining means determining if an element is present or not (for example, detection). These terms can include quantitative, qualitative or quantitative and qualitative determinations. Assessing can be relative or absolute. “Detecting the presence of’ can include determining the amount of something present in addition to determining whether it is present or absent depending on the context.
  • protein may include a polypeptide.
  • a protein may include a eukaryotic protein, or a protein in a cell or subject.
  • treatment or “treating” are used in reference to a pharmaceutical or other intervention regimen for obtaining beneficial or desired results in the recipient.
  • beneficial or desired results include but are not limited to a therapeutic benefit or a prophylactic benefit.
  • a therapeutic benefit may refer to eradication or amelioration of symptoms or of an underlying disorder being treated.
  • a therapeutic benefit can be achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder.
  • a prophylactic effect includes delaying, preventing, or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof.
  • a subject at risk of developing a particular disease, or to a subject reporting one or more of the physiological symptoms of a disease may undergo treatment, even though a diagnosis of this disease may not have been made.
  • Amino refers to the -NH2 radical.
  • Cyano refers to the -CN radical.
  • Niro refers to the -NO2 radical.
  • Oxa refers to the -O- radical.
  • an alkyl comprises one to four carbon atoms (e.g., C1-C4 alkyl). In other embodiments, an alkyl comprises one to three carbon atoms (e.g., C1-C3 alkyl). In other embodiments, an alkyl comprises one to two carbon atoms (e.g., C1-C2 alkyl). In other embodiments, an alkyl comprises one carbon atom (e.g., Ci alkyl). In other embodiments, an alkyl comprises five to fifteen carbon atoms (e.g., C5-C15 alkyl). In other embodiments, an alkyl comprises five to eight carbon atoms (e.g., Cs-Cs alkyl).
  • an alkyl comprises two to five carbon atoms (e.g., C2-C5 alkyl). In other embodiments, an alkyl comprises three to five carbon atoms (e.g., C3-C5 alkyl).
  • the alkyl group is selected from methyl, ethyl, 1 -propyl (w-propyl), 1 -methylethyl (Ao-propyl), 1 -butyl (w-butyl), 1- methylpropyl (sec-butyl), 2 -methylpropyl (Ao-butyl), 1,1 -dimethyl ethyl (ze/7-butyl), 1 -pentyl (n- pentyl).
  • Alkoxy refers to a radical bonded through an oxygen atom of the formula -O-alkyl, where alkyl is an alkyl chain as defined above.
  • alkenyl refers to a straight or branched hydrocarbon chain radical group consisting solely of carbon and hydrogen atoms, containing at least one carbon-carbon double bond, and having from two to twelve carbon atoms. In certain embodiments, an alkenyl comprises two to eight carbon atoms. In other embodiments, an alkenyl comprises two to four carbon atoms. The alkenyl is attached to the rest of the molecule by a single bond, for example, ethenyl (i.e., vinyl), prop-l-enyl (i.e., allyl), but-l-enyl, pent-l-enyl, penta- 1,4-dienyl, and the like.
  • ethenyl i.e., vinyl
  • prop-l-enyl i.e., allyl
  • but-l-enyl pent-l-enyl, penta- 1,4-dienyl, and the like.
  • an alkenyl group is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo, tnmethylsilanyl, -OR a , -SR a , -OC(O)-R a , -N(R a ) 2 , -C(O)R a , -C(O)OR a , -C(O)N(R a ) 2 , - N(R a )C(O)OR a , -OC(O)-N(R a ) 2 , -N(R a )C(O)R a , -N(R a )S(O) t R a (where t is 1 or 2), -S(O) t OR a (where t is 1 or 2), -S(O)tR
  • Alkynyl refers to a straight or branched hydrocarbon chain radical group consisting solely of carbon and hydrogen atoms, containing at least one carbon-carbon triple bond, having from two to twelve carbon atoms.
  • an alkynyl comprises two to eight carbon atoms.
  • an alkynyl comprises two to six carbon atoms.
  • an alkynyl comprises two to four carbon atoms.
  • the alkynyl is attached to the rest of the molecule by a single bond, for example, ethynyl, propynyl, butynyl, pentynyl, hexynyl, and the like.
  • an alkynyl group is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo, trimethylsilanyl, -OR a , -SR a , -OC(O)-R a , -N(R a ) 2 , -C(O)R a , -C(O)OR a , -C(O)N(R a ) 2 , - N(R a )C(O)OR a , -OC(O)-N(R a ) 2 , -N(R a )C(O)R a , -N(R a )S(O) t R a (where t is 1 or 2), -S(O) t OR a (where t is 1 or 2), -S(O)tR
  • Alkylene or "alkylene chain” refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group, consisting solely of carbon and hydrogen, containing no unsaturation and having from one to twelve carbon atoms, for example, methylene, ethylene, propylene, n-butylene, and the like.
  • the alkylene chain is attached to the rest of the molecule through a single bond and to the radical group through a single bond.
  • the points of attachment of the alkylene chain to the rest of the molecule and to the radical group are through one carbon in the alkylene chain or through any two carbons within the chain.
  • an alkylene comprises one to eight carbon atoms (e.g., Ci-Cs alkylene). In other embodiments, an alkylene comprises one to five carbon atoms (e.g., C1-C5 alkylene). In other embodiments, an alkylene comprises one to four carbon atoms (e.g., C1-C4 alkylene). In other embodiments, an alkylene comprises one to three carbon atoms (e.g., C1-C3 alkylene). In other embodiments, an alkylene comprises one to two carbon atoms (e.g., Ci-C 2 alkylene). In other embodiments, an alkylene comprises one carbon atom (e.g., Ci alkylene).
  • an alkylene comprises five to eight carbon atoms (e.g., Cs-Cs alkylene). In other embodiments, an alkylene comprises two to five carbon atoms (e.g., C2-C5 alkylene). In other embodiments, an alkylene comprises three to five carbon atoms (e.g., C3-C5 alkylene).
  • an alkylene chain is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo, trimethylsilanyl, -OR a , - SR a , -OC(O)-R a , -N(R a ) 2 , -C(O)R a , -C(O)OR a , -C(O)N(R a ) 2 , -N(R a )C(O)OR a , -OC(O)- N(R a ) 2 , - N(R a )C(O)R a , -N(R a )S(O)tR a (where t is 1 or 2), -S(O)tOR a (where t is 1 or 2), -S(O)tOR a (where t is 1 or 2),
  • Aryl refers to a radical derived from an aromatic monocyclic or multicyclic hydrocarbon ring system by removing a hydrogen atom from a ring carbon atom.
  • the aromatic monocyclic or multicyclic hydrocarbon ring system contains only hydrogen and carbon from five to eighteen carbon atoms, where at least one of the rings in the ring system is fully unsaturated, i.e., it contains a cyclic, delocalized (4n+2) p-electron system in accordance with the Hiickel theory.
  • the ring system from which aryl groups are derived include, but are not limited to, groups such as benzene, fluorene, indane, indene, tetralin and naphthalene.
  • aryl or the prefix “ar-” (such as in “aralkyl”) is meant to include aryl radicals optionally substituted by one or more substituents independently selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -R b -0R a , -R b -OC(O)-R a , -R b -OC(O)-OR a , -R b -OC(O)- N(R
  • Aralkyl refers to a radical of the formula -R c -aryl where R c is an alkylene chain as defined above, for example, methylene, ethylene, and the like.
  • the alkylene chain part of the aralkyl radical is optionally substituted as described above for an alkylene chain.
  • the aryl part of the aralkyl radical is optionally substituted as described above for an aryl group.
  • Carbocyclyl or “cycloalkyl” refers to a stable non-aromatic monocyclic or polycyclic hydrocarbon radical consisting solely of carbon and hydrogen atoms, which includes fused or bridged ring systems, having from three to fifteen carbon atoms.
  • a carbocyclyl comprises three to ten carbon atoms.
  • a carbocyclyl comprises five to seven carbon atoms.
  • the carbocyclyl is attached to the rest of the molecule by a single bond. Carbocyclyl is saturated (i.e., containing single C-C bonds only) or unsaturated (i.e., containing one or more double bonds or triple bonds).
  • a fully saturated carbocyclyl radical is also referred to as "cycloalkyl.”
  • monocyclic cycloalkyls include, e.g., cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl.
  • An unsaturated carbocyclyl is also referred to as "cycloalkenyl.”
  • Examples of monocyclic cycloalkenyls include, e.g., cyclopentenyl, cyclohexenyl, cycloheptenyl, and cyclooctenyl.
  • Polycyclic carbocyclyl radicals include, for example, adamantyl, norbomyl (i.e., bicyclo[2.2.1]heptanyl), norbomenyl, decalinyl, 7,7-dimethyl-bicyclo[2.2.1]heptanyl, and the like.
  • carbocyclyl is meant to include carbocyclyl radicals that are optionally substituted by one or more substituents independently selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, oxo, thioxo, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -R b -0R a , -R b -OC(O)-R a , -R b -OC(O)-OR a , -R b -OC(O)-N(
  • Carbocyclylalkyl refers to a radical of the formula -R c -carbocyclyl where R c is an alkylene chain as defined above. The alkylene chain and the carbocyclyl radical are optionally substituted as defined above.
  • Halo or "halogen” refers to bromo, chloro, fluoro or iodo substituents.
  • Fluoroalkyl refers to an alkyl radical, as defined above, that is substituted by one or more fluoro radicals, as defined above, for example, trifluoromethyl, difluoromethyl, fluoromethyl, 2,2,2-trifluoroethyl, l-fluoromethyl-2-fluoroethyl, and the like.
  • the alkyl part of the fluoroalkyl radical is optionally substituted as defined above for an alkyl group.
  • Heterocyclyl or “heterocycloalkyl” refers to a stable 3- to 18-membered nonaromatic ring radical that comprises two to twelve carbon atoms and from one to six heteroatoms selected from nitrogen, oxygen and sulfur. Unless stated otherwise specifically in the specification, the heterocyclyl radical is a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which optionally includes fused or bridged ring systems. The heteroatoms in the heterocyclyl radical are optionally oxidized. One or more nitrogen atoms, if present, are optionally quatemized. The heterocyclyl radical is partially or fully saturated.
  • heterocyclyl is attached to the rest of the molecule through any atom of the ring(s).
  • heterocyclyl radicals include, but are not limited to, dioxolanyl, thienyl[l,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2-oxopiperazinyl, 2-oxopiperidinyl, 2-oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4-piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, tetrahydropyr
  • heterocyclyl is meant to include heterocyclyl radicals as defined above that are optionally substituted by one or more substituents selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, thioxo, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -R b -OR a , -R b -OC(O)-R a , -R b -OC(O)-OR a , -R b -OC(O)-N(R a )
  • A-heterocyclyl or “N-attached heterocyclyl” refers to a heterocyclyl radical as defined above containing at least one nitrogen and where the point of attachment of the heterocyclyl radical to the rest of the molecule is through a nitrogen atom in the heterocyclyl radical.
  • An A-heterocyclyl radical is optionally substituted as described above for heterocyclyl radicals. Examples of such A-heterocyclyl radicals include, but are not limited to, 1-morpholinyl,
  • C-heterocyclyl or “C-attached heterocyclyl” refers to a heterocyclyl radical as defined above containing at least one heteroatom and where the point of attachment of the heterocyclyl radical to the rest of the molecule is through a carbon atom in the heterocyclyl radical.
  • a C-heterocyclyl radical is optionally substituted as described above for heterocyclyl radicals. Examples of such C-heterocyclyl radicals include, but are not limited to, 2-morpholinyl,
  • Heteroaryl refers to a radical derived from a 3 - to 18- membered aromatic ring radical that comprises two to seventeen carbon atoms and from one to six heteroatoms selected from nitrogen, oxygen and sulfur.
  • the heteroaryl radical is a monocyclic, bicyclic, tricyclic or tetracyclic ring system, wherein at least one of the rings in the ring system is fully unsaturated, i.e., it contains a cyclic, delocalized (4n+2) p-electron system in accordance with the Hiickel theory.
  • Heteroaryl includes fused or bridged ring systems.
  • the heteroatom(s) in the heteroaryl radical is optionally oxidized.
  • heteroaryl is attached to the rest of the molecule through any atom of the ring(s).
  • heteroaryls include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzindolyl, 1,3-benzodioxolyl, benzofuranyl, benzooxazolyl, benzo[d]thiazolyl, benzothiadiazolyl, benzo[/?][ l ,4]dioxepinyl, benzo[b][l,4]oxazinyl, 1 ,4-benzodioxanyl, benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl, benzopyranyl, benzopyranonyl, benzofuranyl, benzofuranonyl, benzothien
  • heteroaryl is meant to include heteroaryl radicals as defined above which are optionally substituted by one or more substituents selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, haloalkenyl, haloalkynyl, oxo, thioxo, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -R b - 0R a , -R b -0C(0)-R a , -R b -0C(0)-0R a
  • A-heteroaryl refers to a heteroaryl radical as defined above containing at least one nitrogen and where the point of attachment of the heteroaryl radical to the rest of the molecule is through a nitrogen atom in the heteroaryl radical.
  • An A-heteroaryl radical is optionally substituted as described above for heteroaryl radicals.
  • C-heteroaryl refers to a heteroaryl radical as defined above and where the point of attachment of the heteroaryl radical to the rest of the molecule is through a carbon atom in the heteroaryl radical.
  • a C-heteroaryl radical is optionally substituted as described above for heteroaryl radicals.
  • attachment point refers to an atom or molecule that connects the linker to the target ligand and/or the recruiting ligand.
  • the attachment point can be covalently bonded to the linker, target ligand, and the recruiting ligand.
  • the compounds disclosed herein in some embodiments, contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric forms that are defined, in terms of absolute stereochemistry, as (R)- or (5)-. Unless stated otherwise, it is intended that all stereoisomeric forms of the compounds disclosed herein are contemplated by this disclosure. When the compounds described herein contain alkene double bonds, and unless specified otherwise, it is intended that this disclosure includes both E and Z geometric isomers (e.g., cis or trans. ⁇ Likewise, all possible isomers, as well as their racemic and optically pure forms, and all tautomeric forms are also intended to be included.
  • geometric isomer refers to E or Z geometric isomers (e.g., cis or trans) of an alkene double bond.
  • positional isomer refers to structural isomers around a central ring, such as ortho-, meta-, and para- isomers around a benzene ring.
  • a "tautomer” refers to a molecule wherein a proton shift from one atom of a molecule to another atom of the same molecule is possible.
  • the compounds disclosed herein are used in different enriched isotopic forms, e.g., enriched in the content of 2 H, 3 H, n C, 13 C or 14 C.
  • the compound is deuterated in at least one position.
  • deuterated forms can be made by the procedure described in U.S. Patent Nos. 5,846,514 and 6,334,997. As described in U.S. Patent Nos. 5,846,514 and 6,334,997, deuteration can improve the metabolic stability and or efficacy, thus increasing the duration of action of drugs.
  • structures depicted herein are intended to include compounds which differ only in the presence of one or more isotopically enriched atoms.
  • compounds having the present structures except for the replacement of a hydrogen by a deuterium or tritium, or the replacement of a carbon by 13 C- or 14 C-enriched carbon are within the scope of the present disclosure.
  • the compounds of the present disclosure optionally contain unnatural proportions of atomic isotopes at one or more atoms that constitute such compounds.
  • the compounds may be labeled with isotopes, such as for example, deuterium ( 2 H), tritium ( 3 H), iodine- 125 ( 125 I) or carbon- 14 ( 14 C).
  • isotopes such as for example, deuterium ( 2 H), tritium ( 3 H), iodine- 125 ( 125 I) or carbon- 14 ( 14 C).
  • Isotopic substitution with 2 H, "C, 13 C, 14 C, 15 C, 12 N, 13 N, 15 N, 16 N, 16 O, 17 O, 14 F, 15 F, 16 F, 17 F, 18 F, 33 S, 34 S, 35 S, 36 S, 35 C1, 37 C1, 79 Br, 81 Br, 125 I are all contemplated. All isotopic variations of the compounds of the present invention, whether radioactive or not, are encompassed within the scope of
  • the compounds disclosed herein have some or all of the 1 H atoms replaced with 2 H atoms.
  • the methods of synthesis for deuterium-containing compounds are known in the art and include, by way of non-limiting example only, the following synthetic methods.
  • Isotopic labeling can be performed using a variety of readily available reagents not limited to: isotopically -enriched carbon dioxide, dimethylformamide, cyanide salts, acetylenes, ammonium salts, other small organic and inorganic sources.
  • reagents not limited to: isotopically -enriched carbon dioxide, dimethylformamide, cyanide salts, acetylenes, ammonium salts, other small organic and inorganic sources.
  • Various methods are employed such as described in: Neumann, K. T. et al. Synthesis and Selective 2H-, 13C-, and 15N-Labehng of the Tau Protein Binder THK-523.
  • Deuterated starting materials are readily available and are subjected to the synthetic methods described herein to provide for the synthesis of deuterium-containing compounds. Large numbers of deuterium-containing reagents and building blocks are available commercially from chemical vendors, such as Aldrich Chemical Co.
  • “Pharmaceutically acceptable salt” includes both acid and base addition salts.
  • a pharmaceutically acceptable salt of any one of the compounds described herein is intended to encompass any and all pharmaceutically suitable salt forms.
  • Preferred pharmaceutically acceptable salts of the compounds described herein are pharmaceutically acceptable acid addition salts and pharmaceutically acceptable base addition salts.
  • “Pharmaceutically acceptable acid addition salt” refers to those salts which retain the biological effectiveness and properties of the free bases, which are not biologically or otherwise undesirable, and which are formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, hydroiodic acid, hydrofluoric acid, phosphorous acid, and the like. Also included are salts that are formed with organic acids such as aliphatic mono- and di carboxylic acids, phenyl-substituted alkanoic acids, hydroxy alkanoic acids, alkanedioic acids, aromatic acids, aliphatic and. aromatic sulfonic acids, etc.
  • acetic acid trifluoroacetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like.
  • Exemplary salts thus include sulfates, pyrosulfates, bisulfates, sulfites, bisulfites, nitrates, phosphates, monohydrogenphosphates, dihydrogenphosphates, metaphosphates, pyrophosphates, chlorides, bromides, iodides, acetates, trifluoroacetates, propionates, caprylates, isobutyrates, oxalates, malonates, succinate suberates, sebacates, fumarates, maleates, mandelates, benzoates, chlorobenzoates, methylbenzoates, dinitrobenzoates, phthalates, benzenesulfonates, toluenesulfonates, phenylacetates, citrates, lactates, malates, tartrates, methanesulfonates, and the like.
  • “Pharmaceutically acceptable base addition salt” refers to those salts that retain the biological effectiveness and properties of the free acids, which are not biologically or otherwise undesirable. These salts are prepared from addition of an inorganic base or an organic base to the free acid. Pharmaceutically acceptable base addition salts are, in some embodiments, formed with metals or amines, such as alkali and alkaline earth metals or organic amines. Salts derived from inorganic bases include, but are not limited to, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like.
  • Salts derived from organic bases include, but are not limited to, salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, for example, isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, ethanolamine, diethanolamine, 2-dimethylaminoethanol, 2-diethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, N, A-dibenzylethylenedi amine, chloroprocaine, hydrabamine, choline, betaine, ethylenediamine, ethylenedianiline, A-methylglucamine, glucosamine, methylglucamine, theobromine, purines, piperazine, piperidine, A-ethylpiperidine, polyamine resins and the like. See Berge et
  • Step 1 The synthesis of l-(4-methylbenzenesulfonyl)-4-nitro-lH-indole.
  • 4-nitro-lH-indole 50.0 g, 308.56 mmol
  • sodium hydride 18.5 g, 770.92 mmol
  • Step 2 The synthesis of 2-iodo-l-(4-methylbenzenesulfonyl)-4-nitro-lH-indole.
  • the resulting solution was added via cannula needle to the drip funnel and then dropwise to the solution of l-(4-methylbenzenesulfonyl)-4-nitro-lH-indole (5.0 g, 15.82 mmol) in dry THF (50 ml) at -78°C. The mixture was left while stirring at -78 °C for 15 min. After that the solution of iodine (6.02 g, 23.73 mmol) in dry THF (25 mL) was added to the reaction mixture at -78°C. After the addition was completed the reaction mixture was allowed to warm to 0°C.
  • Step 3 The synthesis of 2-iodo-4-nitro-lH-indole.
  • 2-iodo-l-(4- methylbenzenesulfonyl)-4-nitro-lH-indole 9.6 g, 21.72 mmol
  • dioxane 250 mL
  • sodium hydroxide 4.34 g, 108.56 mmol
  • the resulting suspension was then concentrated under reduced pressure, the obtained residue was diluted with water (150 mL) and extracted with ethyl acetate (3 x 100 mL).
  • Step 4 The synthesis of 2-iodo-4-nitro-l-(2,2,2-trifluoroethyl)-lH-indole.
  • 2-iodo-4-nitro-lH-indole 23.0 g, 79.88 mmol
  • sodium hydride 4.15 g, 173.01 mmol
  • the resulting solution was allowed to warm up to room temperature and left to stir at room temperature for 1 hour.
  • Step 5 The synthesis of 2-iodo-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine.
  • 2-iodo-4-nitro-l-(2,2,2-trifluoroethyl)-lH-indole 15.0 g, 40.55 mmol, 231.7 mL, 1.0 eq
  • 4-(pyridin-4-yl)pyridine 316.54 mg, 2.03 mmol
  • anhydrous DMF 250 mL
  • (dihydroxyboranyl)boronic acid (10.9 g, 121.09 mmol
  • the resulting reaction mixture solution was allowed to warm up to room temperature and stirred for 1 h. After that period the mixture was quenched by 10% aqueous solution of K2CO3 (1 L) and stirred for 1 h. Then the mixture was extracted with ethyl acetate (3 x 200 mL). The organic layers were combined, washed with water (3 x 150 ml), brine (200 mL), dried over anhydrous ISfeSCL and filtered.
  • the residue was purified by resolution (column: DAICEL CEURALPAK AD(250mm*50mm, 10 pm);mobile phase: [CO 2 -ACN/MeOH(0.1% NH 3 .H 2 O)];B%:54%, isocratic elution mode) to give N-methylated piperidine 5 as a mixture of stereoisomers (79% yield) as gray solid.
  • Step 4 Recrystallization was performed on the stereoisomers mixture by adding 1 eq of chiral acid N-Acetyl-L-Leucine, stirred for 1 hour at room temperature then heat to 70 °C for 1 hour followed by overnight stirring at room temperature using MeoH/H2O (6:1) solvent ratio. The solid was isolated and further purified by SFC to obtain desired pure enantiomer.
  • Step 1 A solution of amine 1 (1 eq), [(dimethylamino)(3H-[l,2,3]triazolo[4,5- b]pyridin-3-yloxy)methylidene]dimethylazanium; hexafluoro-lambda5-phosphanuide (1.3 eq), acid 2 (1 eq), and ethylbis(propan-2-yl)amine (5 eq) in DMF (0.2 M) was stirred overnight at room temperature. Solvent was evaporated from mixture and re-dissolved in water-acetonitrile for HPLC purification to obtain the amide.
  • General procedure 4 Assembly of BFM through Click coupling.
  • Step 1 To a solution of alkyne 2 (1 eq) in the mixture of t-BuOFLTbO (2:1, 0.2 M) at 0°C was added sodium (2R)-2-[(lS)-l,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3- olate (1 eq), followed by the addition of copper (II) sulfate pentahydrate (0.5 eq). After 5 min of stirring, the solution of azide 1 (1 eq) in THF (0.1 M) was added to the reaction mixture, which was then heated up to 50°C and left while stirring overnight. After the reaction was completed (monitored by LCMS), the mixture was concentrated under reduced pressure and the residue was diluted with minimal DMSO and subjected for prep HPLC without any further work-up to obtain BFM 3.
  • Step 1 To a solution of aniline 1 (1.2 eq) in anhydrous DMF (1 M) dipotassium carbonate (1.5 eq) was added. The reaction mixture was cooled to 0°C and 3 -bromoprop- 1-yne (1 eq) dropwise was added dropwise under an inert atmosphere. The resulting solution was then allowed to warm up to room temperature and left to stir for 18 hrs. The reaction mixture was diluted with saturated solution of NH4CI and extracted with ethyl acetate (3x). The organic layers were combined, washed with water (3x), brine, dried over anhydrous Na2SO4 and filtered. The collected filtrate was concentrated under reduced pressure and the obtained crude was subjected for flash chromatography to afford the desired benzoate 2.
  • Step 2 To a solution of key aryl iodide 3 (1 eq), benzoate 2 (1.2 eq), copper (I) iodide (0.5 eq) and tri ethylamine (3.0 eq) in DMSO (0.1 M) under inert atmosphere Palladium- tetrakis(triphenylphosphine) (10 wt. %) was added. The resulting solution was stirred at room temperature for 18 hours. After that period the reaction mixture was diluted with distilled water, the mixture was stirred for 1 hour. The formed precipitate was collected by filtration, washed with water, dried and subjected for flash chromatography purification to afford the desired alkyne 4.
  • Step 3 To a solution of alkyne 4 (1 eq) in THF/MeOH (1: 1, 0.25M) the solution of lithium hydroxide hydrate (15 eq) in water (0.25 M) was added. The resulting solution was stirred at room temperature for 48 hours. The reaction mixture was then concentrated under reduced pressure, diluted with water and acidified with sodium hydrogen sulfate (15 eq). The mixture was extracted with ethyl acetate/acetonitrile, dried over anhydrous Na2SO4 and filtered. The collected filtrate was concentrated under reduced pressure to afford the desired acid 5.
  • Step 4 To a solution of acid 5 (1 eq) in DMF (0.1 M) was added 3H- [l,2,3]triazolo[4,5-b]pyridin-3-ol (1.5 eq), (3- [(ethylimino)methylidene]aminopropyl)dimethylamine hydrochloride (1.5 eq), and after 5 min, amine linker 6 (1.1 eq). The resulting mixture was stirred at room temperature overnight. The reaction mixture was diluted by water, extracted with ethyl acetate (3x). The organic layers were combined, washed with water (3x), brine, dried over anhydrous Na2SO4 and filtered. The filtrate collected was concentrated under reduced pressure and the residue obtained was subjected to prep HPLC purification to result in the desired amide 7.
  • Step 5 To solution of amide 7 (1 eq) in MeOH (0.1 M) 10% HC1 in dioxane was added. The reaction mixture was stirred at room temperature for 18 hours. After that period the mixture was concentrated under reduced pressure to afford the desired amine 8.
  • General procedure 6 Synthesis of sulfonamide containing Rl-L scaffolds.
  • Step 1 To a solution of amine 1, (1 eq) and triethylamine (1.5 eq) in DCM (0.35 M), solution of sulfonyl chloride (1 eq) in THF (1 M) was added at 0°C under nitrogen atmosphere. The mixture was warmed to room temperature and stirred for 12 hours. Reaction was monitored until completion via LCMS analysis. The mixture was concentrated, diluted with EtOAc and washed with 1 M solution of NaHSO4 in water, saturated solution of NaHCCE, brine, dried over anhydrous Na2SO4 and concentrated under reduced pressure to afford sulfonamide 3 that was used in the next step without further purification.
  • Step 2A To a solution of nitro arene 3 (1 eq) and 4,4’-bipyridine (0.05 eq) in anhydrous DMF (0.15 M), (dihydroxyboranyl)boronic acid (3 eq) was added portion wise under inert atmosphere at 5°C. The resulting solution was warmed up and stirred at room temperature for 1 hour. The reaction mixture was quenched by 10% solution of K2CO3, stirred for 1 hour, and extracted by EtOAc. The organic layer was washed by water (3x), brine, dried over Na2SO4 and concentrated under reduced pressure to afford amine 4 that was used in the next step without purification.
  • Step 2B To a suspension of Pd/C (10 wt. %) in MeOH (0.2 M) under nitrogen atmosphere nitro-containing sulfonamide linker 3 (1 eq) was added. The mixture was degassed and purged with H2 3 times, and then the mixture was stirred under H2 (15 Psi) atmosphere at 25 °C for 12 hrs. When the starting material disappeared by LCMS, the reaction was filtered, and the solid residue was washed by THF (3x). The filtrate was concentrated in vacuo to give desired aniline.
  • Step 3 To a solution of amine 4, (1 eq) in DMF (0.13 M), was added 3 -bromoprop- 1- yne, (1 eq) and dipotassium carbonate (3 eq) at room temperature under nitrogen atmosphere. The mixture was stirred at 60°C for 12 hours. After that another portion of 3 -bromoprop- l-yne (1 eq) was added and the reaction was stirred at 60°C for 8 hours. The addition was continued until 80% conversion by LCMS was achieved.
  • Step 4 solution of Aryl iodide 6, (1 eq), alkyne 5, (2 eq), DiPA, (0.4 eq), and dry DMSO (0.15 M) was degassed by bubbling argon for 2 min. Palladium- tetrakis(triphenylphosphine) (30 wt. %) and Cui (lOwt. %) were added and the mixture was again degassed by bubbling argon and was stirred under argon at room temperature for 12 hours.
  • Step 1 Mono-Boc diamine 1 (1 eq) and pyridine (2.0 eq) were mixed in DCM (0.2M) and mixture was cooled to 0°C. Ditrichloromethyl carbonate (0.4 eq) was added portion wise, mixture was left to stir at 0°C for Ihour and then was stirred overnight at rt. The solution was washed with H2O (lx) and saturated aq solution of NaHSO4 (2x), organic layer dried over Na2SO4, and concentrated under reduced pressure to obtain acid chloride 2 (63.4% yield) which was used in the next step without further purification.
  • Step 3 At 0°C carbamate 4 (1 eq), (dihydroxyboranyl)boronic acid (4 eq) were mixed in DMF, after 10 min (dihydroxyboranyl)boronic acid (4 eq) was added portionwise and the mixture was left to stir at room temperature overnight. The reaction mixture was diluted with distilled water and extracted with DCM (3x). The organic layers were combined, washed with water (3x), brine, dried over anhydrous Na2SO4 and filtered. The filtrate collected was concentrated under reduced pressure to result in the desired aniline 5 (76% yield) which was used in the next step without purification.
  • Step 4 At 0°C aniline 5 (1 eq) and dipotassium carbonate (1.5 eq) were mixed in DMF (0.2 M) after 3 min 3 -bromoprop- l-yne (1.3 eq) was added dropwise and the mixture was left to stir at room temperature overnight. The resulting mixture was extracted with ethyl acetate. The organic layer was washed with water, dried overNa2SO4, and concentrated under reduced pressure to obtain product 6 (33% yield) after FC and HPLC (30-55% 0-5min H2O/ACN, flow: 30ml/min (loading pump 4ml/min ACN) target mass 509.60, column: Chromatorex 18 SMB100- 5T 100x19mm).
  • Step 5 Under argon, iodo 7 (1 eq), carbamate 6 (1.2) copper(I) iodide (10 mol %) tetrakis(triphenylphosphine)palladium (10 mol %) were mixed in DMSO/(i-Pr)2NH (5M, 3:1) and the mixture was left to stir at room temperature overnight. Alkyne 8 (93.4% yield) was obtained after HPLC (40-65% 0-5min H2O/ACN/0.1%NH4OH, flow: 30ml/min (loading pump 4ml/min ACN) target mass 818.94, column: XBridge C18 100x19 mm).
  • General procedure 8 Synthesis of ether-containing Rl-L scaffolds.
  • Step 1 Dipotassium carbonate (1.5 eq) was added to a solution of alkyl halide 1 (1 eq) in DMF (0.35 M). The resulting mixture was stirred at room temperature for 30 min and phenol 2 (1.2 eq), was added in one portion. The reaction was stirred at 50°C for 24 hours (monitored by LCMS). The resulting mixture was diluted with EtOAc then washed with H2O, brine (3x), dried overNa2SO4, and concentrated under reduced pressure to dryness to afford ether 3.
  • Step 2 A solution of ether 3 (1 eq), in methanol (0.15 M) was treated with Pd/C (5 wt. %). The resulting mixture was hydrogenated at 2 atm and ambient temperature until spectral data of an aliquot revealed completion of the reaction (by LCMS). Then the catalyst was fdtered off and the filtrate was concentrated to afford aniline 4. The product was used in further experiments without any additional purification.
  • Step 3 3 -Bromoprop- l-yne (1.05 eq), was added portion wise to the solution of aniline 4 (1 eq) and dipotassium carbonate (1.5 eq) in DMF (0.2 M) and the mixture was stirred at rt for 24 hrs. The resulting mixture was diluted with EtOAc, washed with H2O and aq NaHSOs. The combined organics were then washed with brine (5x), dried over Na2SO4, and concentrated to afford 9 g of crude oil. The crude product obtained was purified by flash chromatography (ISCO® Interchim). As a result, propargyl aniline 5 was obtained.
  • Step 4 A mixture of propargyl aniline 5 (1.2 eq), key intermediate 7 (1 eq), copper iodide (10 wt. %) and palladium-tetrakis(triphenylphosphine) (20 wt. %) was stirred in DMSO:TEA (3:1, 0.1 M) under argon atmosphere at room temperature for 4 hrs. Then the mixture was purified by HPLC to obtain di-substituted alkyne 8.
  • DMSO:TEA 3:1, 0.1 M
  • Step 2 A solution of thiol 2 (1 eq), alkyl halide 3 (1.8 eq), sodium hydroxymethanesulfinate (2.7 eq), and dipotassium carbonate (1.8 eq) in DMF (0.24 M) was stirred overnight at room temperature. The resulting mixture was concentrated under vacuum, diluted with water and then extracted with ethyl acetate (2x). The combined organic layers were washed with brine (4x) and dried over anhydrous Na2SO4, to obtain sulfide 4.
  • Step 3 To cooled to 0°C solution of sulfide 4 (1 eq) in DCM (0.15 M) 3- chlorobenzene-l-carboperoxoic acid (3 eq) was added. The mixture was stirred overnight at room temperature then diluted with water and extracted with DCM. The combined organic layers were washed with 20% K2CO3 (2x), brine (4x), dried over anhydrous Na2SO4, and concentrated under reduced pressure to obtain sulfonyl 5.
  • Step 4 A stirred solution of sulfonyl 5 (leq) and 4-(pyridin-4-yl)pyridine (0.05 eq) in DMF (0.15 M) was cooled to 0 °C and (dihydroxyboranyl)boronic acid (3 eq) was added dropwise at the temperature not exceeding 5 °C. The reaction mixture was allowed to warm up to room temperature and stirred for another 12 hours. Then 20% K2CO3 and ethyl acetate were added, organic layers separated, washed with H2O (2x) and brine (3x), dried overNa2SO4 and concentrated in vacuo to obtain aniline 6.
  • Step 5 A stirred solution of aniline 6 (1 eq), potassium iodide (1.3 eq) and 3- bromoprop-l-yne (1.3 eq) in DMF (0.2 M) dipotassium carbonate (2 eq) was added portion wise at the room temperature. The reaction mixture was stirred at 75 °C for another 48 hours. Then ethyl acetate was added, organic layers separated, washed with H2O (2x) and brine (3x), dried over Na2SO4 and concentrated in vacuo to obtain propargyl aniline 7 after flash chromatography.
  • Step 6 To a stirred solution of propargyl aniline 7 (1.2 eq), iodo indole 8 (1 eq) in THF/EhN (1: 1, 0.1M) palladium-tetrakis(triphenylphosphine) (20 wt. %) and copper iodide (10 wt. %) were added portion wise at the room temperature under Argon atmosphere. Reaction mixture was stirred at room temperature for another 12 hours. Then the mixture was purified by flash chromatography to obtain di-substituted alkyne 9.
  • Step 1 Dipotassium carbonate (1.5 eq) was added to a solution nitrophenol 2 (1 eq) in DMF (0.5 M). The resulting mixture was stirred at room temperature for 30 min then linker intermediate 1 (1.2 eq) and potassium iodide (0.1 eq) were added in one portion. The reaction was stirred at 40 °C for 24 hours (monitored by LCMS). The resulting mixture was diluted with ethyl acetate then washed with H2O, brine (4x), dried overNa2SO4, and concentrated under reduced pressure to dryness to afford 3.
  • Step 2 Copper (I) iodide (10 wt. %) was added to a round bottom flask charged with aryl bromide 3 (1 eq), sodium methanesulfmate (1.2 eq) and (2S)-pyrrolidine-2-carboxylic acid (2 wt. %) in DMSO (0.5 M) at room temperature. The resulting mixture was sparged with argon for 10 minutes, then the reaction mixture was stirred at 100 °C for 12 hours. The mixture was diluted with ethyl acetate, organic layers were separated, washed with H2O, aqua NH3 (2x), brine (3x), dried overNa2SO4, and concentrated under reduced pressure to dryness to afford 4 as a crude oil. The crude product obtained was purified by flash chromatography to obtain pure aryl sulfone 4.
  • Step 3 A solution of aryl sulfone 4 (1 eq) in methanol (5 M) was treated with Pd/C (5 wt. %). The resulting mixture was hydrogenated at 2 atm and ambient temperature until spectral data of an aliquot revealed completion of the reaction (by LCMS). Then the catalyst was filtered off and the filtrate was concentrated to afford aniline 5. The product was used in further experiments without any additional purification.
  • Step 4 3 -Bromoprop- 1-yne (1.2 eq) was added portion wise to the solution of aniline 5 (1 eq), dipotassium carbonate (1.5 eq) and potassium iodide (10 wt. %) in DMF (2 M) and the mixture was stirred at 90°C for 4 days. The resulting mixture was diluted with ethyl acetate, washed with H2O and aq NaHSCh. The combined organic layers were then washed with brine (3x), dried overNa2SO4, and concentrated to afford 6 as a crude oil. The crude product obtained was purified by flash chromatography to obtain alkylated arene 6.
  • Step 5 Key intermediate 7 (1 eq), palladium-tetrakis(triphenylphosphine) (20 wt. %), aryl sulfone 6 (1.2 eq) and copper (I) iodide (10 wt. %) in DMSO/z-Pr2NH (3:1, 0.08 M) were added to round bottom flask at room temperature. The resulting mixture was sparged with argon for 10 minutes and was left to stir at room temperature for 12 hours. The mixture was diluted with ethyl acetate, washed with H2O, aqua NH3 (2x), brine, dried overNa2SO4, and concentrated under reduced pressure to dryness to afford 8 as crude brown oil. The crude product obtained was purified by flash chromatography to obtain alkyne 8.
  • Step 6 Alkyne 8 (1 eq) was dissolved in MeOH (0.02 M). Hydrogen chloride (10.0 eq) was added and the mixture was stirred at room temperature overnight. After consumption of the starting material (monitored by LCMS) the resulting mixture was concentrated under reduced pressure to dryness ( ⁇ 40°C). The obtained residue was quenched with NaHCO? and extracted with dichloromethane (3x). The combined organic extracts were washed with brine, dried over Na2SO4, and concentrated under reduced pressure to afford amine 9.
  • General procedure 11 Synthesis of propargylated aniline-containing NH-sulfonamide linker.
  • Step 1 A mixture of 3 -methoxy-4-nitro-benzenesulfonyl chloride (1.2 eq) and mono- Boc protected diamine linker (1.0 eq) in pyridine (0.68 M) was degassed, purged with N2 3 times, and then stirred at 25 °C for 1 hour under N2 atmosphere. LCMS showed complete consumption of starting 1 and formation of desired product 3. The mixture was concentrated in vacuo to give an oil residue that was purified by flash column chromatography to provide nitro-containing intermediate 2.
  • Step 2 To a solution of NH-sulfonamide containing intermediate 3 (1.0 eq) in DCM (0.18 M) DMAP (0.1 eq) and EtsN (3 eq) were added followed by (Boc)2O (1.4 eq). The mixture was stirred at 25 °C for 12 hours. LCMS showed complete consumption of starting material 3 and formation of the desired Boc-protected sulfonamide product 4. The mixture was concentrated in vacuo to give an oil residue that was further purified by flash column chromatography.
  • Step 3 To a suspension of Pd/C (75 mg/mmol, 10% purity) in MeOH (0.26 M) under nitrogen atmosphere nitro -containing intermediate 4 was added. The mixture was degassed, purged with H23 times, and stirred under H2 (15 Psi) atmosphere at 25°C for 12 hours. LCMS showed complete consumption of starting material and formation of the desired product. The reaction was filtered, solid residue was washed by THF (3x), and collected filtrate was concentrated in vacuo to give the desired aniline intermediate 5.
  • Step 4 A mixture of aniline intermediate 5 (1 eq), 3 -bromoprop- l-yne (1.3 eq), K2CO3 (2 eq), and KI (0.2 eq) in DMF (0.45 M) was degassed, purged with N2 3 times, and stirred under nitrogen atmosphere at 80 °C for 12 hours. LCMS showed complete consumption of starting materials and formation of the desired product. Ethyl acetate and water were added and then layers were separated. The aqueous phase was extracted with ethyl acetate (3x). The combined organic layers were washed with brine, dried over Na2SO4, filtered and concentrated in vacuo to give an oil residue. The residue was purified by prep-WLC to give the propargylated aniline-containing NBoc-sulfonamide linker 6.
  • Step 5 To a solution of the propargylated aniline-containing NBoc-sulfonamide linker 6 (1 eq) in MeOH (1 M), K2CO3 (2 eq) was added. The mixture was stirred at 50 °C for 12 hours. LCMS showed complete consumption of starting material and formation of the desired product. The reaction mixture was concentrated in vacuo to give an oil residue. The residue was purified by flash silica gel chromatography to give the desired propargylated aniline-containing NH sulfonamide linker 7.
  • Step 1 To a stirred suspension of 2,6-dinitroaniline 1 (1 eq) in glacial acetic acid (4 M) was added bromine (1.1 eq) dropwise and heated at 120° C for 2 hours. After cooling to ambient temperature, the resultant mixture was poured into water. The precipitate solid was collected by filtration, washed with water, and then dried in-air to obtain aryl bromide 2.
  • Step 2 A mixture of aryl bromide 2 (1 eq) and diammonium sulfide (1 eq) in ethanol
  • Step 3 To a suspension of dianiline 3 (1 eq) in 4M HC1 (0.3 M) was added formic acid (2.5 eq). The mixture was heated at 100°C for 1.5 hours, and then cooled to room temperature. Water was added and neutralization with concentrated NH4OH gave a precipitate which was collected, washed with water, and dried to give benzimidazole 4.
  • Step 4 A suspension of benzimidazole 4 (1 eq), key intermediate benzyl bromide (1 eq) and dipotassium carbonate (3 eq) in dioxane (0.1 M) was stirred at 75°C for 12 hours, filtered and evaporated to obtain alkylated benzimidazole 5 which was used without further purification.
  • Step 5 A suspension of tricyclic intermediate 5 (1 eq), 3,5-dimethyl-4-(tetramethyl- l,3,2-dioxaborolan-2-yl)-l,2-oxazole 6 (1.2), dipotassium carbonate (3 eq), and palladium- tetrakis(triphenylphosphine) (lOwt. %) in degassed dioxane/H2O (10: 1, 0.05 M) was stirred under argon at 100°C overnight. After cooling to room temperature, the mixture was evaporated, then water and EtOAc were added, and the mixture was filtered to obtain acid 7.
  • Step 6 To a solution of acid 7 (1 eq) in THF/DMF (4: 1, 0.1 M), Pd/C (5wt. %) was added. The resulting mixture was hydrogenated at ambient pressure and ambient temperature until 1 H NMR of an aliquot revealed completion of reaction. The catalyst was filtered off and the filtrate evaporated in vacuo. Then water was added, and the solids were collected and dried to afford benzimidazole 8.
  • Step 1 A suspension of aryl bromide 1 (1 eq), ester 2 (1.2 eq) and dipotassium carbonate (2 eq) in dioxane (2M) was stirred at 100°C for 12 hours, filtered and evaporated to obtain alkylated product 3 (90.8% yield) (1: 1 mixture of isomers) which was used without further purification but later separated and confirmed by 2D-NMR/nOe.
  • Step 2 A suspension of aryl bromide 3 (1 eq), boronic ester 4 (1.5 eq), tetrakis(triphenylphosphine)palladium (10 mol %), and dipotassium carbonate (2.2 eq) in degassed dioxane/H ⁇ O (3M, 10: 1) was stirred under argon at 100°C overnight.
  • Step 3 A solution of ester 5 (1 eq) and sodium hydroxide (10 eq) in Me0H:H20 (0.5M, 10:1) was stirred at room temperature for 12 hours, acidified with TFA to pH ⁇ 3 and purified by HPLC (5-12% 0-7 min H2O/ACN/0.1% FA, flow: 30ml/min (loading pump 4ml/min ACN) target mass 347.88 column: Chromatorex 18 SMB100-5T 100x19mm 5 pm) to obtain free acid 6 (14.2% yield) as a white solid.
  • the regioisomers were separated by prep HPLC, the structure was confirmed by 2D NMR.
  • General procedure 14 Synthesis of imidazo[4,5-b]pyridin containing RL acids.
  • Step 1 A mixture of aldehyde 1 (1 eq), tert-butyl 2-bromoacetate (1.1 eq) and dipotassium carbonate (2.1 eq) in acetonitrile (0.2 M) was stirred overnight at 78°C. Then the mixture was filtered and evaporated to obtain tert butyl ester 2 (91.2% yield) as a yellow oil which was used without further purification.
  • Step 2 A mixture of dianiline 3 (1 eq), boronic ester 4 (1.2 eq), tetrakis(triphenylphosphine)palladium (9 mol %) and dipotassium carbonate (2 eq) in dioxane/H2O (5M, 10: 1) was degassed and purged with Ar for 3x, and then the mixture was stirred at 90 °C for 12 hours under Ar atmosphere. The mixture was diluted with EtOAc and water, separated. The aqueous phase was extracted with EtOAc (3x). The organic phase was washed with brine. The organic phase was dried over anhydrous Na2SO4 and concentrated in vacuum. The residue was triturated with EtOAc. The mixture was filtered. The filter cake was dried in vacuum to afford bi-aryl 5 (49.4% yield) as a brown solid.
  • Step 5 To a solution of amine 7 (1 eq) in dioxane (4M) l-(lH-imidazole-l- carbonyl)-lH-imidazole (4.5 eq) was added. The mixture was stirred at 80 °C for 12 hours, diluted with EtOAc and water, separated. The aqueous phase was extracted with EtOAc (lx), The organic phase was washed with brine (2x). The organic phase was dried over anhydrous ISfeSCE and concentrated in vacuum to obtain urea 8 (78.7% yield) as a yellow solid.
  • Step 6 A solution of urea 8 (1 eq) in POCI3 (5 eq) was stirred at 110°C for 36 hours, diluted with water, extracted with EtOAc (2x), washed with brine, dried under Na2SO4 and evaporated to obtain chloride 9 (53% yield) as a brown oil.
  • Step 7 A solution of chloride 9 (1 eq) in MeNEE in MeOH (excess eq) was stirred at
  • Step 1 To a solution of CD3OH (9.17 g, 254.34 mmol, 10.33 ml, 1.2 equiv) in THF (500ml) sodium hydride (10.6 g, 60.0% purity, 264.94 mmol) was added portion wise at 0-°C under inert atmosphere. After 30min of stirring 5 -bromo-2-chloro-3 -nitropyridine (50.0 g, 211.96 mmol) was added to this mixture at room temperature. After 12 hours solvent was evaporated under reduced pressure and water (500ml) was added. Precipitated solids were collected by fdtration, washed with water and purified by FC (Ok.
  • Step 2 A suspension of 5-bromo-2-(2H3)methoxy-3-nitropyridine (15.0 g, 63.84 mmol), 3,5-dimethyl-4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)-l,2-oxazole (17.09 g, 76.61 mmol), dipotassium carbonate (17.61 g, 127.68 mmol) and tetrakis(triphenylphosphine)palladium (3.7 g, 3.19 mmol) in dioxane:H2O (10: 1, 300ml) was stirred at 100°C under inert atmosphere overnight.
  • Step 4 A mixture of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-(2H3)methoxypyridin-3- amine (75.0 mg, 337.45 pmol), 2-(3-formylphenoxy)acetic acid (60.57 mg, 336.42 pmol) and sodium bis(acetyloxy)boranuidyl acetate (214.01 mg, 1.01 mmol) in 1,2-di chloroethane (20ml) was stirred overnight at room temperature.
  • Step 1 To a solution of aldehyde 1, (1 eq) in MeOH (0.5 M) sodium borohydride (1 eq) was added in portions at 0°C. Then the solution was stirred at room temperature for 2 hours, diluted with 10% HC1, extracted with methyl tert-butyl ether (2x), washed with brine, dried over anhydrous sodium sulfate and filtered. The collected filtrate was concentrated under reduced pressure to obtain the desired alcohol 2, which was used without further purification.
  • Step 2a To a solution of alcohol 2 (1.0 eq) and triethylamine (1.5 eq) in ethyl acetate (0.35 M) methanesulfonyl chloride (1.0 eq) was added at 0°C. The mixture was stirred for 30 min at 0°C, then diluted with distilled water. The organic layer was separated, washed with water and brine, dried over magnesium sulfate, filtered, and concentrated in vacuo to produce the desired mesylate 3, which was immediately used as crude in the next step.
  • Step 3 A suspension of aryl bromide 4 (1 eq), (dimethyl-l,2-oxazol-4-yl)boronic acid (1.3 eq), dipotassium carbonate (2 eq) and [1,1'- bis(diphenylphosphino)ferrocene]dichloropalladium (II) dichloromethane complex (5 wt. %) in a degassed mixture of dioxane and water (10:1, 0.3 M) was stirred under argon at 90°C overnight. After cooling to room temperature, the mixture was diluted with water and extracted with ethyl acetate (2x). The organic layers were combined, washed with water and brine, dried over magnesium sulfate, filtered, and concentrated in vacuo to afford the desired bi-aryl 5.
  • Step 4 To a magnetically stirred solution of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-2- methoxypyridine (1 eq) in EtOH (0.1 M) hydrogen bromide (35 eq) was added. The resulting mixture was heated at 90°C for 4 hours. Then the reaction mixture was cooled down to room temperature and concentrated under reduced pressure. The residue obtained was diluted with brine and the precipitate formed was collected by filtration and washed with small amount of water to result in the desired pyridone 6.
  • Step 5 A solution of pyridone 6 (1 eq), mesylate or bromide 3 (1.7 eq) and dipotassium carbonate (3 eq) in acetonitrile (0.2 M) was heated at 70°C for 2 hours. Then the mixture was filtered, evaporated to dryness and the residue obtained was purified by flash chromatography to obtain the desired ester 7.
  • Step 6 To a solution of methyl ester 7 (1 eq) in Me0H/H20 (6:1, 0.7 M) sodium hydroxide (3 eq) was added at room temperature. The reaction mixture was stirred for 12 hours, then evaporated to dryness, dissolved in water and acidified to pH 2 with NaHSCU The formed precipitate was collected by filtration, washed with water and purified by prep HPLC to provide the desired acid 8.
  • Step 1 A mixture of bromide 1 (1 eq), (dimethyl- l,2-oxazol-4-yl)boronic acid (1.3 eq), dipotassium carbonate (2 eq) Pd(PPhs)4 (0.1 eq) in a degassed mixture of dioxane and water (10: 1, 0.3 M) was stirred under argon at 90°C overnight.
  • the reaction mixture was diluted with ethyl acetate (100 mL) and water (50 mL).
  • Step 2 To a solution of bi-aryl 3 in dioxane was added HBr/HOAc (IM). The mixture was stirred at 90 °C for 12 hours. LCMS showed compound 2 was consumed completely and 63% of desired mass was detected. The mixture was cooled to 0 °C and quenched by adding water. The resulting reaction mixture was extracted with ethyl acetate (3x). Ethyl acetate layer was washed with water (2x), dried over anhydrous Na2SO4 and evaporated under reduced pressure.
  • IM HBr/HOAc
  • Step 4 To a solution of tBu ester 6 (1 eq) was added DCM/TFA (0.2 M, 1:1). The mixture was stirred at 25 °C for 12 hours. LCMS showed 13% compound 8 remained and 78% of desired mass was detected. The reaction mixture was fdtered and concentrated under reduced pressure to remove solvent and give a residue. The residue was purified by prep-WVC (column: Phenomenex luna C18 150*40mm* 15um; mobile phase: [water (FA)-ACN]; gradient: 33%-63% B over 15 min) to afford free acid 7 blue solid.
  • Example 2 Synthesis of2- ⁇ 3-[(4- ⁇ 2-[2-(2-aminoethoxy)ethoxy]ethoxy ⁇ phenyl)amino]prop-l- yn-l-yl ⁇ -N-(l-methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine.
  • Step 1 The synthesis of tert-butyl N-(2- ⁇ 2-[2-(4- nitrophenoxy)ethoxy]ethoxy ⁇ ethyl)carbamate.
  • Dipotassium carbonate (6.65 g, 48.22 mmol) was added to a solution of tert-butyl N-2-[2-(2-bromoethoxy)ethoxy]ethylcarbamate (10.0 g, 32.15 mmol) in DMF (50 mL).
  • the resulting mixture was stirred at room temperature for 30 min and 4- nitrophenol (5.36 g, 38.58 mmol) was added in one portion.
  • the reaction was stirred at 50 °C for 24 hrs and monitored by LCMS.
  • Step 2 The synthesis of tert-butyl N-(2- ⁇ 2-[2-(4- aminophenoxy)ethoxy]ethoxy ⁇ ethyl)carbamate.
  • a solution of tert-butyl N-(2-2-[2-(4- nitrophenoxy)ethoxy]ethoxyethyl)carbamate (9.5 g, 25.65 mmol) in methanol (150 ml) was treated with Pd/C (0.95 g, 5 wt. %).
  • the resulting mixture was hydrogenated at 2 atm and ambient temperature until spectral data of an aliquot revealed completion of the reaction (by LCMS).
  • Step 3 The synthesis of zc/7-butyl N- ⁇ 2-[2-(2- ⁇ 4-[(prop-2-yn-l yl)amino]phenoxy ⁇ ethoxy)ethoxy] ethyl (carbamate.
  • Step 4 The synthesis of zcrz-butyl N- ⁇ 2-[2-(2- ⁇ 4-[(3- ⁇ 4-[(l-methylpiperidin-4- yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]phenoxy(ethoxy)ethoxy] ethyl (carbamate.
  • the resulting mixture was sparged with argon for 10 min and stirred at room temperature for 12 hrs.
  • the mixture was diluted with EtOAc (100 mL), washed with H2O (30 mL), aq. NH3 (2 x 30 mL), brine (20 mL), dried over Na2SO4, and concentrated under reduced pressure to dryness to afford 1.1 g of crude brown oil.
  • Step 5 The synthesis of 2- ⁇ 3-[(4- ⁇ 2-[2-(2- aminoethoxy)ethoxy]ethoxy ⁇ phenyl)amino]prop-l-yn-l-yl ⁇ -N-(l-methylpiperidin-4-yl)-l-(2,2,2- trifluoroethyl)- lH-indol-4-amine.
  • Example 3 Synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-( ⁇ 3-[(6- ⁇ 4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifluoroethyl)- lH-indol-2-yl ⁇ prop-2-yn- 1- yl)amino] phenoxy ⁇ hexyl)oxy] phenyl ⁇ methyl)-l,2-dihydropyridin-2-one.
  • Step 1 The synthesis of 6-(4-nitrophenoxy)hexan-l-ol.
  • Step 2 The synthesis of 6-(4-nitrophenoxy)hexyl methanesulfonate.
  • 6-(4-nitrophenoxy)hexan-l-ol 1.0 g, 4.19 mmol
  • ethylbis(propan-2-yl)amine 1.08 g, 8.39 mmol, 1.46 ml
  • methanesulfonyl chloride 525.72 mg, 4.61 mmol, 360.0 pl
  • Step 3 The synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-[(3- ⁇ [6-(4- nitrophenoxy)hexyl]oxy ⁇ phenyl)methyl]-l,2-dihydropyridin-2-one.
  • Step 4 The synthesis of l-[(3- ⁇ [6-(4-aminophenoxy)hexyl]oxy ⁇ phenyl)methyl]-5- (3,5-dimethyl-l,2-oxazol-4-yl)-l,2-dihydropyridin-2-one.
  • Step 5 The synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-( ⁇ 3-[(6- ⁇ 4-[(prop-2-yn- l-yl)amino]phenoxy ⁇ hexyl)oxy]phenyl ⁇ methyl)-l,2-dihydropyridin-2-one.
  • Step 6 The synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-( ⁇ 3-[(6- ⁇ 4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]phenoxy ⁇ hexyl)oxy]phenyl ⁇ methyl)-l,2-dihydropyridin-2-one.
  • Example 4 Synthesis ofN-(2- ⁇ 2-[2-(2-aminoethoxy)ethoxy]ethoxy ⁇ ethyl)-3-methoxy-N- methyl-4-[(3- ⁇ 4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2- yl ⁇ prop-2-yn-l-yl)amino]benzene-l-sulfonamide.
  • Step 1 The synthesis of tert-butyl N-[2-(2- ⁇ 2-[2-(N-methyl-3-methoxy-4 nitrobenzenesulfonamido)ethoxy]ethoxy ⁇ ethoxy)ethyl]carbamate.
  • Step 2 The synthesis of tert-butyl N-[2-(2- ⁇ 2-[2-(N-methyl-4-amino-3- methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethoxy)ethyl]carbamate.
  • Step 3 The synthesis oftert-butyl N-(2- ⁇ 2-[2-(2- ⁇ N-methyl-3-methoxy-4-[(prop-2- yn-l-yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)carbamate.
  • Step 4 The synthesis of tert-butyl N-(2- ⁇ 2-[2-(2- ⁇ N-methyl-3-methoxy-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)carbamate.
  • Step 5 The synthesis ofN-(2- ⁇ 2-[2-(2-aminoethoxy)ethoxy]ethoxy ⁇ ethyl)-3- methoxy-N-methyl-4-[(3- ⁇ 4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol- 2-yl ⁇ prop-2-yn-l-yl)amino]benzene-l -sulfonamide trihydrochloride.
  • Example 5 Synthesis of 4-(4- ⁇ [5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l- yl] methyl ⁇ phenoxy)-N-(2- ⁇ 2- [2-(2- ⁇ 4- [(3- ⁇ 4- [(l-methylpiperidin-4-yl)amino] - 1-(2,2,2- trifhioroethyl)- lH-indol-2-yl ⁇ prop-2-yn- 1- yl)amino]phenoxy ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)butanamide.
  • Step 1 The synthesis of 4-(4- ⁇ [5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2- dihydropyridin-l-yl]methyl ⁇ phenoxy)-N-(2- ⁇ 2-[2-(2- ⁇ 4-[(3- ⁇ 4-[(l-methylpiperidin-4-yl)amino]- 1 -(2,2,2-trifluoroethyl)- lH-indol-2-yl ⁇ prop-2-yn- 1 - yl)amino]phenoxy ⁇ ethoxy)ethoxy] ethoxy ⁇ ethyl)butanami de. Procedure as described in general procedure 3.
  • Example 6 Synthesis of 2-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl ⁇ phenoxy)-N-(2- ⁇ 2- [2-(N-methyl-4- ⁇ [3-(4- ⁇ [(3S,4R)-3-fhioro-l- methylpiperidin-4-yl]amino ⁇ -l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino ⁇ - 3-methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethyl)acetamide.
  • Step 1 The synthesis of tert-butyl N-[2-(2- ⁇ 2-[N-methyl-4-( ⁇ 3-[4-bromo-l-(2,2,2- trifluoroethyl)-lH-indol-2-yl]prop-2-yn-l-yl ⁇ amino)-3- methoxybenzenesulfonamido]ethoxy ⁇ ethoxy)ethyl]carbamate.
  • reaction mixture was stirred at room temperature for another 12 hrs. Then the mixture was purified by flash column chromatography to obtaintert-butyl N-[2-(2-2-[N-methyl-4-(3-[4-bromo-l-(2,2,2- trifluoroethyl)- 1 H-indol-2-yl]prop-2-yn- 1 -ylamino)-3 - methoxybenzenesulfonamido]ethoxyethoxy)ethyl]carbamate (350.0 mg, 53.6% yield) as yellow gum.
  • Step 2 The synthesis oftert-butyl N-(2- ⁇ 2-[2-(N-methyl-4- ⁇ [3-(4- ⁇ [(3S,4R)-3- fluoro- 1 -methylpiperi din -4-yl] amino ⁇ - 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2-yn- 1 - yl]amino ⁇ -3-methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethyl (carbamate.
  • Step 3 The synthesis of N- ⁇ 2-[2-(2-aminoethoxy)ethoxy]ethyl ⁇ -4- ⁇ [3-(4- ⁇ [(3S,4R)- 3 -fluoro- 1 -methylpiperidin-4-yl] amino ⁇ - 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2-yn- 1 - yl]amino ⁇ -3-methoxy-N-methylbenzene-l-sulfonamide tetrahydrochloride.
  • Step 4 The synthesis of 2-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl ⁇ phenoxy)-N-(2- ⁇ 2-[2-(N-methyl-4- ⁇ [3-(4- ⁇ [(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino ⁇ -l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino ⁇ -3- methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethyl)acetamide.
  • Step 1 The synthesis of 2-[3-(3,5-dimethyl-l,2-oxazol-4-yl)-5- [hydroxy(phenyl)methyl]phenoxy]-N-[2-(2- ⁇ 2-[2-( ⁇ 3-methoxy-4-[(3- ⁇ 4-[(l-methylpiperi din-4- yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]phenyl ⁇ formamido)ethoxy]ethoxy ⁇ ethoxy)ethyl] acetamide.
  • Example 8 Synthesis of5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-( ⁇ 3-[4-(4- ⁇ 4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifluoroethyl)- lH-indol-2-yl ⁇ prop-2-yn- 1- yl)amino] phenoxy ⁇ butoxy) butoxy]phenyl ⁇ methyl)-l,2-dihydropyridin-2-one.
  • Step 1 The synthesis of tert-butyl N- ⁇ 4-[4-(4-hydroxybutoxy)butoxy]phenyl ⁇ -N- (prop-2-yn-l-yl)carbamate.
  • Tert-butyl N-(4-hydroxyphenyl)-N-(prop-2-yn-l-yl)carbamate (1.02 g, 4.12 mmol)
  • 4-(4-chlorobutoxy)butan-l-ol (891.49 mg, 4.95 mmol)
  • dipotassium carbonate (853.36 mg, 6.19 mmol)
  • potassium iodide (684.23 mg, 4.13 mmol) were mixed in MeCN (30 mL) and suspension was heated at 75°C for 3 days.
  • Step 2 The synthesis of tert-butyl N-(4- ⁇ 4-[4- (methanesulfonyloxy)butoxy]butoxy ⁇ phenyl)-N-(prop-2-yn-l-yl)carbamate.
  • Step 3 The synthesis oftert-butyl N-(4- ⁇ 4-[4-(3- ⁇ [5-(3,5-dimethyl-l,2-oxazol-4-yl)- 2-oxo-l, 2-dihydropyri din-1 -yl] methyl ⁇ phenoxy )butoxy]butoxy ⁇ phenyl)-N-(prop-2-yn-l- yl)carbamate.
  • Step 4 The synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-( ⁇ 3-[4-(4- ⁇ 4-[(prop-2- yn-1 -yl)amino]phenoxy (butoxy )butoxy]phenyl ⁇ methyl)- l,2-dihydropyridin-2-one.
  • Step 5 The synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-( ⁇ 3-[4-(4- ⁇ 4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]phenoxy ⁇ butoxy)butoxy]phenyl ⁇ methyl)-l,2-dihydropyridin-2-one.
  • Example 9 Synthesis of 2-(3- ⁇ [5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l- yl] methyl ⁇ phenoxy)-N-(2- ⁇ 2- [2- (4- ⁇ [3-(4- ⁇ [(3S,4R)-3-fhioro- l-methylpiperidin-4-yl] amino ⁇ - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl)prop-2-yn- 1- yl]amino ⁇ phenoxy)ethoxy]ethoxy ⁇ ethyl)acetamide.
  • Step 1 4-Bromo-2-iodo-l-(2,2,2-trifluoroethyl)-lH-indole (1.0 g, 2.48 mmol), tertbutyl N-2-[2-(2-4-[(prop-2-yn-l-yl)amino]phenoxyethoxy)ethoxy]ethylcarbamate (1.13 g, 2.98 mmol) see intermediate 5 from procedure Z8435419477, triphenyl[tris(triphenyl-lambda5- phosphanyl)palladio] -lambda5 -phosphane (575.15 mg, 496.55 pmol) was added to a RB flask charged with 4-bromo-2-iodo-l-(2,2,2-trifluoroethyl)-lH-indole (1.0 g, 2.48 mmol), tert-butyl N- 2-[2-(2-4-[(prop
  • tert-butyl N-[2-(2-2-[4- (3 - [4-bromo- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl]prop-2-yn- 1 - ylamino)phenoxy]ethoxyethoxy)ethyl]carbamate (1.2 g, 66.5% yield) was obtained as brown oil.
  • Step 2 To a RB flask charged with tert-butyl N-[2-(2-2-[4-(3-[4-bromo-l-(2,2,2- trifluoroethyl)-lH-indol-2-yl]prop-2-yn-l-ylamino)phenoxy]ethoxyethoxy)ethyl]carbamate (100.0 mg, 152.78 pmol) , (3 S,4R)-3 -fluoro- l-methylpiperidin-4-amine (60.65 mg, 459.07 pmol) , sodium 2-methylpropan-2-olate (44.1 mg, 459.06 pmol) , [l,l'-biphenyl]-2-yldi-tert- butyl)phosphane (18.25 mg, 61.21 pmol) and sodium 2-methylpropan-2-olate (44.1 mg, 459.06 pmol) was added Toluene (5 ml) at
  • Step 3 Tert-butyl N-(2-2-[2-(4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4- yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l- yl]aminophenoxy)ethoxy]ethoxyethyl)carbamate (13.0 mg, 18.42 pmol) was dissolved in 0.9 ml of MeOH. Hydrogen chloride (6.65 mg, 184.92 pmol, 90.0 pl) was added and resulting mixture was stirred at room temperature overnight. After consumption of the starting material (LCMS control) the resulting mixture was concentrated under reduced pressure to dryness( ⁇ 40°C) and immediately used in further experiment without any additional purification.
  • Step 4 following general procedure 3. The mixture obtained was subjected for prep HPLC purification (33-40-65% 0-2-7-7.1min; 30ml/min water-acn+nh3 (loading pump 4 ml/min acn+nh3); target mass 943 column Xbridge C18 5 uM 19*100mm) to afford 2-(3-[5-(3,5- dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l-yl]methylphenoxy)-N-(2-2-[2-(4-[3-(4- [(3 S,4R)-3 -fluoro- 1 -methylpiperidin-4-yl] amino- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2- yn-l-yl]aminophenoxy)ethoxy]ethoxyethyl)acetamide (2.1 mg,
  • Example 10 Synthesis of 2-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl ⁇ phenoxy)-N- [2-(2- ⁇ 2- [2-(N-methyl-4- ⁇ [3-(4- ⁇ [(3S,4R)-3-fhioro- 1- methylpiperidin-4-yl]amino ⁇ -l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino ⁇ - 3-methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethoxy)ethyl]acetamide.
  • Step 1 The synthesis of tert-butyl N-[2-(2- ⁇ 2-[2-(N-methyl-3-methoxy-4- nitrobenzenesulfonamido)ethoxy]ethoxy ⁇ ethoxy)ethyl]carbamate.
  • Step 2 The synthesis of tert-butyl N-[2-(2- ⁇ 2-[2-(N-methyl-4-amino-3- methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethoxy)ethyl]carbamate.
  • Step 3 The synthesis of tert-butyl N-(2- ⁇ 2-[2-(2- ⁇ N-methyl-3-methoxy-4-[(prop-2- yn-l-yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)carbamate.
  • Step 4 The synthesis of tert-butyl N- ⁇ 2-[2-(2- ⁇ 2-[N-methyl-4-( ⁇ 3-[4-bromo-l- (2,2,2-trifluoroethyl)- 1 H-indol-2-yl]prop-2-yn- 1 -yl ⁇ amino)-3 - methoxybenzenesulfonamido] ethoxy ⁇ ethoxy)ethoxy] ethyl ⁇ carbamate.
  • Step 5 The synthesis of tert-butyl N-[2-(2- ⁇ 2-[2-(N-methyl-4- ⁇ [3-(4- ⁇ [(3S,4R)-3- fluoro- 1 -methylpiperi din -4-yl] amino ⁇ - 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2-yn- 1 - yl]amino ⁇ -3-methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethoxy)ethyl]carbamate.
  • Step 6 The synthesis of N-(2- ⁇ 2-[2-(2-aminoethoxy)ethoxy]ethoxy ⁇ ethyl)-4- ⁇ [3-(4- ⁇ [(3 S,4R)-3 -fluoro- 1 -methylpiperi din-4-yl]amino ⁇ -l -(2,2, 2-trifluoroethyl)-lH-indol-2-yl)prop-2- yn-l-yl]amino ⁇ -3-methoxy-N-methylbenzene-l-sulfonamide tetrahydrochloride.
  • Step 7 The synthesis of 2-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl ⁇ phenoxy)-N-[2-(2- ⁇ 2-[2-(N-methyl-4- ⁇ [3-(4- ⁇ [(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino ⁇ -l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino ⁇ -3- methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethoxy)ethyl]acetamide.
  • Example 11 Synthesis of 2-[(4- ⁇ [5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin- 1 -y 1 ] methyl ⁇ pyridin-2-yl)oxy] -N-(2- ⁇ 2- [2- (2- ⁇ N-methyl-3-methoxy-4- [(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl ⁇ prop-2-yn- 1- yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)acetamide.
  • Step 1 The synthesis of 2-[(4- ⁇ [5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2- dihydropyridin-l-yl]methyl ⁇ pyridin-2-yl)oxy]-N-(2- ⁇ 2-[2-(2- ⁇ N-methyl- >xy-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)acetamide.
  • Step 1 The synthesis of 2-[(4- ⁇ [5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2- dihydropyridin-l-yl]methyl ⁇ pyridin-2-yl)oxy]-N- ⁇ 2-[2-(2- ⁇ N-methyl-3-methoxy-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethyl ⁇ acetamide.
  • Example 13 Synthesis of 4-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl ⁇ phenoxy)-N- ⁇ 2- [2-(2- ⁇ N-methyl-3-methoxy-4- [(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl ⁇ prop-2-yn- 1- yl)amino]benzenesulfonamido ⁇ ethoxy) ethoxy]ethyl ⁇ butanamide (Z8772414956).
  • Step 1 The synthesis of tert-butyl N-(2- ⁇ 2-[2- (methylamino)ethoxy]ethoxy ⁇ ethyl)carbamate.
  • Tert-butyl N-2-[2-(2- bromoethoxy)ethoxy]ethylcarbamate (5.0 g, 16.07 mmol) was dissolved in MeOH (5 mL) and added dropwise to methanamine (49.9 g, 1.61 mol, 317.82 ml) over 30 min. Reaction mixture left stirring overnight.
  • Step 3 The synthesis of tert-butyl N-(2- ⁇ 2-[2-(N-methyl-4-amino-3- methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethyl)carbamate.
  • Step 4 The synthesis of tert-butyl N- ⁇ 2-[2-(2- ⁇ N-methyl-3-methoxy-4-[(prop-2-yn- l-yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethyl ⁇ carbamate.
  • Step 5 The synthesis of tert-butyl N- ⁇ 2-[2-(2- ⁇ N-methyl-3-methoxy-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethyl ⁇ carbamate.
  • Step 6 The synthesis ofN- ⁇ 2-[2-(2-aminoethoxy)ethoxy]ethyl ⁇ -3-methoxy-N- methyl-4-[(3- ⁇ 4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2- yn-l-yl)amino]benzene-l -sulfonamide tetrahydrochloride.
  • Step 7 The synthesis of 4-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl ⁇ phenoxy)-N- ⁇ 2-[2-(2- ⁇ N-methyl-3-methoxy-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethyl ⁇ butanamide.
  • Example 14 Synthesis of 2-(3- ⁇ [4-(2- ⁇ 2-[2-(2-aminoethoxy)ethoxy]ethoxy ⁇ ethanesulfonyl)-2- methoxyphenyl] amino ⁇ prop- 1-yn- l-yl)-N-(l-methylpiperidin-4-yl)- l-(2,2,2-trifluoroethyl)- lH-indol-4-amine.
  • Step 1 The synthesis of 3-methoxy-4-nitrobenzene-l-thiol.
  • Step 2 The synthesis of tert-butyl N- ⁇ 2-[2-(2- ⁇ 2-[(3-methoxy-4- nitrophenyl)sulfanyl]ethoxy ⁇ ethoxy)ethoxy]ethyl ⁇ carbamate.
  • Step 3 The synthesis of tert-butyl N-[2-(2- ⁇ 2-[2-(3-methoxy-4- nitrobenzenesulfonyl)ethoxy]ethoxy ⁇ ethoxy)ethyl]carbamate.
  • tert-butyl N-2-[2- (2-2-[(3-methoxy-4-nitrophenyl)sulfanyl]ethoxyethoxy)ethoxy]ethylcarbamate (5.9 g, 12.82 mmol) in DCM (100 mL)
  • 3 -chlorobenzene- 1 -carboperoxoic acid (6.62 g, 38.46 mmol) was added at 0°C.
  • Step 4 The synthesis of tert-butyl N-[2-(2- ⁇ 2-[2-(4-amino-3- methoxybenzenesulfonyl)ethoxy]ethoxy ⁇ ethoxy)ethyl]carbamate.
  • Step 5 The synthesis of tert-butyl N-(2- ⁇ 2-[2-(2- ⁇ 3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonyl ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)carbamate.
  • Step 6 The synthesis of tert-butyl N-(2- ⁇ 2-[2-(2- ⁇ 3-methoxy-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonyl ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)carbamate.
  • reaction mixture was stirred at room temperature for another 12 hrs. Then the mixture was purified by flash column to obtain tert-butyl N-(2-2-[2-(2-3-methoxy-4-[(3-4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l- yl)amino]benzenesulfonylethoxy)ethoxy]ethoxyethyl)carbamate (240.0 mg, 84.4% yield, 95.0% purity) as a yellow gum.
  • Example 15 Synthesis of 2- ⁇ 3- [(4- ⁇ 2- [2-(2-aminoethoxy)ethoxy] ethanesulfonyl ⁇ -2- methoxyphenyl)amino]prop-l-yn-l-yl ⁇ -N-(l-methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)- lH-indol-4-amine.
  • Step 1 The synthesis of 3-methoxy-4-nitrobenzene-l-thiol.
  • Step 2 The synthesis of tert- Nb-u[t2y-l(2- ⁇ 2-[(3-methoxy-4- nitrophenyl)sulfanyl]ethoxy ⁇ ethoxy)ethyl]carbamate.
  • Step 3 The synthesis of tert- Nb-u(t2y-l ⁇ 2-[2-(3-methoxy-4- nitrobenzenesulfonyl)ethoxy] ethoxy ⁇ ethyl)carbamate.
  • Step 4 The synthesis of tert-butyl N-(2- ⁇ 2-[2-(4-amino-3- methoxybenzenesulfonyl)ethoxy]ethoxy ⁇ ethyl)carbamate.
  • Step 6 The synthesis of tert-butyl N- ⁇ 2-[2-(2- ⁇ 3-methoxy-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonyl ⁇ ethoxy)ethoxy]ethyl ⁇ carbamate.
  • Reaction mixture was stirred at room temperature for another 12 hrs. Then the mixture was purified by flash column (Interchim, 40 g C18, water/acetonitrile (0-100%), flow rate: 70 ml/min, 20-25 CV) to obtain tert-butyl N-2- [2-(2-3-methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2- ylprop-2-yn-l-yl)amino]benzenesulfonylethoxy)ethoxy]ethylcarbamate (210.0 mg, 67.5% yield, 90.0% purity) as yellow gum.
  • Example 16 Synthesis of 2-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl ⁇ phenoxy)-N-(ll- ⁇ N-methyl-3-methoxy-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifluoroethyl)- lH-indol-2-yl ⁇ prop-2-yn- 1- yl)amino]benzenesulfonamido ⁇ undecyl)acetamide.
  • Step 1 The synthesis of tert-butyl N-(l l- ⁇ N-methyl-3-methoxy-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonamido ⁇ undecyl)carbamate.
  • Step 2 The synthesis ofN-(l l-aminoundecyl)-3-methoxy-N-methyl-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzene-l -sulfonamide hydrochloride.
  • Step 3 The synthesis of 2-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl ⁇ phenoxy)-N-(l l- ⁇ N-methyl-3-methoxy-4-[(3- ⁇ 4-[(l-methylpiperi din-4- yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonamido ⁇ undecyl)acetamide.
  • Example 17 Synthesis of 2-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl ⁇ phenoxy)-N- [ 1 l-(N-methyl-4- ⁇ [3-(4- ⁇ [(3S,4R)-3-fhioro-l- methylpiperidin-4-yl]amino ⁇ -l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino ⁇ - 3-methoxybenzenesulfonamido) undecyl] acetamide.
  • Step 1 The synthesis of tert-butyl N-(l l-hydroxyundecyl)carbamate.
  • 11- Aminoundecan-l-ol (6.0 g, 32.05 mmol) was dissolved in methanol (100 mL), then di-tert-butyl dicarbonate (7.34 g, 33.65 mmol, 7.74 ml) and sodium hydroxide (1.35 g, 33.65 mmol) were added. The solution was stirred until the reaction was completed. Then solvent was evaporated under reduced pressure and the resulting oil dissolved in chloroform (100 mL) and washed with water (3 x 50 mL). The organic phase was dried over Na2SO4 and the solvent removed under reduced pressure to give tert-butyl N-(l l-hydroxyundecyl)carbamate (8.7 g, 80.3% yield).
  • Step 2 The synthesis of tert-butyl N-[l l-(methanesulfonyloxy)undecyl]carbamate.
  • the reaction mixture was diluted with saturated solution of NaHCCh (50 mL) and extracted with ethyl acetate (3 x 50 mL). The organic layers were combined, washed with water (3 x 50 mL), brine (50 mL), dried over anhydrous Na2SO4, and fdtered. The collected fdtrate was concentrated under reduced pressure to afford the desired tert-butyl N-[l 1- (methanesulfonyloxy)undecyl]carbamate (10.0 g, 76.3% yield)
  • Step 3 The synthesis of tert-butyl N-[l l-(methylamino)undecyl]carbamate.
  • tert-butyl N-[ll-(methanesulfonyloxy)undecyl]carbamate (11.0 g, 30.12 mmol) in anhydrous MeOH (100 mL) methanamine (9.35 g, 301.18 mmol, 59.55 ml) was added at room temperature and the reaction mixture was left to stir at 60°C for 18 hrs. Then solvent was evaporated under reduced pressure, the resulting oil dissolved in EtOAc (100 mL) and washed with water (3 x 50 mL). The organic phase was dried overNa2SO4 and the solvent removed under reduced pressure to give tert-butyl N-[l l-(methylamino)undecyl] carbamate (9.0 g, 84.5% yield).
  • Step 4 The synthesis of tert-butyl N-[l l-(N-methyl-3-methoxy-4- nitrobenzenesulfonamido)undecyl]carbamate.
  • tert-butyl N-[l l- (methylamino)undecyl]carbamate 5.0 g, 90.0% purity, 14.98 mmol
  • anhydrous DCM 100 mL
  • triethylamine (2.27 g, 22.47 mmol, 3.13 ml) was added followed by 3 -methoxy-4-nitrobenzene-l -sulfonyl chloride (3.76 g, 14.98 mmol) at 0°C.
  • Step 5 The synthesis of tert-butyl N-[l l-(N-methyl-4-amino-3- methoxybenzenesulfonamido)undecyl]carbamate.
  • tert-butyl N-[l l-(N-methyl-3- methoxy-4-nitrobenzenesulfonamido)undecyl]carbamate 7.0 g, 13.57 mmol, 77.57 ml
  • 4-(pyridin-4-yl)pyridine 105.93 mg, 678.74 pmol
  • Step 6 The synthesis of tert-butyl N-(l l- ⁇ N-methyl-3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonamido ⁇ undecyl)carbamate.
  • reaction mixture was diluted with saturated solution of NH4CI (250 mL) and extracted with ethyl acetate (3 x 150 mL). The organic layers were combined, washed with water (3 x 150 mL), brine (150 mL), dried over anhydrous ISfeSCL and filtered.
  • Step 7 The synthesis of tert-butyl N- ⁇ 1 l-[N-methyl-4-( ⁇ 3-[4-bromo-l-(2,2,2- trifluoroethyl)-lH-indol-2-yl]prop-2-yn-l-yl ⁇ amino)-3- methoxybenzenesulfonamido]undecyl ⁇ carbamate.
  • Step 8 The synthesis of tert-butyl N-[l l-(N-methyl-4- ⁇ [3-(4- ⁇ [(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino ⁇ -l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino ⁇ -3- methoxybenzenesulfonamido)undecyl]carbamate.
  • Step 9 The synthesis ofN-(l l-aminoundecyl)-4- ⁇ [3-(4- ⁇ [(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino ⁇ -l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino ⁇ -3- methoxy-N-methylbenzene-1 -sulfonamide hydrochloride.
  • Step 10 The synthesis of2-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl ⁇ phenoxy)-N-[l l-(N-methyl-4- ⁇ [3-(4- ⁇ [(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino ⁇ -l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino ⁇ -3- methoxybenzenesulfonamido)undecyl]acetamide.
  • Example 18 Synthesis of 2-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl ⁇ phenoxy)-N- ⁇ 2- [2- (2- ⁇ 3-methoxy-4- [(3- ⁇ 4- [(l-methylpiperidin-4- yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl ⁇ prop-2-yn- 1- yl)amino]benzenesulfonyl ⁇ ethoxy)ethoxy] ethyl ⁇ acetamide.
  • Step 1 The synthesis of 2- ⁇ 3-[(4- ⁇ 2-[2-(2-aminoethoxy)ethoxy]ethanesulfonyl ⁇ -2- methoxyphenyl)amino]prop- 1 -yn- 1 -yl ⁇ -N-(l -methylpiperi din -4-yl)- 1 -(2,2, 2-tri fluoroethyl)- 1H- indol-4-amine tetrahydrochloride.
  • Step 2 The synthesis of 2-(3- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzo di azol-l-yl]methyl ⁇ phenoxy)-N- ⁇ 2-[2-(2- ⁇ 3-methoxy-4-[(3- ⁇ 4-[(l-methylpiperi din-4- yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonyl ⁇ ethoxy)ethoxy]ethyl ⁇ acetamide.
  • Step 1 The synthesis of rac-2-[3-(3,5-dimethyl-l,2-oxazol-4-yl)-5-[(R)- hydroxy(phenyl)methyl]phenoxy]-N-(2- ⁇ 2-[2-(2- ⁇ N-methyl-3-methoxy-4-[(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)acetamide.
  • Example 20 Synthesis of 2-(4- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl ⁇ phenoxy)-N-(2- ⁇ 2- [2-(2- ⁇ 4- [(3- ⁇ 4- [(l-methylpiperidin-4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl ⁇ prop-2-yn- 1- yl)amino]phenoxy ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)acetamide.
  • Step 1 The synthesis of 2-(4- ⁇ [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl ⁇ phenoxy)-N-(2- ⁇ 2-[2-(2- ⁇ 4-[(3- ⁇ 4-[(l-methylpiperidin-4-yl)amino]-l- (2,2,2-trifluoroethyl)-lH-indol-2-yl ⁇ prop-2-yn-l- yl)amino]phenoxy ⁇ ethoxy)ethoxy] ethoxy ⁇ ethyl)acetami de.
  • Example 21 Synthesis of 2-[3-( ⁇ [5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-methoxypyridin-3- yl] amino ⁇ methyl)phenoxy] -N- [2-(2- ⁇ 2- [2-(N-methyl-4- ⁇ [3-(4- ⁇ [(3S,4R)-3-fhioro- 1- methylpiperidin-4-yl]amino ⁇ -l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino ⁇ - 3-methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethoxy)ethyl]acetamide.
  • Step 1 A stirred solution of tert-butyl N-(2-2-[2-(2-N-methyl-3-methoxy-4-[(prop-2- yn-l-yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)carbamate (585.0 mg, 1.1 mmol) N- [(3 S,4R)-3 -fluoro- 1 -methylpiperi din-4-yl]-2-iodo- 1 -(2,2, 2-trifluoroethyl)- lH-indol-4- amine (419.13 mg, 920.69 pmol) in THF (9 mL), and EbN (9 mL) was prepared.
  • Tetrakis(triphenylphosphane) palladium (212.54 mg, 184.14 pmol) and copper(I) iodide (17.48 mg, 92.07 pmol) were added dropwise at room temperature under an argon atmosphere. The reaction mixture was stirred at room temperature for 12 hours.
  • Step 2 A stirred solution of tert-butyl N-[2-(2-2-[2-(N-methyl-4-[3-(4-[(3S,4R)-3- fluoro-1 -methylpiperi din -4-yl]amino-l -(2,2, 2-tri fluoroethyl)-lH-indol-2-yl)prop-2-yn-l - yl]amino-3-methoxybenzenesulfonamido)ethoxy]ethoxyethoxy)ethyl]carbamate (170.0 mg, 198.37 pmol) in MeOH (0.2 ml) and dioxane/hcl(0.2 ml) at the room temperature.
  • Step 3 A solution of N-(2-2-[2-(2-aminoethoxy)ethoxy]ethoxyethyl)-4-[3-(4- [(3 S,4R)-3 -fluoro- 1 -methylpiperidin-4-yl] amino- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2- yn-l-yl]amino-3-methoxy-N-methylbenzene-l-sulfonamide (88.3 mg, 116.67 pmol), [(dimethylamino)(3H-[l,2,3]triazolo[4,5-b]pyridin-3-yloxy)methylidene]dimethylazanium hexafhrorophosphamiide (57.68 mg, 151.75 pmol), 2-[3-([5-(3,5-dimethyl-l,2-oxazol-4-
  • Example 22 Synthesis of 2- ⁇ [6-( ⁇ [5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2- dihydropyridin-3-yl] amino ⁇ methyl)pyridin-2-yl] oxy ⁇ -N- [2-(2- ⁇ 2- [2-(N-methyl-4- ⁇ [3- (4- ⁇ [(3S,4R)-3-fluoro- l-methylpiperidin-4-yl] amino ⁇ - l-(2,2,2-trifluoroethyl)- lH-indol-2- yl)prop-2-yn- 1-yl] amino ⁇ -3- methoxybenzenesulfonamido)ethoxy]ethoxy ⁇ ethoxy)ethyl]acetamide.
  • Step 1 A stirred solution of tert-butyl N-(2-2-[2-(2-N-methyl-3-methoxy-4-[(prop-2- yn-l-yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)carbamate (585.0 mg, 1.1 mmol), N-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]-2-iodo-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine (419.13 mg, 920.69 pmol) in THF (9 mL), and EbN (9 mL) was prepared.
  • Tetrakis(triphenylphosphane) palladium (212.54 mg, 184.14 pmol) and copper(I) iodide (17.48 mg, 92.07 pmol) were added dropwise at room temperature under an argon atmosphere. The reaction mixture was stirred at room temperature for 12 hours.
  • Step 2 A stirred solution of tert-butyl N-[2-(2-2-[2-(N-methyl-4-[3-(4-[(3S,4R)-3- fluoro-l-methylpiperidin-4-yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l- yl]amino-3-methoxybenzenesulfonamido)ethoxy]ethoxyethoxy)ethyl]carbamate (170.0 mg, 198.37 pmol) in MeOH (0.2 ml) and dioxane/HCL(0.2 ml) at the room temperature.
  • Step 3 A solution of N-(2-2-[2-(2-aminoethoxy)ethoxy]ethoxyethyl)-4-[3-(4- [(3 S,4R)-3 -fluoro- 1 -methylpiperidin-4-yl] amino- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2- yn-l-yl]amino-3-methoxy-N-methylbenzene-l-sulfonamide (48.0 mg, 63.42 pmol), [(dimethylamino)(3H-[l,2,3]triazolo[4,5-b]pyridin-3-yloxy)methylidene]dimethylazanium hexafluorophosphamiide (31.32 mg, 82.39 pmol), 2-[6-([5-(3,5-dimethyl-l,2-oxazol-4-yl)-2
  • Example 23 Synthesis of 2-[3-( ⁇ [5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin- 3-y 1 ] amino ⁇ methyl)phenoxy] -N-(2- ⁇ 2- [2-(2- ⁇ N-methyl-3-methoxy-4- [(3- ⁇ 4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl ⁇ prop-2-yn- 1- yl)amino]benzenesulfonamido ⁇ ethoxy)ethoxy]ethoxy ⁇ ethyl)acetamide.
  • Step 1 A solution of the N-(2-2-[2-(2-aminoethoxy)ethoxy]ethoxyethyl)-3-methoxy- N-methyl-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2- yn-l-yl)amino]benzene-l -sulfonamide (30.0 mg, 40.6 pmol), the 2-[3-([5-(3,5-dimethyl-l,2- oxazol-4-yl)-2-oxo-l,2-dihydropyridin-3-yl]aminomethyl)phenoxy]acetic acid (15.01 mg, 40.63 pmol), the [(dimethylamino)(3H-[l,2,3]triazolo[4,5-b]pyridin-3- yloxy)methyliden
  • Example 24 Synthesis of tert- butyl 3-[2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]propanoate.
  • Step 1 The synthesis of 2-methoxy-4-[(4-methoxyphenyl)methylsulfanyl]-l-nitro- benzene.
  • compound 1 4-fluoro-2-methoxy-l -nitro-benzene (compound 1, 10.0 g, 58.4 mmol) and (4-methoxyphenyl)methanethiol (9.91 g, 64.3 mmol) in DMF (100 mL) K2CO3 (16.15 g, 116.9 mmol) was added . The mixture was stirred at 60 °C for 12 hrs.
  • Step 2 The synthesis of 3-methoxy-4-nitro-benzenesulfonyl chloride.
  • 2-methoxy-4-[(4-methoxyphenyl)methylsulfanyl]-l-nitro-benzene (8 g, 26.2 mmol) in MeCN (72 mL)
  • AcOH (6 mL)
  • H2O (2 mL)
  • l,3-dichloro-5,5-dimethyl-imidazolidine-2, 4-dione (10.32 g, 52.4 mmol) was added. The mixture was stirred at 0 °C for Ih.
  • Step 3 The synthesis of tert 3--b[u2t-y[2l -[2-[(3-methoxy-4-nitro-phenyl)sulfonyl- methylamino]ethoxy]ethoxy]ethoxy]propanoate.
  • Step 4 The synthesis of tert 3--b[u2t-y[2l -[2-[(3-methoxy-4-nitro-phenyl)sulfonyl- methylamino] ethoxy] ethoxy] ethoxy ]propanoate.
  • Step 5 The synthesis of tert 3--b[u2t-y[2l -[2-[(4-amino-3-methoxy-phenyl)sulfonyl- methylamino] ethoxy] ethoxy] ethoxy ]propanoate.
  • tert-but 3y-l To a suspension of Pd/C (300 mg, 10% purity) in MeOH (20 mL), tert-but 3y-l [2-[2-[2-[(3-methoxy-4-nitro-phenyl)sulfonyl- methylamino] ethoxy] ethoxy] ethoxy ]propanoate (3 g, 5.92 mmol) was added under nitrogen atmosphere.
  • Step 6 The synthesis of tert-butyl 3-[2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]propanoate.
  • Example 25 Synthesis of tert- butyl N-[2-[2-[2-[2-[2-[[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]ethyl]carbamate.
  • Step 2 The synthesis of tert-butyl /V-[2-[2-[2-[2-[2-[2-[2-[2- (methylamino)ethoxy] ethoxy] ethoxy]ethyl]carbamate.
  • tert-butyl N- [2- [2- [2- [2- [2- [2- [2- [2- [2- [2- [2- [2- [2- [2- [2- [benzyl(methyl)amino]ethoxy]ethoxy]ethoxy]ethyl]carbamate (2.1 g, 4.77 mmol) was added.
  • Step 3 The synthesis of tert-butyl N-[2-[2-[2-[2-[(3-methoxy-4-nitro- phenyl)sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]ethyl]carbamate.
  • Step 4 The synthesis of tert-butyl JV-[2-[2-[2-[2-[(4-amino-3-methoxy- phenyl)sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]ethyl]carbamate.
  • Step 5 The synthesis of tert-butyl N-[2-[2-[2-[2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]ethyl]carbamate.
  • Example 26 Synthesis of tert- butyl N-[8-[[3-methoxy-4-(prop-2-ynylamino)phenyl]sulfonyl- methyl-amino] octyl] carbamate.
  • Step 1 The synthesis of tert-butyl A-[8-(methylamino)octyl]carbamate.
  • a solution of tert-butyl A-(8-bromooctyl)carbamate (3.0 g, 9.73 mmol) and methanamine (2 M, 29.20 mL) in THF (5 mL) was stirred at 60 °C for 12 hours in a 30 mL sealed tube.
  • the mixture was concentrated in vacuo to give tert-butyl TV- [8- (methylamino)octyl]carbamate (2.4 g) as a white solid, which was used into the next step without further purification.
  • Step 2 The synthesis of N-[8-[(3-methoxy-4-nitro-phenyl)sulfonyl-methyl- amino]octyl]carbamate.
  • Step 3 The synthesis of tert-butyl N-[8-[(4-amino-3-methoxy-phenyl)sulfonyl- methyl-amino]octyl]carbamate.
  • a suspension of Pd/C 100 mg, 2.11 mmol, 10% purity
  • MeOH MeOH
  • tert-butyl N-[8-[(3-methoxy-4- nitro-phenyl)sulfonyl- methyl-amino]octyl]carbamate (1 g, 2.11 mmol) was added.
  • Step 4 The synthesis of tert-butyl A-[8-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonyl-methyl-amino]octyl]carbamate.
  • Example 27 Synthesis of tert- butyl N-[2-[2- [2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl] sulfonylamino] ethoxy] ethoxy] ethyl] carbamate.
  • Step 1 The synthesis of A-[2-[2-[2-[(3-methoxy-4- nitrophenyl)sulfonylamino]ethoxy] ethoxy]ethoxy]ethyl]carbamate.
  • Step 2 The synthesis of tert-butyl A-[2-[2-[2-[2-[2-(tert- butoxycarbonylamino)ethoxy] ethoxy] ethoxy ] ethyl] -N-(3 -methoxy-4-ni trophenyl)sulfonyl- carbamate.
  • Step 3 The synthesis of tert A-b-(u4ty-almino-3-methoxy-phenyl)sulfonyl-A-[2-[2- [2-[2-(tertbutoxycarbonylamino)ethoxy]ethoxy]ethyl]carbamate.
  • Step 4 The synthesis of tert- Ab-u[t2y-l[2-[2-[2-(tert- butoxycarbonylamino)ethoxy] ethoxy] ethoxy ] ethyl] -N- [3 -methoxy-4-(prop2- ynylamino)phenyl]sulfonyl-carbamate.
  • a mixture of A-(4t-eartm-binuoty-3l -methoxy - phenyl (sulfonyl -A- [2- [2- [2- [2- [2-(tertbutoxycarbonylamino)ethoxy]ethoxy] ethoxy ] ethyl] carbamate (1.3 g, 2.25 mmol), 3 -bromoprop- 1-yne (435 mg, 2.93 mmol), K2CO3 (622 mg, 4.50 mmol), and KI (75 mg, 450 pmol) in DMF (5 mL) was degassed, purged with N2 3 times, and stirred under nitrogen atmosphere at 80 °C for 12 hrs.
  • Step 5 The synthesis of tert- Ab-u [t2y-l [2- [2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonylamino]ethoxy]ethoxy]ethyl]carbamate.
  • Example 28 Cell viability assays showing bifunctional molecule induced cell death
  • OmniTAC compounds are created that include targeting ligands for p53 and recruiting ligands for proteins capable of modulating p53 activity. Linkers connect the targeting and recruiting ligands. A screening of the compounds determines the best binders to certain modifier proteins and p53 using a cell viability assay. Cell viability in p53 WT, p53 mutant and/or p53 null cell lines is compared. The compounds are then tested in vitro. Cells are cultured at 37 °C at proper humidity levels. A control group is created that only contains cells and vehicle treatment. A treatment group with OmniTAC is tested, and compared to the control group.
  • Selected OmniTAC compounds are added to the treated cells at various concentrations, for example, 250 nM, 500 nM, and 1,000 nM.
  • the compounds are incubated with the cells for various time intervals such as 24, 48, and 72 hours. Following incubation, cell viability is measured by monitoring luminescence.
  • NUGC3 500 cells per well
  • NUGC3 Y220C KO cells 375 cells per well
  • BFMs 50 pL media per well
  • Cell viability was measured through measuring the amount of available ATP via luciferase activity as detailed in the Promega’s CellTiter GioTM protocol: 25 pL of 20% solution of Promega’s Cell Titer Gio 2.0 (CTG) reagent in PBS was added to each well. Plates with cells and CTG reagent were placed on orbital shaker for 15-30 min and luminescence was recorded for each well (0.3s integration time).
  • CTG Cell Titer Gio 2.0
  • Table 6 Summary of the Effects of OmniTAC treatment on the Viability of NUGC3 and NUGC3 p53 Y220C KO Cells. IC50 indicates the concentration of compound at which 50% of maximum of cell viability is observed. a 3 -day viability instead of 5 -day b H1299 Y220C cells were used instead of NUGC-3 c Hl 299 cells were used instead of NUGC-3 KO d NUGC-4 cells were used instead of NUGC-3 KO
  • OmniTAC compounds are created that include targeting ligands for p53 and recruiting ligands for proteins capable of modulating p53 activity. Linkers connect the targeting and recruiting ligands. A screening of the compounds determines the best binders to certain modifier proteins and p53 using ternary complex formation assay. Cells are cultured at 37 °C and proper humidity levels. A control group is created using a reference compound, here compound 1.
  • H1299 cells stably expressing SmBiT-p53 Y220C and LgBiT-BRD4 were plated in each well of 384 well plate using phenol red-free OPTI-MEM media (30 pL per well).
  • Tested compounds, reference compound 1 and DMSO control were added to cells using Tecan D300e compound printer (12 concentration in triplicates, two-fold dilution from 20 or 10 pM highest concentration). Cells were incubated with compounds for 3 h, then plates were cooled to room temperature over 15 min. Furimazine was added (50 pM final concentration) and luminescence was read immediately in kinetics mode until signal reached its maximum value.
  • Table 7 Summary of the ternary complex formation results in cell lysate.
  • TC50 indicates the concentration of compound at which 50% of maximum luminescence is observed;
  • TC max indicates the percentage of maximum luminescence compared to reference compound 1.
  • OmniTAC compounds are created that include targeting ligands for p53 and recruiting ligands for proteins capable of modulating p53 activity. Linkers connect the targeting and recruiting ligands. A screening of the compounds determines the best binders to certain modifier proteins and p53 using ternary complex formation assay. Cells are cultured at 37 °C and proper humidity levels. A control group is created using a reference compound, here reference compound 1.
  • H1299 cells stably expressing SmBiT-p53 Y220C and LgBiT-BRD4 were harvested from confluent T175 flask and lysed by sonication in 50 mM HEPES buffer supplemented with 200 mM KC1 and protease/phosphatase inhibitor cocktail. Lysate was separated from cell debris using centrifugation at 15 000 rpm for 15 min (4 °C). Cell lysate concentration was measured using PierceTM BCA Protein Assay Kits and concentration of proteins adjusted to 0.5 pg/pL. 20 pL of cell lysate was added to each well of 384 well plates.
  • Tested compounds, reference compound 1 and DMSO control were added to lysate using Tecan D300e compound printer (12 concentration in triplicates, two-fold dilution from 20 or 10 pM highest concentration). Cell lysate was incubated with compounds for 15 min at room temperature, furimazine was added (50 pM final concentration) and luminescence was read immediately in kinetics mode until signal reached its maximum value. Signal was normalized by DMSO and maximum luminescence observed in this experiment with reference compound. TCso and TCmax values were obtained after removal of points at higher doses and automatic fitting of remaining data using “[inhibitor] vs response - variable slope (four parameters)” method using GraphPad PRISM 10 software. Results are shown in FIG. 5 and Table 8.
  • Table 8 Summary of the ternary complex formation results in cells. TCso indicates the concentration of compound at which 50% of maximum luminescence is observed; TC max indicates the percentage of maximum luminescence compared to reference compound 1.

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Abstract

Provided are heterobifunctional compounds, pharmaceutical compositions, and methods of treating disease, such as cancer.

Description

TARGETED PROTEIN MODIFICATION
CROSS-REFERENCE
[0001] This application claims the benefit of U.S. Provisional Application Serial No. 63/560,123 filed March 1, 2024, which is hereby incorporated by reference in its entirety.
BACKGROUND
[0002] A need exists for compounds that, when used, result in the modification of a protein. A need exists in the medicinal arts for selective modification of target proteins.
SUMMARY
[0003] Provided herein is a modifier protein targeting chimeric (OmniTAC) compound which targets the transcription factor p53, comprising a targeting ligand, a recruiting ligand, and a linker, wherein the targeting ligand is attached to the recruiting ligand via the linker; wherein the targeting ligand is configured to bind to target protein, wherein the target protein is a wild-type (WT) or a mutant p53, and the recruiting ligand is configured to bind to a modifier protein such that the modifier protein induces a change to the WT or mutant p53; and wherein the modifier protein comprises a non-degradative protein that activates, stabilizes, and/or corrects misfolding of the target protein.
[0004] Described herein is a platform for modifying a target protein. In some embodiments, modifying the target protein can include activating or reactivating a target protein. In some embodiments, the platform may include compounds such as modifier protein targeting chimeric (OmniTAC) compounds, methods of their preparation, and methods of using them.
[0005] In one aspect, described herein is a modifier protein targeting chimeric (OmniTAC) compound which targets a transcription factor p53, comprising a targeting ligand, a recruiting ligand, and a linker, wherein the targeting ligand is attached to the recruiting ligand via the linker; wherein the targeting ligand is configured to bind to a target protein, wherein the target protein is a wild-type (WT) p53 or a mutant p53, and the recruiting ligand is configured to bind to a modifier protein such that the modifier protein induces a change to the WT p53 or mutant p53; and wherein the modifier protein comprises a non-degradative protein that activates, stabilizes, and/or corrects misfolding of the target protein.
[0006] In some embodiments, the modifier protein targeting chimeric (OmniTAC) compound has a structure of Formula (I): wherein:
R1 is the targeting ligand with a structure of Formula (II):
R2 is a recruiting ligand;
L is a linker with the following structure: -(AP)m-L1A-L1B-(AP)m-;
AP is PEG, ether, amide, sulfonamide, sulfone, sulfoxide, sulfonate, phosphonate, ester, urea, carbamate, substituted phosphine oxide, optionally substituted C1-6 alkyl, optionally substituted C3-12 cycloalkyl, optionally substituted 3- to 12- membered heterocycloalkyl, optionally substituted 3- to 12- membered heteroaryl, or optionally substituted Ce-12 aryl;
L1A and L1B are each independently polyethylene glycol (PEG), C1-50 alkylene-PEG, C2-50 alkenylene-PEG, C2-50 alkynylene-PEG, C1-50 alkylene, C2-50 alkenylene, C2-50 alkynylene, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, C6-12 aryl, 3- to 12- membered heteroaryl, 3- to 12- membered heterocycloalkyl-C1-10 alkylene, 3- to 12- membered heterocycloalkyl-PEG, or PEG-3- to 12- membered heterocycloalkyl-PEG, spirocyclic cores, or a combination thereof, each of which may be substituted with one or more halogen, deuterium, methyl, deuterated methyl, trifluoromethyl, amide, sulfonamide, sulfone, ester, urea, carbamate, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, C6-12 aryl, or 3- to 12- membered heteroaryl;
RA is C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl or 3- to 12- membered heteroaryl;
Y1, Y2, Y3, Y4, Y5, and Y6 are each independently CH, C, NH, N, NO, S, SO, or absent, wherein at least two of Y1, Y2, Y3 and Y4 is CH, C, NH, N, NO, S, or SO, and wherein at least one of Y5 and Y6 is CH, C, NH, N, NO, S, or SO;
Y7 and Y8 are each independently C or N;
R1A is a cysteine reactive group, C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, -SOR1A1, or -COR1A1, wherein the C1-6 alkyl and C3 -12 cycloalkyl is optionally substituted with -CN, halogen, or C1-6 alkylamines;
R1B is deuterium, halogen, -CN, -OH, -OC1-6 alkyl, -OC1-6 haloalkyl, -NH2, NHC1-6 alkyl, -N(C1-6 alkyl)2, -NHCOMe, -OCOMe, -OCONR1BAR1BB, C1-6 alkyl, -COOR1BB, -CONR1BAR1BB, - NR1BACOR1BB, _N02, _NRIBSO25 -SO2(C1-6alkyl), -SO2NR1BAR1BB, -SO2NH-heteroaryl, or two R1G taken together form an aryl or heteroaryl ring;
R1BA is hydrogen or C1-6 alkyl; R1BB is hydrogen, -COC1-6 alkyl, C1-6alkyl, C6-12 aryl, 3- to 12- membered heteroaryl;
R1C is deuterium, halogen, -OH, -OC1-6 alkyl, -OC1-6 haloalkyl, -NH2, NHC1-6 alkyl, - N(C1-6 alkyl)2, -NO2, -NHCOMe, or -OCOMe;
R1D is hydrogen or C1-6 alkyl;
R1E is C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, or 3- to 12- membered heteroaryl, wherein the C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, C6-12 aryl, and 3- to 12- membered heteroaryl are optionally substituted with halogen, C1-6 alkyl, C1-6 alkoxy, C1-6 carboxylic acid, -NH2, or -N(C1-6alkyl)2; or R1D and R1E combine with the carbon to which is attached to form a cyclic structure, wherein the cyclic structure is C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, C6-12 aryl, and 3- to 12- membered heteroaryl, wherein the cyclic structure is optionally substituted with one or more R1DE;
R1DE is deuterium, halogen, -CN, -OH, -NH2, -NH(C1-6 alkyl), -NH(C1-6 haloalkyl), - N(C1-6 alkyl )2, -OC1-6 alkyl, -OC1-6 haloalkyl, C1-6 alkyl, C1-6 alkoxy, C1-6 haloalkyl, C1-6 haloalkoxy, -NHCO(C 1-6 haloalkyl), -CO2(C 1-6 alkyl), -CONH(C 1-6 alkyl), -SO2NH(C1-6 alkyl), - SO2N(C1-6 alkyl)2, -SO2(C1-6 alkyl), or -SO2NMe(C1-6 alkyl);
R1F is hydrogen or C1-6 alkyl; m is 0 or 1; n is 0 to 5; o is 0 or 1; and wherein an atom on one of R1B, R1DE, or R1E or the cyclic structure of R1D and R1E is covalently linked to L.
[0007] In some embodiments, the compound of Formula (I) has the structure of Formula (II- A): wherein:
RB is 3- to 12- membered heterocycloalkyl;
R1DE is deuterium, halogen, -OH, -OMe, -OCF3, -NH2, -NH(C1-6alkyl), or -N(C1-6alkyl)2; and p is 0 to 5. [0008] In some embodiments, the compound of Formula (II- A) has the structure of Formula (II-B): wherein:
X1, X2, X3, and X4 are each independently C, CH, NH, N, NO, S, SO or absent, wherein at least two of X1, X2, X3, and X4 are C, CH, NH, N, NO, S, or SO; and p is 1 to 3.
[0009] In some embodiments, the compound of Formula (II- A) has the structure of Formula
(III- A) or Formula (III-B):
[0010] In some embodiments, the compound of Formula (III- A) or Formula (III-B) has the structure of Formula (III-A1) or Formula (III-B1):
wherein:
B is a absent, -NH-, -0-, CO, amide, C1-6 alkylene, C2-6 alkenylene, or C2-6 alkynylene, wherein the C1-6 alkylene, C2-6 alkenylene, and C2-6 alkynylene is optionally substituted with deuterium, halogen, or C1-3 alkoxy;
W1 and W2 are each independently NH, N, O, or S;
Rc and RD are each independently optionally substituted C3-12 cycloalkyl, optionally substituted 3- to 12- membered heterocycloalkyl, optionally substituted C6-12 aryl or optionally substituted 3- to 12- membered heteroaryl; and
R1H and R11 are each independently hydrogen or C1-6 alkyl, wherein the C1-6 alkyl is optionally substituted with deuterium or halogen.
[0011] In some embodiments, the compound of Formula (III-A1) or Formula (III-B1) has the structure of Formula (III-A2) or Formula (III-B2):
(III-A2) or
(III-B2) wherein:
X1, X2, X3, and X4 are each independently C, CH, NH, N, NO, S, SO or absent, and wherein at least two of X1, X2, X3, and X4 is C, CH, NH, N, NO, S, SO.
[0012] In some embodiments, the compound of Formula (III-A1) or Formula (III-B1) has the structure of Formula (IV-A), Formula (IV-B), Formula (IV-C), or Formula (IV-D):
[0013] In some embodiments, the compound of Formula (IV-A), Formula (IV-B), Formula
(IV-C), or Formula (IV-D) has the structure of Formula (IV-A1), Formula (IV-B1), Formula (IV- Cl), or Formula (IV-D1):
Bl),
X1, X2, X3, and X4 are each independently CH, N, NO, S, SO or absent, and wherein at least two of X1, X2, X3, and X4 is CH, N, NO, S, SO;
R1B, R1C, and R1L are each independently halogen, -OH, -NH2, -NH(C1-6 alkyl), -NH(C1-6 alkyl)2, -OC1-6 alkyl, -OCH3, -OCF3, -NO2, -NHAc, or -OAc;
R1DE is halogen, deuterium, hydroxyl, trifluoromethoxy, or amine; or wherein when R1DE is in (R1DE)p-i, then R1DE is deuterium, halogen, -CN, -OH, -NH2, - NH(C 1-6 alkyl), -NH(C1-6haloalkyl), -OC1-6 alkyl, -OC1-6 haloalkyl, C1-6 alkyl, C1-6 haloalkyl, - NHCO(C1-6 haloalkyl), -CO2(C1-6 alkyl), -CONH(C1-6 alkyl), -SO2NH(C1-6 alkyl), -SO2N(C1-6 alkyl)2, -SO2(C 1-6 alkyl), or -SO2NMe(C1-6 alkyl); and q is 0 to 5.
[0014] In some embodiments, the compound of Formula (III- A) or Formula (III-B) has the structure of Formula (IV-A2) or Formula (IV-C2):
[0015] In some embodiments, the modifier protein targeting chimeric (OmniTAC) compound has the structure of Formula V:
R1 - L - Y1
(V) or a pharmaceutically acceptable salt thereof; wherein:
R1 is one of the following:
• -(phenyl substituted with 0 or 1 C1-4 alkoxyl, 0 or 1 C1-4 deuteroalkoxyl, and 0, 1, or 2 occurrences of halo, hydroxyl, -S(O)2(C1-6 alkyl), or C1-4 alkyl)-N(R2)-(C2-4 alkynylene)-(indolyl substituted with C1-4haloalkyl and 0 or 1 -N(R3)-(3-6 membered saturated heterocyclyl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclyl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); or
• -(3-6 membered saturated heterocyclylene containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R2)-(indolyl substituted with C1-4haloalkyl and 0 or 1 -N(R3)-(C2-4alkynylene)-N(R2)-(phenyl substituted with 0 or 1 C1-4alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl or -S(O)2-( C1-4 alkyl));
R2, R3, R4 and independently hydrogen or C1-4 alkyl);
Y1 is one of the following:
• -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -( C1-4 alkylene)-(3-7 membered heterocyclyl))-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -( C1-4 alkylene)-(3-7 membered heterocyclyl))-(5- membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(imidazo[4,5-b]pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -( C1-4 alkylene)-(3-7 membered heterocyclyl))- (5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)- (pyridinylene substituted with C1-4alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl, and 5-membered heteroaryl)- (C1-6 alkylene substituted by 1 or 2 hydroxyl)-(phenyl or pyridinyl substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl), wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(pyridin-2- onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)- (5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); or
• -(phenylene or pyridinylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)-(pyridin-2-onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(O)-(pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, or 5- membered heteroaryl, wherein the 5 -membered heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R4)-(C1-6 alkylene)-(phenyl or pyridinyl substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl)-(5-10 membered heteroaryl substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and 5 -membered heteroaryl, wherein the 5- membered heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene, wherein the C1-6 alkylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of C1-4 alkyl and 6-membered heteroaryl); and
L is a bivalent, saturated or unsaturated, straight or branched Ci-60 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -S-, - N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O)2-, -N(H)S(O)2-, -N(C1-6 alkyl)S(O)2-, -S(O)2N(H)-, -S(O)2N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, - C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6 alkyl)-, -N(H)C(O)O-, -N(C1-6 alkyl)C(O)O-, - N(C3-6 cycloalkyl)-, -C(H)(C3-6 cycloalkyl)-, optionally substituted 3-10 membered carbocyclyl, or optionally substituted 3-11 membered heterocyclyl containing 1, 2, 3, or 4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
[0016] In some embodiments, the modifier protein targeting chimeric (OmniTAC) compound has the structure of Formula VI:
R1 - L - Y1
(VI) or a pharmaceutically acceptable salt thereof; wherein:
R1 is -(phenyl substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-N(R2)-(C2-4alkynylene)-(indolyl substituted with C1-4haloalkyl and -N(R3)-(3-6 membered saturated heterocyclyl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclyl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
R2, R3, R4 and independently hydrogen or C1-4 alkyl);
Y1 is one of the following:
• -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); or • -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(Ci-6 alkylene)-N(R4)- (pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); and
L is a bivalent, saturated or unsaturated, straight or branched Ci-60 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -S-, - N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O)2-, -N(H)S(O)2-, -N(C1-6 alkyl)S(O)2-, -S(O)2N(H)-, -S(O)2N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, - C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6 alkyl)-, -N(H)C(O)O-, -N(C1-6 alkyl)C(O)O-, - N(C3-6 cycloalkyl)-, -C(H)(C3-6 cycloalkyl)-, optionally substituted 3-10 membered carbocyclyl, or optionally substituted 3-11 membered heterocyclyl containing 1, 2, 3, or 4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
BRIEF DESCRIPTION OF THE DRAWINGS
[0017] FIG. 1 illustrates a non-limiting list of modifier proteins and associated ligands that can be used to design recruiting ligands, organized by mechanism of action.
[0018] FIG. 2 illustrates a non-limiting list of modifier proteins and references for associated ligands that can be used to design recruiting ligands, organized by mechanism of action.
[0019] FIG. 3 illustrates effects of OmniTAC treatment on the viability of NUGC3 and NUGC3 p53 Y220C KO cells.
[0020] FIG. 4 illustrates ternary complex formation between the target protein, p53 Y220C, and the modifier protein, in lysate.
[0021] FIG. 5 illustrates ternary complex formation between the target protein, p53 Y220C, and the modifier protein, in live cells.
DETAILED DESCRIPTION
[0022] Disclosed herein is a platform which may be useful for modifying a target protein. Modifying the target protein can include activating or reactivating a target protein. The platform may include compounds such as modifier protein targeting chimeric (OmniTAC) compounds, methods of their preparation, and methods of using them.
[0023] TP53 is the most frequently mutated gene in cancer, with mutations identified in at least half of all human cancers. Widely known as the “Guardian of the Genome”, TP53 is a crucial tumor suppressor. One might expect mutations in the TP53 gene to result in loss of WTp53 function, as seen with other tumor suppressor genes. Strikingly, most of the cancer- associated TP53 mutations lead to the production of full-length p53 protein with only a single amino acid change. This mutant accumulates in tumor cells at levels much higher than in normal cells, contrary to the common loss of function modality. Despite 40 years of research on this gene and over 130,000 studies, there has been no clinical success against this pivotal target.
Accumulated mutant p53 is only present in cancer cells, representing a unique therapeutic opportunity to develop a first-in-class, selective therapy against a target that is present in half of all cancers. Compounds of the present disclosure can provide this precise selectivity using a targeted protein modification approach.
[0024] Compounds of the present disclosure are capable of providing selective, targeted protein modifications. Current drug approaches to therapeutics generally involve using small molecules, biologies, and/or genetic therapies to modify a biological target of interest, e.g., a protein target. Such approaches are limited in that small molecules generally have a small range of method of action and may not be catalytic; and biologic or genetic therapies may have poor oral bioavailability and cell permeability, making targeting of intracellular proteins challenging. The compounds of the present disclosure advantageously bring a target protein in proximity with a modifier protein, which provides a modification to the target protein to exert a therapeutic effect. This approach leverages the protein modification capabilities of existing modifier proteins and desired properties of small molecules to induce changes in disease-associated target proteins in vivo, enabling the development of highly specific and potent drugs.
I. OmniTAC compounds
[0025] Provided herein, in some embodiments, are compounds and pharmaceutical compositions comprising said compounds. In some embodiments a compound described herein comprises a targeting ligand, a linker, and a recruiting ligand. In some embodiments a compound described herein comprises a targeting ligand, a linker, and a recruiting ligand, connected via attachment points. The compound may comprise or consist of a modifier protein targeting chimeric (OmniTAC) compound.
[0026] Disclosed herein, in some embodiments, are OmniTAC compounds. The OmniTAC compound may comprise a heterobifunctional compound (BFM). The OmniTAC compound may include a targeting ligand. The OmniTAC compound may include a recruiting ligand. The OmniTAC compound may include a linker. The linker may attach the targeting ligand to the recruiting ligand. The linker may attach the targeting ligand to the recruiting ligand via an attachment point. Some embodiments include a modifier protein targeting chimeric (OmniTAC) compound comprising a targeting ligand, a recruiting ligand, and a linker; wherein the targeting ligand is attached to the recruiting ligand via the linker. Some embodiments include a modifier protein targeting chimeric (OmniTAC) compound comprising a targeting ligand, a recruiting ligand, and a linker; wherein the targeting ligand is attached to the recruiting ligand via the linker through an attachment point.
A. Compounds of Formula I
[0027] In some embodiments, the compound has a structure of Formula I: wherein R1 is the targeting ligand; L is the linker; and R2 is the recruiting ligand. As used throughout the present disclosure, “R1”, “targeting ligand”, and “TL” are used interchangeably; “L” and “linker” are used interchangeably; and “R2”, “recruiting ligand”, and “RL” are used interchangeably.
[0028] In some embodiments, the compound has a structure of Formula IA1 :
R1— L— R2 (IA1), wherein R1 is ligand that binds a target protein; L is the linker; and R2 is a ligand that binds an effector protein.
[0029] In some embodiments, the compound has a structure of Formula IA2:
RJ(p53)— L— R2(BRD) (IA2), wherein R\p53) is ligand that binds WT, mutant, truncated or full length p53; L is the linker; and R2(BRD) is a ligand that binds to a bromodomain.
[0030] In some embodiments, the compound includes some aspect of a natural or organic compound. In some embodiments, the compound is synthetic. In some embodiments, the compound is engineered. The compound may be purified. In some embodiments, the compound is substantially pure. As used herein, “substantially pure” means that the compound is substantially separated or isolated from contaminants or impurities. In some embodiments, a substantially pure compound comprises less than 10%, less than 5%, less than 2%, less than 1%, less than 0.5%, or less than 0.1% by weight of impurities.
[0031] In some embodiments, the compound comprises or consists of a small molecule. An example of a small molecule includes an organic compound having a molecular weight of less than 900 daltons. The compound may have a molecular weight below 2500 daltons, below 2250 daltons, below 2000 daltons, below 1750 daltons, below 1500 daltons, or below 1250 daltons. The compound may have a molecular weight below 1000 daltons, below 900 daltons, below 800 daltons, below 700 daltons, below 600 daltons, or below 500 daltons. The compound may have a molecular weight greater than 2500 daltons, greater than 2250 daltons, greater than 2000 daltons, greater than 1750 daltons, greater than 1500 daltons, or greater than 1250 daltons. The compound may have a molecular weight greater than 1000 daltons, greater than 900 daltons, greater than 800 daltons, greater than 700 daltons, greater than 600 daltons, or greater than 500 daltons. [0032] The compound may be included in a pharmaceutical composition. The compound may be administered to a subject. The compound may be included in the method described herein. For example, the compound may be used in a protein modification method or in a treatment method. Some embodiments include a method of making a compound disclosed herein.
B. Targeting ligands and target proteins
[0033] Disclosed herein, in some embodiments, are targeting ligands. The targeting ligand may include a ligand of a protein such as a target protein. The targeting ligand may be configured to bind to a target protein. The targeting ligand may bind the target protein. The targeting ligand may include a moiety that binds the target protein. The targeting ligand may be a part of a heterobifunctional compound such as an OmniTAC compound. The targeting ligand may connect to a linker or recruiting ligand. In some embodiments, the targeting ligand is incorporated into an in vivo engineered protein.
[0034] The targeting ligand may include a small molecule. In some embodiments, the targeting ligand comprises a small molecule moiety. In some embodiments, the targeting ligand has a molecular weight of 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, or 2500 daltons, or a range defined by any two of the aforementioned numbers of daltons. [0035] Disclosed herein, in some embodiments, are targeting ligands that bind a target protein. The targeting ligand may bind directly to the target protein. In some embodiments, the binding between the targeting ligand and the target protein is covalent. The covalent binding may be with a cysteine, lysine, or methionine, or any other reactive residue of the target protein. In some embodiments, the binding between the targeting ligand and the target protein is non- covalent.
[0036] Electrophiles reactive to lysines, cysteines and methionines can be inserted between the ligand and the linker, or independently attached to the recruiting ligand (RL), or the targeting ligand (TL), or to the linker. Examples of the target ligand or recruiting ligand binding with cysteine, lysine, or methionine are shown below (R=TL or RL, attachment point shows linker-TL or linker-RL):
N-acyl-N-alkyl N-acyl-N-alkyl a-substituted ^-substituted Oxaziridine for sulfonamide for sulfonamide for acrylamides acrylamides methionine lysine lysine for cysteine for cysteine X=N or O
[0037] Non-limiting, exemplary cysteine reactive groups that can be attached to the RL or the TL are shown below:
[0038] In some embodiments, the binding between the target protein and the targeting ligand comprises a binding affinity with an equilibrium dissociation constant (Kd) below 100 μM, a Kd below 90 μM, a Kd below 80 μM, a Kd below 70 μM, a Kd below 60 μM, a Kd below 50 μM, a Kd below 45 μM, a Kd below 40 μM, a Kd below 35 μM, a Kd below 30 μM, a Kd below 25 μM, a Kd below 20 μM, a Kd below 15 μM, a Kd below 14 μM, a Kd below 13 μM, a Kd below 12 μM, a Kd below 11 μM, a Kd below 10 μM, a Kd below 9 μM, a Kd below 8 μM, a Kd below 7 μM, a Kd below 6 μM, a Kd below 5 μM, a Kd below 4 μM, a Kd below 3 μM, a Kd below 2 μM, or a Kd below 1 pM. In some embodiments, the binding between the target protein and the targeting ligand comprises a binding affinity with an equilibrium dissociation constant (Kd) of at least 100 μM, a Kd of at least 90 μM, a Kd of at least 80 μM, a Kd of at least 70 μM, a Kd of at least 60 μM, a Kd of at least 50 μM, a Kd of at least 45 μM, a Kd of at least 40 μM, a Kd of at least 35 μM, a Kd of at least 30 μM, a Kd of at least 25 μM, a Kd of at least 20 μM, a Kd of at least 15 μM, a Kd of at least 14 μM, a Kd of at least 13 μM, a Kd of at least 12 μM, a Kd of at least 11 μM, a Kd of at least 10 μM, a Kd of at least 9 μM, a Kd of at least 8 μM, a Kd of at least
7 μM, a Kd of at least 6 μM, a Kd of at least 5 μM, a Kd of at least 4 μM, a Kd of at least 3 μM, a Kd of at least 2 μM, or a Kd of at least 1 pM.
[0039] Disclosed herein, in some embodiments, are target proteins. A target protein may include a protein intended to be modified, e.g. by a modifier protein. The target protein may be an enzymatic interacting partner for the modifier protein. The target protein may be modified by the modifier protein. The target protein may be any protein upon which the modifier protein exerts its effects. In some embodiments, the modifier protein may be modified by the target protein.
[0040] Examples of target proteins may include, in non-limiting examples, structural proteins, signaling proteins such as receptor proteins, channel proteins, or enzymes. In some embodiments, the target protein comprises a tumor suppressor, metabolic enzyme, protein aggregate, or haploinsufficient protein. The target protein may include a tumor suppressor. The target protein may be a metabolic protein. The target protein may include an enzyme. The target protein may include an aggregate protein. The target protein may include a haploinsufficient protein.
[0041] In some embodiments, the target protein includes a tumor suppressor. An example of a tumor suppressor includes tumor protein P53 (P53 or p53). P53 is also an example of protein that can activate DNA repair, arrest growth, or initiate apoptosis. P53 is controlled by a multitude of post-translational modifications (PTMs) such as phosphorylation. Phosphorylation of P53 may dictate its activation status. The target protein may include P53 or another protein that modulates DNA repair, cell growth, or apoptosis. P53 is an example of a transcription factor. A mutation in p53 is observed in over 50% of all cancers. 90% of these mutations are missense and result in inactive or dominant forms of p53. P53 has generally been an undruggable target. Previous approaches, mostly small molecules, have had only limited success in rescuing wild-type p53 function. Compared to existing pharmacochaperones, BFMs that recruit proteins capable of modulating p53 activity have a better chance of effectively re-activating p53. The linker may be further attached to a recruiting ligand, for example, via click or amide coupling. In some embodiments, the compound provided herein targets p53 for modification by a modifier protein described herein. In some embodiments, the modification comprises a post -translation modification of p53. Further modifications are provided herein. [0042] The p53 may include any detail as described at uniprot.org under accession number P04637 (as last accessed Nov. 10, 2022). p53 may include a polypeptide having the following amino acid sequence: MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPH HERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVWPYEPPEVGSDCTTIHYNYM CNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHH ELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGK EPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD (SEQ ID NO: 1). Unless otherwise specified, all references herein to amino acid residues numbering of p53 is relative to SEQ ID NO: 1. In some embodiments, the p53 of SEQ ID NO: 1 is wild-type p53. The p53 may include a mutant form of p53. The mutant form may be with regard to SEQ ID NO: 1. The mutant form may include a functional fragment or SEQ ID NO: 1. In some embodiments, a functional fragment of SEQ ID NO: 1 has at least some of the function of wild type p53. The mutant form of p53 may include an amino acid sequence at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, or at least 99% identical, to SEQ ID NO: 1. The mutant form of p53 may in some instances include an amino acid sequence less than 75% identical, less than 80% identical, less than 85% identical, less than 90% identical, less than 91% identical, less than 92% identical, less than 93% identical, less than 94% identical, less than 95% identical, less than 96% identical, less than 97% identical, less than 98% identical, less than 99% identical, or less than 100% identical, to SEQ ID NO: 1.
[0043] The p53 may comprise a mutant p53. The targeting ligand may bind the p53 mutant. Some aspects relate to a heterobifunctional compound comprising: a p53 binding moiety attached to a recruiting ligand that binds a modifier protein, wherein the p53 binding moiety binds to one of a plurality of mutant forms of p53. Some aspects relate to a heterobifunctional compound comprising: a p53 binding moiety attached to a recruiting ligand that binds a modifier protein, wherein the p53 binding moiety binds a mutant form of p53. In some embodiments, the mutant form of p53 is the p53 Y220C mutant, wherein the tyrosine at amino acid position 220 of p53 is substituted with a cysteine. Some aspects include a method of activating ap53 mutant protein, comprising contacting the p53 mutant protein with a compound disclosed herein.
[0044] In some embodiments, p53 binding ligands can bind to p53’s DNA binding domain (amino acids 92-312) of wild-type (WT) or mutant p53. In some embodiments, p53 binding ligands can bind to a cleft in C-terminus of p53 WT or mutant. In some embodiments, p53 binding ligands can bind p53 (WT or mutant) at the edge of DNA binding domain (site of CDB3 binding). In some embodiments, p53 binding ligands can interact with Asp268 of p53 WT or mutant.
[0045] In some embodiments, the p53 mutant is the Y220C mutant. In some embodiments, the p53 binding ligands may interact with Cys220, Asp228, Thrl50, Ser227, and Leul45. The p53 binding ligands may interact with Cys220, Asp228, Thrl50, Ser227, or Leul45 of the p52 Y220C mutant. In some embodiments, the p53 binding ligands may interact with any combination of Cys220, Asp228, Thrl50, Ser227, and Leul45 of the p53 Y220C mutant. The interaction may comprise a covalent binding. For the p53 Y220C mutant, the p53 binding ligand may interact with Cys220. For the p53 Y220C mutant, the p53 binding ligand may interact with Asp228. For p53 binding ligands that react covalently with cysteines, the binding ligand may interact with Cysl24, Cysl82, Cys220 (in p53 Y220C mutant), Cys 229, or Cys277. For p53 binding ligands that react covalently with cysteines, the binding ligands may interact with Cys220 of the p53 Y220C mutant.
[0046] Some aspects include a heterobifunctional compound (BFM) comprising: a p53 binding moiety attached to a recruiting ligand that binds a modifier protein, wherein the p53 binding moiety binds to one of a plurality of mutant forms of p53. Some aspects include a heterobifunctional compound comprising: a p53 binding moiety attached to a recruiting ligand that binds a modifier protein. The p53 binding moiety may bind to a mutant form of p53, such as a mutant form of p53 selected from a mutant form described herein. The mutant form may include a substitution such as a Y220C mutation. In some aspects, the modifier protein comprises BRIM. Some aspects include a method of activating a p53 mutant protein, comprising contacting the p53 mutant protein with a compound disclosed herein.
[0047] In some embodiments, a target protein comprises a protein associated with a disease state. For example, the target protein may be present, upregulated, or downregulated in the disease state, or a mutation in the target protein may contribute to the disease state. The target protein may play a role in the disease state, such as a deleterious role or a protective role with regard to the disease state. In some embodiments, a target protein comprises a protein with a modification status associated with a disease state. In some embodiments, the compound provided herein targets the target protein for modification by a modifier protein described herein such that the target protein is no longer associated with the disease state. For example, the phosphorylation status of the target protein may be associated with the disease state. Examples of disease states may include cancer. In some embodiments, the disease state includes cancer. [0048] The target protein may be in a subject. The target protein may be in a cell. The target protein may be intrinsic to the cell. The target protein may be endogenous to the cell. In some embodiments, the target protein is extrinsic to the cell. In some embodiments, the target protein is exogenous to the cell. The cell may be a cell of the subject.
[0049] In some embodiments, the target protein undergoes a change because of contact or proximity with the modifier protein. For example, the target protein may undergo a modification. The modification may be an enzymatic modification. The modification may include a post- translational modification. Some examples of modifications may include phosphorylation, palmitoylation, methylation, glycosylation, ligation, sulfonation, ubiquitylation, SUMOylation, fucosylation, sialylation, tyrosylation, acylation, acetylation, or tetradecanoylation. The modification may be added to the target protein or may be removed from the target protein. The modification may include phosphorylation, dephosphorylation, methylation, demethylation, deacylation, deacetylation, glycosylation, deglycosylation, ubiquitylation, or deubiquitylation. The modification may be covalent. The modification may be non-covalent. The target protein may undergo a structural change. Examples of structural changes may include protein folding or misfolding. The structural change may include cleavage. The modification may include changes in cellular localization. The structural change may include changes in oligomerization state. The modification may include the change in stability of target protein, its half-life, or concentration in certain subcellular compartments. The structural change may include the ability of protein to interact with other proteins.
[0050] The target protein may be more active as a result of the change. The target protein may be less active as a result of the change. When the target protein is an enzyme, the enzymatic activity of the target protein may be affected as a result of the change. In some embodiments, the target protein activity is increased or decreased by about 1.5 -fold, 2-fold, 3 -fold, 4-fold, 5 -fold, 10-fold, 20-fold, 50-fold, 100-fold as a result of the change.
[0051] In certain embodiments of a compound of Formula (I), R1 is a targeting ligand with a structure of Formula (II): Formula (II), wherein:
RA is C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl or 3- to 12- membered heteroaryl; Y1, Y2, Y3, Y4, Y5, and Y6 are each independently CH, C, NH, N, NO, S, SO, or absent, wherein at least two of Y1, Y2, Y3 and Y4 is CH, C, NH, N, NO, S, or SO, and wherein at least one of Y5 and Y6 is CH, C, NH, N, NO, S, or SO;
Y7 and Y8 are each independently C or N;
R1A is a cysteine reactive group, C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, -SOR1A1, or -COR1A1, wherein the C1-6 alkyl and C3 -12 cycloalkyl is optionally substituted with -CN, halogen, or C1-6 alkylamines;
R1B is deuterium, halogen, -CN, -OH, -OC1-6 alkyl, -OC1-6 haloalkyl, -NH2, NHC1-6 alkyl, -N(C1-6 alkyl)2, -NHCOMe, -OCOMe, -OCONR1BAR1BB, C1-6 alkyl, -COOR1BB, -CONR1BAR1BB, - NR1BACOR1BB, -NO2, -NR1BSO2, -SO2(C1-6alkyl), -SO2NR1BAR1BB, -SO2NH-heteroaryl, or two R1G taken together form an aryl or heteroaryl ring;
R1BA is hydrogen or C1-6 alkyl;
R1BB is hydrogen, -COC1-6 alkyl, Ci-ealkyl, Ce-12 aryl, 3- to 12- membered heteroaryl;
R1C is deuterium, halogen, -OH, -OC1-6 alkyl, -OC1-6 haloalkyl, -NH2, NHC1-6 alkyl, - N(C1-6 alkyl)2, -NO2, -NHCOMe, or -OCOMe;
R1D is hydrogen or C1-6 alkyl;
R1E is C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, or 3- to 12- membered heteroaryl, wherein the C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, and 3- to 12- membered heteroaryl are optionally substituted with halogen, C1-6 alkyl, C1-6 alkoxy, C1-6 carboxylic acid, -NH2, or -N(Ci-ealkyl)2; or R1D and R1E combine with the carbon to which is attached to form a cyclic structure, wherein the cyclic structure is C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, and 3- to 12- membered heteroaryl, wherein the cyclic structure is optionally substituted with one or more R1DE;
R1DE is deuterium, halogen, -CN, -OH, -NH2, -NH(C1-6 alkyl), -NH(C1-6 haloalkyl), - N(C1-6 alkyl)2, -OC1-6 alkyl, -OC1-6 haloalkyl, C1-6 alkyl, C1-6 alkoxy, C1-6 haloalkyl, C1-6 haloalkoxy, -NHCO(C 1-6 haloalkyl), -CO2(C 1-6 alkyl), -CONH(C 1-6 alkyl), -SO2NH(C1-6 alkyl), - SO2N(C1-6 alkyl)2, -SO2(C1-6 alkyl), or -SO2NMe(C1-6 alkyl);
R1F is hydrogen or C1-6 alkyl; n is 0 to 5; o is 0 or 1; and
[0052] wherein an atom on one of R1B, R1DE, or R1E or the cyclic structure of R1D and R1E is covalently linked to L. In certain embodiments, R1D and R1E combine to form a cyclic structure, wherein the cyclic structure is 3- to 7- membered heterocycloalkyl. In certain embodiments, the cyclic structure is pyridinyl. [0053] In certain embodiments of a compound of Formula (I), R1 is a targeting ligand with a structure of Formula (II- A): wherein:
RB is 3- to 12- membered heterocycloalkyl;
R1DE is deuterium, halogen, -OH, -OMe, -OCF3, -NH2, -NH(C1-6alkyl), or -N(C1-6alkyl)2; and p is 0 to 5.
[0054] In certain embodiments of a compound of Formula (I), R1 is a targeting ligand with a structure of Formula (II-B): wherein:
X1, X2, X3, and X4 are each independently C, CH, NH, N, NO, S, SO or absent, wherein at least two of X1, X2, X3, and X4 are C, CH, NH, N, NO, S, or SO; and p is 1 to 3.
C. Recruiting ligands and modifier proteins
[0055] Disclosed herein, in some embodiments, are recruiting ligands. The recruiting ligand may be configured to bind to a modifier protein. The recruiting ligand may include a moiety that binds the modifier protein. The recruiting ligand may bind the modifier protein. The recruiting ligand may bind the protein or other macromolecule that interacts with a modifier protein. Upon binding, the modifier may induce a change in the target protein. In some embodiments, the recruiting ligand is configured to bind to a modifier protein such that the modifier protein induces a change to the target protein. The recruiting ligand may be a part of a heterobifunctional compound (BFM) such as an OmniTAC compound. The recruiting ligand may connect to a linker or targeting ligand. In some embodiments, the recruiting ligand is incorporated into an in vivo engineered protein.
[0056] The recruiting ligand may include a small molecule. In some embodiments, the recruiting ligand comprises a small molecule moiety. In some embodiments, the recruiting ligand has a molecular weight of 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, or 2500 daltons, or a range defined by any two of the aforementioned numbers of daltons. [0057] Disclosed herein, in some embodiments, are recruiting ligands that bind a modifier protein. The recruiting ligand may bind directly to the modifier protein. In some embodiments, the binding between the recruiting ligand and the modifier protein is covalent. The covalent binding may be with a cysteine, lysine, methionine, or any other reactive residue of the modifier protein. In some embodiments, the binding between the recruiting ligand and the modifier protein is non-covalent.
[0058] Disclosed herein R2 comprises a recruiting ligand (RL) that binds to modifier proteins. The recruiting ligands can be synthesized from parent ligands. Parent ligands are small molecule binders for modifier proteins; these binders can be activators, inhibitors or have no effect on the modifier protein. Recruiting ligands comprise parent ligands with a chemical handle to attach to L or R1 directly through appropriate chemical transformation. In some cases, the parent ligand may already contain a suitable chemical handle that can be utilized without affecting the binding ability of the ligand. In some embodiments, the recruiting ligand is the parent ligand. In some embodiments, the recruiting ligand is a truncated analogue of the parent ligand. In some embodiments, the recruiting ligand is an analogue of the parent ligand where a functional group or ring has been replaced by an appropriate bioisostere. In some cases, R2 is designed as an analogue of the parent ligand by attaching a chemical handle that (1) is solvent exposed and (2) does not impair the binding to the modifier protein. In some embodiments, the exit vector is defined as the orientation and area projected by attachment of a linker to a parent ligand. One parent ligand can lead to several R2 designs with varied exit vector and/or chemical handles. The attachment point should have a minimal impact on the binding mode and affinity of the parent ligand. To do so, the following guidelines can be followed:
(a) Exit vector choice
- if crystal structures data is available, the binding mode is analyzed to identify solvent exposed regions of the ligand.
- if structure activity relationship (SAR) data is available, it should be used to determine regions of the ligands that can be modified without resulting in large drop of binding affinity (measured by direct binding, e.g. KD, or through effectives concentrations e.g. EC50, IC50, etc.). - if the parent ligands have previously been described as components of bifunctional molecules (BFMs), the described attachment point will be identified.
- if no structural and SAR data is available, then a minimum of 3 exit vectors will be explored to empirically determine a suitable R2.
(b) chemical handle choice
- a chemical group that can be reacted with compatible functional groups to form a new chemical bond in high yields by anyone skilled in the field of organic chemistry. Such reactions include amide coupling, carbamate formation, Click reaction, sulfonamide formation, alkylation, reductive amination, etc.
- the chemical handle can be: carboxylic acid, alkyne, amine, azide, isocyanide, sulfonyl chloride, sulfonyl fluoride, alkyl bromide, alkyl chloride, alkyl iodide, alkyl mesylate, aldehydes, ketone.
- The chemical handle should be chosen such that it is compatible with other functional groups within the parent ligand.
[0059] In some embodiments, the parent ligand is selected from the compounds listed in FIG. 1 or FIG. 2. In some embodiments, the parent ligand is selected from the compounds listed in FIG. 1. In some embodiments, the parent ligand is selected from the compounds listed in FIG. 2.
D. Linkers
[0060] Disclosed herein, in some embodiments, are linkers. The linker may be a part of a heterobifunctional compound such as an OmniTAC compound. The linker may connect a targeting ligand to a recruiting ligand. The linker may directly connect to both the targeting ligand and the recruiting ligand. The linker may include a ligand of a protein such as a target protein.
[0061] In some embodiments, the linker comprises a polyethylene glycol. In some embodiments, the linker comprises an aromatic group. In some embodiments, the linker comprises an alkyl chain. In some embodiments, the linker comprises an alkenyl. In some embodiments, the linker comprises an alkyl phosphate. In some embodiments, the linker comprises an alkyl siloxane. In some embodiments, the linker comprises an epoxy. In some embodiments, the linker comprises an acrylamide. In some embodiments, the linker comprises an N-acyl-N-alkyl sulfonamide. In some embodiments, the linker comprises an oxaziridine. In some embodiments, the linker comprises a glycidyl. In some embodiments, the linker comprises a carboxylate. In some embodiments, the linker comprises an anhydride. In some embodiments, the linker comprises a polypeptide. In some embodiments, the linker comprises piperazine. In some embodiments, the linker comprises piperidyl. In some embodiments, the linker comprises triazole. In some embodiments, the linker comprises enamines. [0062] In some embodiments, the linker comprises a chain length of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 carbon atoms, or a range defined by any two of the aforementioned numbers of atoms. In some embodiments, the linker comprises a chain length of between 2 to 24 atoms. In some embodiments, the linker comprises a chain length of between 2 to 18 atoms.
[0063] In some embodiments, the linker comprises: (a) a structure selected from the nonlimiting group consisting of polyethylene glycol, an aromatic group, an alkyl, an alkenyl, an alkyl phosphate, an alkyl siloxane, an epoxy, a glycidyl, a carboxylate, an anhydride, a piperazine, a piperidyl, a triazole, or a combination thereof; or (b) a polypeptide of natural or synthetic source having a chain length of between 2 to 24 amino acids.
[0064] In some embodiments, the linker comprises one or more covalently connected structural units of A (e.g., -Ai . . . Aq~), wherein Ai is a group coupled to at least one of a recruiting ligand, a targeting ligand, or a combination thereof. In some embodiments, A i links a recruiting ligand, a targeting ligand, or a combination thereof directly to another recruiting ligand, targeting ligand, or combination thereof. In some embodiments, Ai links a recruiting ligand, a targeting ligand, or a combination thereof indirectly to another recruiting ligand, targeting ligand, or combination thereof through Aq.
[0065] In some embodiments, Ai to Aq are, each independently , a bond, CRL1RL2, (), S, SO, so2, NRLS, SO2NRL3, SONRL3, CONRL3, NRL3CONRL4, NRL3SO2NRL4, CO, CRLi=CRL2, C=C, SIRL1RL2, P(O)RLi, P(O)ORL1, NRL3C(=NCN)NRL4, NRL 3C(=NCN), NRL3C(=CNO2)NRL4, C3- ncycloalkyl optionally substituted with 0-6 R! j or R1'2 groups, Cri-nheterocyclyl optionally substituted with 0-6 RL1 or RL2 groups, aryl optionally substituted with 0-6 RL1 or RL2 groups, heteroaryl optionally substituted with 0-6 RL1 or RL2 groups, where Rljl or RL2, each independently, can be linked to other A groups to form cycloalkyl or heterocyclyl moiety which can be further substituted with 0-4 R; ': groups. In some embodiments, RL1, R: 2_ RL3, RL4 and RL5 are, each independently, H, halo, C1-8alkyl, OC1-8alkyl, SC1-8alkyl, NHCusalkyl, N(Cj.
8alkyl)2, Cs-iicycloalkyl, aryl, heteroaryl, Cs-nheterocyclyl, OC1-8cycloalkyl, SC1-8cycloalkyl, NHC1-8cycloalkyl, N(C1-8Cycloalkyl)2, N(C1-8cycloalkyl)(C1-8alkyl), OH, NH2, SH, SO2C1-8alkyl, P(O)(OC1-8alkyl)(C1-8alkyl), P(())(OC1-8alkyl)2, CC- -C1-8alky 1, CCH, CH==CH(C1-8alkyl), ( (( 1. 8alkyl)=CH(Ci.8alkyl), C(C1-8alkyl)= C(C1-8alkyl)2, SI(OH)3, Si(C1-8alkyl)3, Si(OH)(C1-8alkyl)2, COC3-8alkyl, CO2H, halogen, CN, CF3, CHF2, CH2F, NO?„ SF5, SO2NHC3-8alkyl, SO2N(C1- 8aikyl)2, SONHC1-8alkyl, S()N(C1-8alkyl)2, CONHCusalkyl, C()N(C1-8alkyl)2, N(C1- 8alkyl)CONH(C1-8alkyl), N(C1-8alkyl)CON(Ci..galkyl)2, NHCONH(C1-8alkyl), NHCON(Ci- 8alkyl)2, NHCONH2, N(C1-8alkyl)SO2NH(C1-8alkyl), N(C1-8alkyl) SO2N(C1-8alkyl)2, NH SO2NH(C1-8alkyl), NH SO2N(C1-8alkyl)2, NH SO2NH2. In some embodiments, q is an integer greater than or equal to 0. In some embodiments, q is an integer greater than or equal to 1. In some embodiments, e.g., where q is greater than 2, Aq is a group which is connected to a recruiting ligand or recruiting ligand moiety, and Ai and Aq are connected via structural units of A (number of such structural units of A: q-2). In some embodiments, e.g., where q is 2, Aq is a group which is connected to Ai and to a recruiting ligand or recruiting ligand moiety. In some embodiments, e.g., where q is 1, the structure of the linker is -Ai-, and Ai is a group which is connected to a recruiting ligand or recruiting ligand moiety and a targeting ligand moiety. In some embodiments, q is an integer from 1 to 100, 1 to 90, 1 to 80, 1 to 70, 1 to 60, 1 to 50, 1 to 40, 1 to 30, 1 to 20, or 1 to 10.
[0066] In some embodiments, the linker comprises or consists of optionally substituted (poly)ethyleneglycol having about 1 to about 100 ethylene glycol units, about 1 to about 50 ethylene glycol units, about 1 to about 25 ethylene glycol units, about 1 to about 10 ethylene glycol units, about 1 to about 8 ethylene glycol units, about 1 to about 6 ethylene glycol units, about 2 to about 4 ethylene glycol units, or optionally substituted alkyl groups interdispersed with optionally substituted (), N, S, P or Si atoms. In some embodiments, the linker is substituted with an aryl, phenyl, benzyl, alkyl, alkylene, halogen, or heterocycle group. In some embodiments, the linker may be asymmetric or symmetrical.
[0067] In any of the embodiments of the compounds described herein, the linker may be any suitable moiety' as described herein. In some embodiments, the linker is or includes a substituted or unsubstituted polyethylene glycol group ranging in size from about 1 to about 12 ethylene glycol units, from about 1 to about 10 ethylene glycol units, from about 2 to about 6 ethylene glycol units, from about 2 to 5 ethylene glycol units, and from about 2 to about 4 ethylene glycol units.
[0068] In some embodiments, the linkers comprise a structure -(AP)m-L1A-L1B-(AP)m-. AP, L1A, and L1B are as described in the specification and claims herein.
[0069] In some embodiments, AP is PEG, ether, amide, sulfonamide, sulfone, sulfoxide, sulfonate, phosphonate, ester, urea, carbamate, substituted phosphine oxide, optionally substituted C1-6 alkyl, optionally substituted C3-12 cycloalkyl, optionally substituted 3- to 12- membered heterocycloalkyl, optionally substituted 3- to 12- membered heteroaryl, or optionally substituted C6-12 aryl.
[0070] In some embodiments, L1A and L1B are each independently polyethylene glycol (PEG), Ci-50 alkylene-PEG, C2-50 alkenylene-PEG, C2-50 alkynylene-PEG, C1-50 alkylene, C2-50 alkenylene, C2-50 alkynylene, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-naryl, 3- to 12- membered heteroaryl, 3- to 12- membered heterocycloalkyl-Ci-10 alkylene, 3- to 12- membered heterocycloalkyl-PEG, or PEG-3- to 12- membered heterocycloalkyl-PEG, spirocyclic cores, or a combination thereof, each of which may be substituted with one or more halogen, deuterium, methyl, deuterated methyl, trifluoromethyl, amide, sulfonamide, sulfone, ester, urea, carbamate, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, or 3- to 12- membered heteroaryl.
[0071] In some embodiments, the linker comprises the following structure, wherein n is any integer from I to 30:
[0072] In some embodiments, L is one of the following:
[0073] In certain embodiments, L is one of the following: [0074] In certain embodiments, L is one of the following:
[0075] In certain embodiments, L is one of the following:
[0076] In certain embodiments, L is one of the following:
E. Compounds of Formula III
[0077] In certain embodiments, the compound is a compound of Formula (III- A) or Formula
(III-B):
[0078] In certain embodiments, the compound is a compound of Formula (III-A1) or
Formula (III-B1): wherein: B is a absent, -NH-, -O-, CO, amide, C1-6 alkylene, C2-6 alkenylene, or C2-6 alkynylene, wherein the C1-6 alkylene, C2-6 alkenylene, and C2-6 alkynylene is optionally substituted with deuterium, halogen, or C1-3 alkoxy;
W1 and W2 are each independently NH, N, O, or S;
Rc and RD are each independently optionally substituted C3-12 cycloalkyl, optionally substituted 3- to 12- membered heterocycloalkyl, optionally substituted Ce-12 aryl or optionally substituted 3- to 12- membered heteroaryl; and
R1H and R11 are each independently hydrogen or C1-6 alkyl, wherein the C1-6 alkyl is optionally substituted with deuterium or halogen.
[0079] In certain embodiments, B is C1-3 alkylene. In certain embodiments, B is methylene. In certain embodiments, Rc and RD are each independently 3- to 7- membered heterocycloalkyl, Ce-io aryl, or 3- to 7- membered heteroaryl.
[0080] In certain embodiments, the compound is a compound of Formula (III-A2) or Formula (III-B2): wherein:
X1, X2, X3, and X4 are each independently C, CH, NH, N, NO, S, SO or absent, and wherein at least two of X1, X2, X3, and X4 is C, CH, NH, N, NO, S, SO. [0081] In certain embodiments, R2 is: wherein:
X5, X6, X7, X8, and X14 are each independently C, CH, CD, CF, NH, N, NO, S, SO or absent, and wherein at least one of X5 and X6 is C, CH, CD, CF, NH, N, NO, S, or SO;
X9, X10, X11, X12, and X13 are each independently C, CH, CD, CF, NH, N, NO, S, SO or absent, and wherein at least two of X9, X10, X11, X12, and X13 are C, CH, CD, CF, CCH3, CCD3, CCF3, N, NH, NO, S, or SO;
R1Jis NH2, NH(C1-6 alkyl), N(C1-6 alkyl)2 or absent; and
Z is C=O, C=S, C-NH2, C-C1-6 alkyl, C-NH(C1-6 alkyl), NH, N(C1-6 alkyl), N, O, S, SO, SO2, or CH.
F. Compounds of Formula IV
[0082] In certain embodiments, the compound is a compound of Formula (IV-A), Formula (IV-B), Formula (IV-C), or Formula (IV-D):
[0083] In certain embodiments, the compound is a compound of Formula (IV-A1), Formula
(IV-B1), Formula (IV-C1), or Formula (IV-D1):
wherein:
X1, X2, X3, and X4 are each independently CH, N, NO, S, SO or absent, and wherein at least two of X1, X2, X3, and X4 is CH, N, NO, S, SO;
R1B, R1C, and R1L are each independently halogen, -OH, -NH2, -NH(C1-6 alkyl), -NH(CI-6 alkyl)2, -OC1-6 alkyl, -OCH3, -OCF3, -NO2, -NHAc, or -OAc;
R1DE is halogen, deuterium, hydroxyl, trifluoromethoxy, or amine; or wherein when R1DE is in (R1DE)p-i, then R1DE is deuterium, halogen, -CN, -OH, -NH2, - NH(C 1-6 alkyl), -NH(C1-6haloalkyl), -OC1-6 alkyl, -OC1-6 haloalkyl, C1-6 alkyl, C1-6 haloalkyl, - NHCO(C1-6 haloalkyl), -CO2(C1-6 alkyl), -CONH(C1-6 alkyl), -SO2NH(C1-6 alkyl), -SO2N(C1-6 alkyl)2, -SO2(C 1-6 alkyl), or -SO2NMe(C1-6 alkyl); and q is 0 to 5. [0084] In certain embodiments, R2 is: wherein:
X15, X16, X17, X18, and X19 are each independently C, CH, CMe, CCD3, N, NH, NMe, NCD3, CF, CD;
X20 is absent, -NH-, -CH2-, -CH(OH)-, -CH(C1-6alkyl)-, -NHCH2-, or -NHCH(Me)-;
X21 is C, CH, or N;
X22, and X23 are each independently C, CH, CO, N, NH, CNH2, or CO(C1-6 alkyl); and
X22 and X23 can optionally be linked to form a second 5- or 6- membered heterocycle, resulting in a fused bicycle.
[0085] In certain embodiments, the compound is a compound of Formula (IV-A2) or Formula (IV-C2):
(IV-C2). [0086] In certain embodiments, R1A is a cysteine reactive group or C1-6 alkyl, wherein the Ci- 6 alkyl is optionally substituted with halogen. In certain embodiments, R1B is -OC1-6 alkyl, -OC1-6 haloalkyl, -OCON(C1-6 alkyl)2, -SO2(C1-6 alkyl), or -SO2N(C1-6 alkyl)2. In certain embodiments, R1DE is deuterium, halogen, -OH, -OMe, or -OCF3. In certain embodiments, R1F is hydrogen or methyl.
G. Compounds of Formula V
[0087] Another aspect provides a compound represented by Formula V :
R1 - L - Y1
(V) or a pharmaceutically acceptable salt thereof; wherein:
R1 is one of the following:
• -(phenyl substituted with 0 or 1 C1-4 alkoxyl, 0 or 1 C1-4 deuteroalkoxyl, and 0, 1, or 2 occurrences of halo, hydroxyl, -S(O)2(C1-6 alkyl), or C1-4 alkyl)-N(R2)-(C2-4 alkynylene)-(indolyl substituted with C1-4 haloalkyl and 0 or 1 -N(R3)-(3-6 membered saturated heterocyclyl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclyl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); or
• -(3-6 membered saturated heterocyclylene containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R2)-(indolyl substituted with C1-4 haloalkyl and 0 or 1 -N(R3)-(C2-4alkynylene)-N(R2)-(phenyl substituted with 0 or 1 C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl or -S(O)2-(C1-4 alkyl));
R2, R3, R4 and independently hydrogen or C1-4 alkyl);
Y1 is one of the following:
• -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5- membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(imidazo[4,5-b]pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))- (5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)- (pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl, and 5-membered heteroaryl)- (C1-6 alkylene substituted by 1 or 2 hydroxyl)-(phenyl or pyridinyl substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl), wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(pyridin-2- onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)- (5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); or
• -(phenylene or pyridinylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)-(pyridin-2-onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(O)-(pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, or 5- membered heteroaryl, wherein the 5 -membered heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R4)-(C1-6 alkylene)-(phenyl or pyridinyl substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl)-(5-10 membered heteroaryl substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and 5-membered heteroaryl, wherein the 5- membered heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene, wherein the C1-6 alkylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of C1-4 alkyl and 6-membered heteroaryl); and L is a bivalent, saturated or unsaturated, straight or branched Ci-60 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -S-, - N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O)2-, -N(H)S(O)2-, -N(C1-6 alkyl)S(O)2-, -S(O)2N(H)-, -S(O)2N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, - C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6 alkyl)-, -N(H)C(O)O-, -N(C1-6 alkyl)C(O)O-, - N(C3-6 cycloalkyl)-, -C(H)(C3-6 cycloalkyl)-, optionally substituted 3-10 membered carbocyclyl, or optionally substituted 3-11 membered heterocyclyl containing 1, 2, 3, or 4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
[0088] In certain embodiments, R1 is -(phenyl substituted with 0 or 1 C1-4 alkoxyl, 0 or 1 C1-4 deuteroalkoxyl, and 0, 1, or 2 occurrences of halo, hydroxyl, -S(O)2(C1-6 alkyl), or C1-4 alkyl)- N(R2)-(C2-4 alkynylene)-(indolyl substituted with C1-4haloalkyl and 0 or 1 -N(R3)-(3-6 membered saturated heterocyclyl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclyl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl). In certain embodiments, R1 is -(3-6 membered saturated heterocyclylene containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R2)-(indolyl substituted with C1-4haloalkyl and 0 or 1 -N(R3)-(C2-4 alkynylene)-N(R2)-(phenyl substituted with 0 or 1 C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl or -S(O)2-(C1-4 alkyl)). In certain embodiments, R1 is
[0089] In certain embodiments, Y1 is -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl). [0090] In certain embodiments, Y1 is -(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl). In certain embodiments, Y1 is -(imidazo[4,5-b]pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl). [0091] In certain embodiments, Y1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)-(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl). [0092] In certain embodiments, Y1 is -(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
[0093] In certain embodiments, Y1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl, and 5-membered heteroaryl)-(C1-6 alkylene substituted by 1 or 2 hydroxyl)-(phenyl or pyridinyl substituted with 0,
1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl), wherein the heteroaryl is substituted by 0, 1,
2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
[0094] In certain embodiments, Y1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(pyridin-2-onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
In certain embodiments, Y1 is -(phenylene or pyridinylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)-(pyridin-2-onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
[0095] In certain embodiments, Y1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(O)- (pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, or 5-membered heteroaryl, wherein the 5 -membered heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R4)-(C1-6 alkylene)-(phenyl or pyridinyl substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl).
[0096] In certain embodiments, Y1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl)-(5-10 membered heteroaryl substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and 5 -membered heteroaryl, wherein the 5 -membered heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene, wherein the C1-6 alkylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of C1-4 alkyl and 6-membered heteroaryl).
[0097] In certain embodiments, Y1 is one of the following:
[0098] In certain embodiments, L is a bivalent, saturated or unsaturated, straight or branched C5-30 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O)2-, - N(H)S(O)2-, -N(C1-6 alkyl)S(O)2-, -S(O)2N(H)-, -S(O)2N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, -C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6 alkyl)-, optionally substituted 3-10 membered carbocyclyl, or optionally substituted 3-11 membered heterocyclyl containing 1, 2, 3, or 4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In certain embodiments, L is a bivalent, saturated or unsaturated, straight or branched C5-30 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -N(H)-, -N(C 1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O)2-, -N(H)S(O)2-, - N(C1-6 alkyl)S(O)2-, -S(O)2N(H)-, or -S(O)2N(C1-6 alkyl)-.
H. Compounds of Formula VI
[0099] Another aspect provides a compound represented by Formula VI:
R1 - L - Y1
(VI) or a pharmaceutically acceptable salt thereof; wherein:
R1 is -(phenyl substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-N(R2)-(C2-4alkynylene)-(indolyl substituted with C1-4haloalkyl and -N(R3)-(3-6 membered saturated heterocyclyl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclyl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
R2, R3, R4 and independently hydrogen or C1-4 alkyl);
Y1 is one of the following:
• -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)- (pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
L is a bivalent, saturated or unsaturated, straight or branched Ci-60 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -S-, - N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O)2-, -N(H)S(O)2-, -N(C1-6 alkyl)S(O)2-, -S(O)2N(H)-, -S(O)2N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, - C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6 alkyl)-, -N(H)C(O)O-, -N(C1-6 alkyl)C(O)O-, - N(C3-6 cycloalkyl)-, -C(H)(C3-6 cycloalkyl)-, optionally substituted 3-10 membered carbocyclyl, or optionally substituted 3-11 membered heterocyclyl containing 1, 2, 3, or 4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
[0100] In certain embodiments, R1 is -(phenyl substituted with methoxy and 0 or 1 occurrences of halo, hydroxyl, or C1-4 alkyl)-N(R2)-(C3 alkynylene)-(indolyl substituted with - CH2CF3 and -N(R3)-(piperidinyl substituted by 1 or 2 substituents independently selected from the group consisting of fluoro and methyl). In certain embodiments, R1 is
[0101] In certain embodiments, Y1 is -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl). In certain embodiments, Y1 is -(phenylene substituted by 0 or 1 substituent independently selected from the group consisting of halo and C1-4 alkyl)-(C1-4 alkylene)-(benzo[d]imidazolylene substituted with 0 or 1 occurrences of halo or C1-4 alkyl)-(5- isoxazolyl substituted by 1, 2, or 3 C1-4 alkyl). In certain embodiments, Y1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)-(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl). In certain embodiments, Y1 is -(phenylene substituted by 0 or 1 substituent independently selected from the group consisting of halo and C1-4 alkyl)-(C1-4 alkylene)-N(R4)-(pyridinylene substituted with C1-4alkoxyl and 0 or 1 occurrences of halo or C1-4 alkyl)-(isoxazolyl substituted by 1, 2, or 3 C1-4 alkyl).
[0102] In certain embodiments, Y1 is one of the following:
[0103] In certain embodiments, L is -S(O)2N(C1-6 alkyl)-, -S(O)2N(C1-6 alkyl)-(Co-e-alkylene)- (3-6 membered heterocyclyl containing 1 nitrogen atom)-C(O)-, -S(O)2N(C1-6 alkyl)-(C3-6- cycloalkylene)-N(H)C(O)-, or -S(O)2N(C1-6 alkyl)-(C3-6-cycloalkylene)-(C1-6-alkylene)- N(H)C(O)-. In certain embodiments, L is -S(O)2N(C1-6 alkyl)-. In certain embodiments, L is - S(0)2N(C1-6 alkyl)-(Co-6-alkylene)-(3-6 membered heterocyclyl containing 1 nitrogen atom)- C(O)-. In certain embodiments, L is -S(O)2N(C1-6 alkyl)-(C3-6-cycloalkylene)-N(H)C(O)-. In certain embodiments, L is -S(O)2N(C1-6 alkyl)-(C3-6-cycloalkylene)-(C1-6-alkylene)-N(H)C(O)-.
I. Exemplary Specific Compounds
[0104] Exemplary specific compounds are provided in Tables 1-5 below. In certain embodiments, the compound is a compound in any of Tables 1-5 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in any of tables 1- 5. In certain embodiments, the compound is a compound in Table 1 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in Table 1. In certain embodiments, the compound is a compound in Table 2 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in Table 2. In certain embodiments, the compound is a compound in Table 3 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in Table 3. In certain embodiments, the compound is a compound in Table 4 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in Table 4. In certain embodiments, the compound is a compound in Table 5 or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound is a compound in Table 5.
Table 1.
-Ill-
II. Pharmaceutical compositions
[0105] Disclosed herein, in some embodiments, are pharmaceutical compositions. The pharmaceutical composition may include a compound described herein. For example, the pharmaceutical composition may include an OmniTAC compound. In some embodiments, the pharmaceutical composition comprises a heterobifunctional compound. In some embodiments, the pharmaceutical composition is sterile. The pharmaceutical composition may include the compound and a pharmaceutically acceptable carrier.
[0106] In some embodiments, the pharmaceutically acceptable carrier comprises a water. In some embodiments, the pharmaceutically acceptable carrier comprises a buffer. In some embodiments, the pharmaceutically acceptable carrier comprises a saline solution. In some embodiments, the pharmaceutically acceptable carrier comprises water, a buffer, or a saline solution.
[0107] The pharmaceutical compositions may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained- release formulation; (3) topical application, for example, as a cream, ointment, or a controlled- release patch or spray applied to the skin; (4) intravaginally or intrarectally, for example, as a pessary, cream or foam; (5) sublingually; (6) ocularly; (7) transdermally; or (8) nasally. In certain embodiments, the invention provides a pharmaceutical composition comprising a compound described herein (such as a compound of Formula I, or other compounds in Section I) and a pharmaceutically acceptable carrier.
[0108] Wetting agents, emulsifiers and lubricants, such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, release agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the compositions. [0109] Examples of pharmaceutically-acceptable antioxidants include: (1) water soluble antioxidants, such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like; (2) oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol, and the like; and (3) metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.
[0110] Formulations of the present invention include those suitable for oral, nasal, topical (including buccal and sublingual), rectal, vaginal and/or parenteral administration. The formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, the particular mode of administration. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound which produces a therapeutic effect. Generally, out of one hundred percent, this amount will range from about 0.1 percent to about ninety -nine percent of active ingredient, preferably from about 5 percent to about 70 percent, most preferably from about 10 percent to about 30 percent.
[0111] In certain embodiments, a formulation of the present invention comprises an excipient selected from the group consisting of cyclodextrins, celluloses, liposomes, micelle forming agents, e.g., bile acids, and polymeric carriers, e.g., polyesters and polyanhydrides; and a compound of the present invention. In certain embodiments, an aforementioned formulation renders orally bioavailable a compound of the present invention.
[0112] Methods of preparing these formulations or compositions include the step of bringing into association a compound of the present invention with the carrier and, optionally, one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association a compound of the present invention with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product.
[0113] Formulations of the invention suitable for oral administration may be in the form of capsules, cachets, pills, tablets, lozenges (using a flavored basis, usually sucrose and acacia or tragacanth), powders, granules, or as a solution or a suspension in an aqueous or non-aqueous liquid, or as an oil-in-water or water-in-oil liquid emulsion, or as an elixir or syrup, or as pastilles (using an inert base, such as gelatin and glycerin, or sucrose and acacia) and/or as mouth washes and the like, each containing a predetermined amount of a compound of the present invention as an active ingredient. A compound of the present invention may also be administered as a bolus, electuary or paste.
[0114] In solid dosage forms of the invention for oral administration (capsules, tablets, pills, dragees, powders, granules, trouches and the like), the active ingredient is mixed with one or more pharmaceutically-acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and/or silicic acid; (2) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose and/or acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds and surfactants, such as poloxamer and sodium lauryl sulfate; (7) wetting agents, such as, for example, cetyl alcohol, glycerol monostearate, and non-ionic surfactants; (8) absorbents, such as kaolin and bentonite clay; (9) lubricants, such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, zinc stearate, sodium stearate, stearic acid, and mixtures thereof; (10) coloring agents; and (11) controlled release agents such as crospovidone or ethyl cellulose. In the case of capsules, tablets and pills, the pharmaceutical compositions may also comprise buffering agents. Solid compositions of a similar type may also be employed as fillers in soft and hard-shelled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols and the like.
[0115] A tablet may be made by compression or molding, optionally with one or more accessory ingredients. Compressed tablets may be prepared using binder (for example, gelatin or hydroxypropylmethyl cellulose), lubricant, inert diluent, preservative, disintegrant (for example, sodium starch glycolate or cross-linked sodium carboxymethyl cellulose), surface-active or dispersing agent. Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.
[0116] The tablets, and other solid dosage forms of the pharmaceutical compositions of the present invention, such as dragees, capsules, pills and granules, may optionally be scored or prepared with coatings and shells, such as enteric coatings and other coatings well known in the pharmaceutical-formulating art. They may also be formulated so as to provide slow or controlled release of the active ingredient therein using, for example, hydroxypropylmethyl cellulose in varying proportions to provide the desired release profile, other polymer matrices, liposomes and/or microspheres. They may be formulated for rapid release, e.g., freeze-dried. They may be sterilized by, for example, filtration through a bacteria-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved in sterile water, or some other sterile injectable medium immediately before use. These compositions may also optionally contain opacifying agents and may be of a composition that they release the active ingredient(s) only, or preferentially, in a certain portion of the gastrointestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes. The active ingredient can also be in micro-encapsulated form, if appropriate, with one or more of the above-described excipients.
[0117] Liquid dosage forms for oral administration of the compounds of the invention include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredient, the liquid dosage forms may contain inert diluents commonly used in the art, such as, for example, water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3 -butylene glycol, oils (in particular, cottonseed, groundnut, com, germ, olive, castor and sesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.
[0118] Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, coloring, perfuming and preservative agents.
[0119] Suspensions, in addition to the active compounds, may contain suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.
[0120] Formulations of the pharmaceutical compositions of the invention for rectal or vaginal administration may be presented as a suppository, which may be prepared by mixing one or more compounds of the invention with one or more suitable nonirritating excipients or carriers comprising, for example, cocoa butter, polyethylene glycol, a suppository wax or a salicylate, and which is solid at room temperature, but liquid at body temperature and, therefore, will melt in the rectum or vaginal cavity and release the active compound.
[0121] Formulations of the present invention which are suitable for vaginal administration also include pessaries, tampons, creams, gels, pastes, foams or spray formulations containing such carriers as are known in the art to be appropriate.
[0122] Dosage forms for the topical or transdermal administration of a compound of this invention include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants. The active compound may be mixed under sterile conditions with a pharmaceutically - acceptable carrier, and with any preservatives, buffers, or propellants which may be required.
[0123] The ointments, pastes, creams and gels may contain, in addition to an active compound of this invention, excipients, such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.
[0124] Powders and sprays can contain, in addition to a compound of this invention, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances. Sprays can additionally contain customary propellants, such as chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, such as butane and propane.
[0125] Transdermal patches have the added advantage of providing controlled delivery of a compound of the present invention to the body. -Such dosage forms can be made by dissolving or dispersing the compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate of such flux can be controlled by either providing a rate controlling membrane or dispersing the compound in a polymer matrix or gel.
[0126] Ophthalmic formulations, eye ointments, powders, solutions and the like, are also contemplated as being within the scope of this invention.
[0127] Injectable depot forms are made by forming microencapsule matrices of the subject compounds in biodegradable polymers such as polylactide-polyglycolide. Depending on the ratio of drug to polymer, and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissue.
III. Engineered proteins
[0128] Disclosed herein, in some embodiments, are in vivo engineered proteins. Some embodiments include an in vivo engineered protein complex comprising a compound such as an OmniTAC compound directly bound to a target protein at one end of the compound and a modifier protein at another end of the compound.
[0129] Some embodiments include an in vivo engineered protein comprising: a target protein directly bound to a compound such as OmniTAC compound. In some embodiments, the compound comprises a targeting ligand. In some embodiments, the targeting ligand binds to a binding region on the target protein. In some embodiments, the binding region on the target protein comprises a particular domain or amino acid residue. In some embodiments, the target protein is directly bound to the targeting ligand by a non-covalent interaction between the target protein and the targeting ligand. In some embodiments, the binding between the target protein and the targeting ligand comprises a binding affinity described herein. In some embodiments, the compound described herein further comprises a recruiting ligand. In some embodiments, the recruiting ligand is attached to the targeting ligand via a linker such as a linker described herein. The target protein may include a structural change and/or modification, as compared to the same target protein not bound to the compound, such as a modification and/or structural change resulting from association with the modifier protein.
[0130] Some embodiments include an in vivo engineered protein comprising a modifier protein directly bound to a compound such as an OmniTAC compound. In some embodiments, the compound comprises a recruiting ligand. In some embodiments, the recruiting ligand binds to a binding region on the modifier protein. In some embodiments, the binding region on the modifier protein comprises a particular domain or amino acid residue. In some embodiments, the modifier protein is directly bound to the recruiting ligand by a non-covalent interaction between the modifier protein and the recruiting ligand. In some embodiments, the binding between the modifier protein and the recruiting ligand comprises a binding affinity described herein. In some embodiments, the compound described herein further comprises a targeting ligand. In some embodiments, the targeting ligand is attached to the recruiting ligand via a linker such as a linker described herein.
[0131] The modifier protein may be any modifier protein disclosed herein. The target protein may be any target protein disclosed herein. In some embodiments, the compound comprises a heterobifunctional compound. In some embodiments, the compound comprises an OmniTAC compound. In some embodiments, the compound comprises a targeting ligand, a recruiting ligand, and a linker. In some embodiments, a modified protein disclosed herein is formed in vivo upon administration of the compound or pharmaceutical composition to a subject. Some embodiments relate to a method of forming an in vivo engineered protein, comprising administering the compound or pharmaceutical composition to the subject.
IV. Methods of using OmniTAC compounds
[0132] Disclosed herein, in some embodiments, are methods of using a compound or pharmaceutical composition disclosed herein. For example, a method may include use of an OmniTAC compound. In some embodiments, a method includes use of a heterobifunctional compound. Some embodiments include a method for inducing a change in a target protein, comprising: contacting the target protein with a modifier protein via a modifier protein targeting chimeric compound (OmniTAC) such that the modifier protein induces a change to the target protein. The change may be or may include a modification described herein, and/or a structural change described herein. The change may include a change in activity of the target protein. The change may include a change in cellular location and/or cellular sublocalization of the target protein.
[0133] Some embodiments include a method for inducing a change in a p53 protein, comprising contacting the p53 protein with a modifier protein via a compound described herein, e.g. OmniTAC compound, such that the modifier protein induces a change to the p53 protein. [0134] Some embodiments include a method for inducing a change in a p53 protein, comprising contacting the P53 protein with a modifier protein via a modifier protein targeting chimeric compound (OmniTAC) such that the modifier protein induces a change to the p53 protein. The change may include phosphorylation. Some embodiments include a method of activating a p53 mutant protein. The method may comprise contacting the p53 mutant protein with a compound disclosed herein, e.g, an OmniTAC compound.
[0135] The change in the target protein, e.g. p53, may be or may include any change described herein. In some embodiments, the change includes phosphorylation. In some embodiments, the change includes dephosphorylation. In some embodiments, the change includes palmitoylation. In some embodiments, the change includes depalmitoylation. In some embodiments, the change includes methylation. In some embodiments, the change includes demethylation. In some embodiments, the change includes glycosylation. In some embodiments, the change includes deglycosylation. In some embodiments, the change includes ligation. In some embodiments, the change includes cleavage. In some embodiments, the change includes sulfonation. In some embodiments, the change includes desulfonation. In some embodiments, the change includes ubiquitylation. In some embodiments, the change includes deubiquitylation. In some embodiments, the change includes SUMOylation. In some embodiments, the change includes deSUMOylation. In some embodiments, the change includes fucosylation. In some embodiments, the change includes defucosylation. In some embodiments, the change includes sialylation. In some embodiments, the change includes desialylation. In some embodiments, the change includes tyrosylation. In some embodiments, the change includes detyrosylation. In some embodiments, the change includes acylation. In some embodiments, the change includes deacylation. In some embodiments, the change includes acetylation. In some embodiments, the change includes deacetylation. In some embodiments, the change includes decanoylation. In some embodiments, the change includes dedecanoylation. In some embodiments, the change includes a structural change. In some embodiments, the change includes binding or aggregation with another protein. In some embodiments, the change includes protein folding. In some embodiments, the change includes protein misfolding. In some embodiments, the change includes changes in cellular sub-localization. In some embodiments, the change includes nuclear localization. In some embodiments, the change includes mitochondrial localization.
[0136] The method may include measuring the change. The measurement may be made after administration of the compound to a cell or subject. The measurement may be made in relation to a control or baseline measurement.
[0137] The measurement may be made by any of a variety of methods. Measuring the change may include using a detection reagent that binds to a target protein and yields a detectable signal. After use of the detection reagent that binds to the target protein and yields the detectable signal, a readout may be obtained that is indicative of the presence, absence or amount of the change in the target protein. Measuring the change may include concentrating, filtering, or centrifuging a sample, e.g. comprising the target protein, the modifier protein, and/or the compound described herein.
[0138] Measuring the change may include using an assay method such as microscopy, spectrophotometry, mass spectrometry, chromatography, liquid chromatography, high- performance liquid chromatography, solid-phase chromatography, a lateral flow assay, an immunoassay, an enzyme-linked immunosorbent assay, a western blot, a dot blot, or immunostaining, or a combination thereof. The measurement may be obtained using mass spectrometry. Some examples of assay methods may include using mass spectrometry, a protein chip, or a reverse-phased protein microarray. A measurement may be generated using an immunoassay such as an enzyme-linked immunosorbent assay, western blot, dot blot, or immunohistochemistry. The measurement may be obtained using sequencing. A measurement may be obtained using flow cytometry. A measurement may be obtained using chromatography, for example high performance liquid chromatography.
[0139] The change may be measured or assessed using an enzyme activity assay. The change may be measured or assessed using histochemistry or immunohistochemistry. The change may be measured or assessed using microscopy. The change may be assessed using an assay such as an immunoassay, a colorimetric assay, a lateral flow assay, a fluorescence assay, a proteomics assay, or a cell-based assay.
[0140] The change may be measured using a reporter gene assay, e.g., a luciferase reporter gene assay. The change may be measured or assessed using luminescence or fluorescence. The change may be measured or assessed using microscopy. The change may be measured or assessed or normalized using cell viability.
[0141] Any compound described herein may be used in a method herein. For example, the compound comprises a targeting ligand, a recruiting ligand, and a linker. In some embodiments, the targeting ligand is configured to bind to a target protein described herein. In some embodiments, the recruiting ligand is configured to bind to a modifier protein described herein. [0142] The method may be performed in a subject. The method may be performed in a cell or a sample of a subject. Examples of subjects include vertebrates, animals, mammals, dogs, cats, cattle, rodents, mice, rats, primates, monkeys, and humans. In some embodiments, the subject is a mammal. In some embodiments, the subject is a human.
[0143] In certain embodiments, the compounds described herein are used to treat a subject. The method may include administering a compound, e.g., a heterobifunctional compound described herein such as an OmniTAC compound. In some embodiments, a pharmaceutical composition described herein is administered. The subject may have a disease and may be in need of treatment thereof. In some embodiments, the administration improves a symptom or parameter of the disease. In some embodiments, the disease is caused by a dysfunction and/or dysregulation of a target protein described herein, e.g., p53. In some embodiments, the disease is cancer. The symptoms may be improved as assessed by a measurement made in relation to a baseline measurement.
[0144] The heterobifunctional compounds described herein, such as a compound of Formula I, II, III, IV, V, VI or other compounds in Section I, provide therapeutic benefits to patients suffering from cancer. Accordingly, one aspect of the invention provides a method of treating cancer. The method comprises administering to a patient in need thereof a therapeutically effective amount of a compound described herein, such as a compound of Formula I, II, III, IV, V, VI or other compounds in Section I, to treat the cancer. In certain embodiments, the compound is a compound of Formula I. In certain embodiments, the particular compound of Formula I is a compound defined by one of the embodiments described above.
Cancer
[0145] In certain embodiments, the cancer is ovarian cancer, uterine cancer, endometrial cancer, cervical cancer, prostate cancer, testicular cancer, breast cancer, brain cancer, lung cancer, oral cancer, esophageal cancer, head and neck cancer, stomach cancer, colon cancer, rectal cancer, skin cancer, sebaceous gland carcinoma, bile duct and gallbladder cancers, liver cancer, pancreatic cancer, bladder cancer, urinary tract cancer, kidney cancer, eye cancer, thyroid cancer, lymphoma, or leukemia. In certain embodiments, the cancer is prostate cancer.
[0146] In certain embodiments, the cancer is squamous cell cancer, lung cancer including small cell lung cancer, non-small cell lung cancer, vulval cancer, thyroid 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, hepatic carcinoma, anal carcinoma, penile carcinoma, and head and neck cancer. In certain embodiments, the cancer is at least one selected from the group consisting of ALL, T-Iineage Acute lymphoblastic Leukemia (T-ALL), T-Iineage lymphoblastic Lymphoma (T-LL), Peripheral T-cell lymphoma, Adult T-cell Leukemia, Pre-B ALL, Pre-B Lymphomas, Large B-cell Lymphoma, Burkitts Lymphoma, B-cell ALL, Philadelphia chromosome positive ALL, Philadelphia chromosome positive CML , lymphoma, leukemia, multiple myeloma myeloproliferative diseases, large B cell lymphoma, or B cell Lymphoma.
[0147] In certain embodiments, the cancer is a solid tumor or leukemia. In certain other embodiments, the cancer is colon cancer, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, lung cancer, leukemia, bladder cancer, stomach cancer, cervical cancer, testicular cancer, skin cancer, rectal cancer, thyroid cancer, kidney cancer, uterus cancer, espophagus cancer, liver cancer, an acoustic neuroma, oligodendroglioma, meningioma, neuroblastoma, or retinoblastoma. In certain other embodiments, the cancer is small cell lung cancer, non-small cell lung cancer, melanoma, cancer of the central nervous system tissue, brain cancer, Hodgkin’s lymphoma, non-Hodgkin ’s lymphoma, cutaneous T-Cell lymphoma, cutaneous B-Cell lymphoma, or diffuse large B-Cell lymphoma. In certain other embodiments, the cancer is breast cancer, colon cancer, small -cell lung cancer, non-small cell lung cancer, prostate cancer, renal cancer, ovarian cancer, leukemia, melanoma, or cancer of the central nervous system tissue. In certain other embodiments, the cancer is colon cancer, small-cell lung cancer, non-small cell lung cancer, renal cancer, ovarian cancer, renal cancer, or melanoma.
[0148] In certain embodiments, the cancer is a fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangio endothelio sarcoma, Ewing’s tumor, leiomyosarcoma, rhabdomyosarcoma, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adeno carcinomas, cystadeno carcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms’ tumor, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, or hemangioblastoma.
[0149] In certain embodiments, the cancer is a neuroblastoma, meningioma, hemangiopericytoma, multiple brain metastase, glioblastoma multiforms, glioblastoma, brain stem glioma, poor prognosis malignant brain tumor, malignant glioma, anaplastic astrocytoma, anaplastic oligodendroglioma, neuroendocrine tumor, rectal adeno carcinoma, Dukes C & D colorectal cancer, unresectable colorectal carcinoma, metastatic hepatocellular carcinoma, Kaposi’s sarcoma, karotype acute myeloblastic leukemia, Hodgkin’s lymphoma, non-Hodgkin’s lymphoma, cutaneous T-Cell lymphoma, cutaneous B-Cell lymphoma, diffuse large B-Cell lymphoma, low grade follicular lymphoma, metastatic melanoma, localized melanoma, malignant mesothelioma, malignant pleural effusion mesothelioma syndrome, peritoneal carcinoma, papillary serous carcinoma, gynecologic sarcoma, soft tissue sarcoma, scelroderma, cutaneous vasculitis, Langerhans cell histiocytosis, leiomyosarcoma, fibrodysplasia ossificans progressive, hormone refractory prostate cancer, resected high-risk soft tissue sarcoma, unrescectable hepatocellular carcinoma, Waldenstrom ’s macroglobulinemia, smoldering myeloma, indolent myeloma, fallopian tube cancer, androgen independent prostate cancer, androgen dependent stage IV non-metastatic prostate cancer, hormone-insensitive prostate cancer, chemotherapy -insensitive prostate cancer, castrate resistant prostate cancer, castrate resistant metastatic prostate cancer, papillary thyroid carcinoma, follicular thyroid carcinoma, medullary thyroid carcinoma, or leiomyoma.
[0150] In certain embodiments, the cancer is bone cancer, pancreatic cancer, skin cancer, cancer of the head or neck, cutaneous or intraocular melanoma, ovarian cancer, colon cancer, rectal cancer, cancer of the anal region, stomach cancer, gastrointestinal (gastric, colorectal, and duodenal), uterine cancer, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the cervix, carcinoma of the vagina, carcinoma of the vulva, Hodgkin's Disease, cancer of the esophagus, cancer of the small intestine, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer of the adrenal gland, sarcoma of soft tissue, cancer of the urethra, cancer of the penis, prostate cancer, testicular cancer, chronic or acute leukemia, chronic myeloid leukemia, lymphocytic lymphomas, cancer of the bladder, cancer of the kidney or ureter, renal cell carcinoma, carcinoma of the renal pelvis, non- Hodgkins's lymphoma, spinal axis tumors, brain stem glioma, pituitary adenoma, adrenocortical cancer, gall bladder cancer, multiple myeloma, cholangiocarcinoma, fibrosarcoma, neuroblastoma, retinoblastoma, or a combination of one or more of the foregoing cancers.
[0151] In certain embodiments, the cancer is hepatocellular carcinoma, ovarian cancer, ovarian epithelial cancer, or fallopian tube cancer; papillary serous cystadeno carcinoma or uterine papillary serous carcinoma (UPSC); prostate cancer; testicular cancer; gallbladder cancer; hcpatocholangio carcinoma; soft tissue and bone synovial sarcoma; rhabdomyosarcoma; osteosarcoma; chondrosarcoma; Ewing sarcoma; anaplastic thyroid cancer; adreno corticaladenoma; pancreatic cancer; pancreatic ductal carcinoma or pancreatic adenocarcinoma; gastrointestinal/stomach (GIST) cancer; lymphoma; squamous cell carcinoma of the head and neck (SCCHN); salivary gland cancer; glioma, or brain cancer; neurofibromatosis- 1 associated malignant peripheral nerve sheath tumors (MPNST); Waldenstrom's macroglobulinemia; or medulloblastoma.
[0152] In certain embodiments, the cancer is hepatocellular carcinoma (HCC), hepatoblastoma, colon cancer, rectal cancer, ovarian cancer, ovarian epithelial cancer, fallopian tube cancer, papillary serous cystadeno carcinoma, uterine papillary serous carcinoma (UPSC),hepatocholangio carcinoma, soft tissue and bone synovial sarcoma, rhabdomyosarcoma, osteosarcoma, anaplastic thyroid cancer, adrenocortical adenoma, pancreatic cancer, pancreatic ductal carcinoma, pancreatic adenocarcinoma, glioma, neurofibromatosis- 1 associated malignant peripheral nerve sheath tumors (MPNST), Waldenstrom's macroglobulinemia, or medulloblastoma.
[0153] In certain embodiments, the cancer is a solid tumor, such as a sarcoma, carcinoma, or lymphoma. In certain embodiments, the cancer is kidney cancer; hepatocellular carcinoma(HCC) or hepatoblastoma, or liver cancer; melanoma; breast cancer; colorectal carcinoma, or colorectal cancer; colon cancer; rectal cancer; anal cancer; lung cancer, such as non-small cell lung cancer (NSCLC) or small cell lung cancer (SCLC); ovarian cancer, ovarian epithelial cancer, ovarian carcinoma, or fallopian tube cancer; papillary serous cystadeno carcinoma oruterine papillary serous carcinoma (UPSC); prostate cancer; testicular cancer; gallbladder cancer; hepatochol angiocarcinoma; soft tissue and bone synovial sarcoma; rhabdomyo sarcoma; osteosarcoma; chondro sarcoma; Ewing sarcoma; anaplastic thyroid cancer; adrenocortical carcinoma; pancreatic cancer; pancreatic ductal carcinoma or pancreatic adenocarcinoma; gastrointestinal/stomach (GIST) cancer; lymphoma; squamous cell carcinoma of the head and neck (SCCHN); salivary gland cancer; glioma, or brain cancer; neurofibromatosis- 1 associated malignant peripheral nerve sheath tumors (MPNST); Waldenstrom's macroglobulinemia; ormedulloblastoma.
[0154] In certain embodiments, the cancer is renal cell carcinoma, hepatocellular carcinoma (HCC), hepatoblastoma, colorectal carcinoma, colorectal cancer, colon cancer, rectal cancer, anal cancer, ovarian cancer, ovarian epithelial cancer, ovarian carcinoma, fallopian tube cancer, papillary serous cystadenocarcinoma, uterine papillary serous carcinoma (UPSC), hepatocholangio carcinoma, soft tissue and bone synovial sarcoma, rhabdomyosarcoma, osteosarcoma, chondrosarcoma, anaplastic thyroid cancer, adrenocortical carcinoma, pancreatic cancer, pancreatic ductal carcinoma, pancreatic adenocarcinoma, glioma, brain cancer, neurofibromatosis- 1 associated malignant peripheral nerve sheath tumors (MPNST), Waldenstrom's macroglobulinemia, or medulloblastoma.
[0155] In certain embodiments, the cancer is hepatocellular carcinoma (HCC), hepatoblastoma, colon cancer, rectal cancer, ovarian cancer, ovarian epithelial cancer, ovarian carcinoma, fallopian tube cancer, papillary serous cystadenocarcinoma, uterine papillary serous carcinoma (UPSC), hepatocholangio carcinoma, soft tissue and bone synovial sarcoma, rhabdomyosarcoma, osteosarcoma, anaplastic thyroid cancer, adrenocortical carcinoma, pancreatic cancer, pancreatic ductal carcinoma, pancreatic adenocarcinoma, glioma, neurofibromatosis- 1 associated malignant peripheral nerve sheath tumors (MPNST), Waldenstrom's macroglobulinemia, or medulloblastoma.
[0156] In certain embodiments, the cancer is hepatocellular carcinoma (HCC). In some embodiments, the cancer is hepatoblastoma. Tn some embodiments, the cancer is colon cancer. In some embodiments, the cancer is rectal cancer. In some embodiments, the cancer is ovarian cancer, or ovarian carcinoma. In some embodiments, the cancer is ovarian epithelial cancer. In some embodiments, the cancer is fallopian tube cancer. In some embodiments, the cancer is papillary serous cystadenocarcinoma. In some embodiments, the cancer is uterine papillary serous carcinoma (UPSC). In some embodiments, the cancer is hepatocholangiocarcinoma. In some embodiments, the cancer is soft tissue and bone synovial sarcoma. In some embodiments, the cancer is rhabdomyosarcoma. In some embodiments, the cancer is osteosarcoma. In some embodiments, the cancer is anaplastic thyroid cancer. In some embodiments, the cancer isadrenocortical carcinoma. In some embodiments, the cancer is pancreatic cancer, or pancreatic ductal carcinoma. In some embodiments, the cancer is pancreatic adenocarcinoma. In some embodiments, the cancer is glioma. In some embodiments, the cancer is malignant peripheral nerve sheath tumors (MPNST). In some embodiments, the cancer is neurofibromatosis- 1 associated MPNST. In some embodiments, the cancer is Waldenstrom's macroglobulinemia. In some embodiments, the cancer is medulloblastoma.
[0157] In certain embodiment, the cancer has a p53 mutation.
Causing Death of Cancer Cell
[0158] Another aspect of the invention provides a method of causing death of a cancer cell. The method comprises contacting a cancer cell with an effective amount of a compound described herein, such as a compound of Formula I, II, III, IV, V or VI, or other compounds in Section I, to cause death of the cancer cell. In certain embodiments, the particular compound of Formula I or II is a compound defined by one of the embodiments described above.
[0159] In certain embodiments, the cancer cell is selected from ovarian cancer, uterine cancer, endometrial cancer, cervical cancer, prostate cancer, testicular cancer, breast cancer, brain cancer, lung cancer, oral cancer, esophageal cancer, head and neck cancer, stomach cancer, colon cancer, rectal cancer, skin cancer, sebaceous gland carcinoma, bile duct and gallbladder cancers, liver cancer, pancreatic cancer, bladder cancer, urinary tract cancer, kidney cancer, eye cancer, thyroid cancer, lymphoma, or leukemia. In certain embodiments, the cancer cell is one or more of the cancers recited in the section above entitled “Cancer.” In certain embodiments, the cancer is a prostate cancer cell.
V. Combination Therapy
[0160] The compounds useful within the methods of the invention may be used in combination with one or more additional therapeutic agents useful for treating any disease contemplated herein. These additional therapeutic agents may comprise compounds that are commercially available or synthetically accessible to those skilled in the art. These additional therapeutic agents are known to treat, prevent, or reduce the symptoms, of a disease or disorder contemplated herein.
[0161] Accordingly, in certain embodiments, the method further comprises administering to the subject an additional therapeutic agent that treats the disease contemplated herein.
[0162] In certain embodiments, administering the compound of the invention to the subject allows for administering a lower dose of the additional therapeutic agent as compared to the dose of the additional therapeutic agent alone that is required to achieve similar results in treating the disease contemplated herein. For example, in certain embodiments, the compound of the invention enhances the therapeutic activity of the additional therapeutic compound, thereby allowing for a lower dose of the additional therapeutic compound to provide the same effect.
[0163] A synergistic effect may be calculated, for example, using suitable methods such as, for example, the Sigmoid-Emax equation (Holford & Scheiner, 1981, Clin. Pharmacokinet. 6:429- 453), the equation of Loewe additivity (Loewe & Muischnek, 1926, Arch. Exp. Pathol Pharmacol. 114:313-326) and the median-effect equation (Chou & Talalay, 1984, Adv. Enzyme Regul. 22:27-55). Each equation referred to above may be applied to experimental data to generate a corresponding graph to aid in assessing the effects of the drug combination. The corresponding graphs associated with the equations referred to above are the concentration-effect curve, isobologram curve and combination index curve, respectively.
[0164] In certain embodiments, the compound of the invention and the therapeutic agent are coadministered to the subject. In other embodiments, the compound of the invention and the therapeutic agent are coformulated and co-administered to the subject.
[0165] In certain embodiments, the compound is administered in combination with a second therapeutic agent having activity against cancer. In certain embodiments, the second therapeutic agent is mitomycin, tretinoin, ribomustin, gemcitabine, vincristine, etoposide, cladribine, mitobronitol, methotrexate, doxorubicin, carboquone, pentostatin, nitracrine, zinostatin, cetrorelix, letrozole, raltitrexed, daunorubicin, fadrozole, fotemustine, thymalfasin, sobuzoxane, nedaplatin, cytarabine, bicalutamide, vinorelbine, vesnarinone, aminoglutethimide, amsacrine, proglumide, elliptinium acetate, ketanserin, doxifluridine, etretinate, isotretinoin, streptozocin, nimustine, vindesine, flutamide, drogenil, butocin, carmofur, razoxane, sizofilan, carboplatin, mitolactol, tegafur, ifosfamide, prednimustine, picibanil, levamisole, teniposide, improsulfan, enocitabine, lisuride, oxymetholone, tamoxifen, progesterone, mepitiostane, epitiostanol, formestane, interferon-alpha, interferon-2 alpha, interferon-beta, interferon-gamma, colony stimulating factor- 1, colony stimulating factor-2, denileukin diftitox, interleukin-2, and leutinizing hormone releasing factor.
[0166] In certain embodiments, the second therapeutic agent is an mTOR inhibitor, which inhibits cell proliferation, angiogenesis and glucose uptake. Approved mTOR inhibitors useful in the present invention include everolimus (Afinitor®, Novartis); temsirolimus (Torisel®, Pfizer); and sirolimus (Rapamune®, Pfizer).
[0167] In certain embodiments, the second therapeutic agent is a Poly ADP ribose polymerase (PARP) inhibitor. Approved PARP inhibitors useful in the present invention include olaparib (Lynparza®, AstraZeneca); rucaparib (Rubraca®, Clovis Oncology); and niraparib (Zejula®, Tesaro). Other PARP inhibitors being studied which may be used in the present invention include talazoparib (MDV3800/BMN 673/LT00673, Medivation/Pfizer/Biomarin); veliparib (ABT-888, AbbVie); and BGB-290 (BeiGene, Inc.).
[0168] In certain embodiments, the second therapeutic agent is a phosphatidylinositol 3 kinase (PI3K) inhibitor. Approved PI3K inhibitors useful in the present invention include idelalisib (Zydelig®, Gilead). Other PI3K inhibitors being studied which may be used in the present invention include alpelisib (BYL719, Novartis); taselisib (GDC-0032, Genentech/Roche); pictilisib (GDC-0941, Genentech/Roche); copanlisib (BAY806946, Bayer); duvelisib (formerly IPI-145, Infinity Pharmaceuticals); PQR309 (Piqur Therapeutics, Switzerland); and TGR1202 (formerly RP5230, TG Therapeutics).
[0169] In certain embodiments, the second therapeutic agent is a proteasome inhibitor. Approved proteasome inhibitors useful in the present invention include bortezomib (Velcade®, Takeda); carfilzomib (Kyprolis®, Amgen); and ixazomib (Ninlaro®, Takeda).
[0170] In certain embodiments, the second therapeutic agent is a histone deacetylase (HDAC) inhibitor. Approved HDAC inhibitors useful in the present invention include vorinostat (Zolinza®, Merck); romidepsin (Istodax®, Celgene); panobinostat (Farydak®, Novartis); and belinostat (Beleodaq®, Spectrum Pharmaceuticals). Other HDAC inhibitors being studied which may be used in the present invention include entinostat (SNDX-275, Syndax Pharmaceuticals) (NCT00866333); and chidamide (Epidaza®, HBI-8000, Chipscreen Biosciences, China). [0171] In certain embodiments, the second therapeutic agent is a CDK inhibitor, such as a CDK 4/6 inhibitor. Approved CDK 4/6 inhibitors useful in the present invention include palbociclib (Ibrance®, Pfizer); and ribociclib (Kisqali®, Novartis). Other CDK 4/6 inhibitors being studied which may be used in the present invention include abemaciclib (Ly2835219, Eli Lilly); and trilaciclib (G1T28, G1 Therapeutics).
[0172] In certain embodiments, the second therapeutic agent is an indoleamine (2,3)-dioxygenase (IDO) inhibitor. IDO inhibitors being studied which may be used in the present invention include epacadostat (INCB024360, Incyte); indoximod (NLG-8189, NewLink Genetics Corporation); capmanitib (INC280, Novartis); GDC-0919 (Genentech/Roche); PF-06840003 (Pfizer);
BMS:F001287 (Bristol-Myers Squibb); Phy906/KD108 (Phytoceutica); and an enzyme that breaks down kynurenine (Kynase, Kyn Therapeutics).
[0173] In certain embodiments, the second therapeutic agent is a growth factor antagonist, such as an antagonist of platelet-derived growth factor (PDGF), or epidermal growth factor (EGF) or its receptor (EGFR). Approved PDGF antagonists which may be used in the present invention include olaratumab (Lartruvo®; Eli Lilly). Approved EGFR antagonists which may be used in the present invention include cetuximab (Erbitux®, Eh Lilly); necitumumab (Portrazza®, Eh Lilly), panitumumab (Vectibix®, Amgen); and osimertinib (targeting activated EGFR, Tagrisso®, AstraZeneca).
[0174] In certain embodiments, the second therapeutic agent is an aromatase inhibitor. Approved aromatase inhibitors which may be used in the present invention include exemestane (Aromasin®, Pfizer); anastazole (Arimidex®, AstraZeneca) and letrozole (Femara®, Novartis). [0175] In certain embodiments, the second therapeutic agent is an antagonist of the hedgehog pathway. Approved hedgehog pathway inhibitors which may be used in the present invention include sonidegib (Odomzo®, Sun Pharmaceuticals); and vismodegib (Erivedge®, Genentech), both for treatment of basal cell carcinoma.
[0176] In certain embodiments, the second therapeutic agent is a folic acid inhibitor. Approved folic acid inhibitors useful in the present invention include pemetrexed (Alimta®, Eh Lilly).
[0177] In certain embodiments, the second therapeutic agent is a CC chemokine receptor 4 (CCR4) inhibitor. CCR4 inhibitors being studied that may be useful in the present invention include mogamulizumab (Poteligeo®, Kyowa Hakko Kirin, Japan).
[0178] In certain embodiments, the second therapeutic agent is an isocitrate dehydrogenase (IDH) inhibitor. IDH inhibitors being studied which may be used in the present invention include AG120 (Celgene; NCT02677922); AG221 (Celgene, NCT02677922; NCT02577406);
BAY1436032 (Bayer, NCT02746081); IDH305 (Novartis, NCT02987010). [0179] In certain embodiments, the second therapeutic agent is an arginase inhibitor. Arginase inhibitors being studied which may be used in the present invention include AEB1102 (pegylated recombinant arginase, Aeglea Biotherapeutics), which is being studied in Phase 1 clinical trials for acute myeloid leukemia and myelodysplastic syndrome (NCT02732184) and solid tumors (NCT02561234); and CB-1158 (Calithera Biosciences).
[0180] In certain embodiments, the second therapeutic agent is a glutaminase inhibitor. Glutaminase inhibitors being studied which may be used in the present invention include CB-839 (Calithera Biosciences).
[0181] In certain embodiments, the second therapeutic agent is an antibody that binds to tumor antigens, that is, proteins expressed on the cell surface of tumor cells. Approved antibodies that bind to tumor antigens which may be used in the present invention include rituximab (Rituxan®, Genentech/Biogenldec); ofatumumab (anti-CD20, Arzerra®, GlaxoSmithKline); obinutuzumab (anti-CD20, Gazyva®, Genentech), ibritumomab (anti-CD20 and Yttrium-90, Zevalin®, Spectrum Pharmaceuticals); daratumumab (anti-CD38, Darzalex®, Janssen Biotech), dinutuximab (anti-glycolipid GD2, Unituxin®, United Therapeutics); trastuzumab (anti-HER2, Herceptin®, Genentech); ado-trastuzumab emtansine (anti-HER2, fused to emtansine, Kadcyla®, Genentech); and pertuzumab (anti-HER2, Perjeta®, Genentech); and brentuximab vedotin (anti- CD30-drug conjugate, Adcetris®, Seattle Genetics).
[0182] In certain embodiments, the second therapeutic agent is a topoisomerase inhibitor. Approved topoisomerase inhibitors useful in the present invention include irinotecan (Onivyde®, Merrimack Pharmaceuticals); topotecan (Hycamtin®, GlaxoSmithKline). Topoisomerase inhibitors being studied which may be used in the present invention include pixantrone (Pixuvri®, CTI Biopharma).
[0183] In certain embodiments, the second therapeutic agent is a nucleoside inhibitor, or other therapeutic that interfere with normal DNA synthesis, protein synthesis, cell replication, or will otherwise inhibit rapidly proliferating cells. Such nucleoside inhibitors or other therapeutics include trabectedin (guanidine alkylating agent, Yondelis®, Janssen Oncology), mechlorethamine (alkylating agent, Valchlor®, Aktelion Pharmaceuticals); vincristine (Oncovin®, Eli Lilly; Vincasar®, Teva Pharmaceuticals; Marqibo®, Talon Therapeutics); temozolomide (prodrug to alkylating agent 5-(3-methyltriazen-l-yl)-imidazole-4-carboxamide (MTIC) Temodar®, Merck); cytarabine injection (ara-C, antimetabolic cytidine analog, Pfizer); lomustine (alkylating agent, CeeNU®, Bristol-Myers Squibb; Gleostine®, NextSource Biotechnology); azacitidine (pyrimidine nucleoside analog of cytidine, Vidaza®, Celgene); omacetaxine mepesuccinate (cephalotaxine ester) (protein synthesis inhibitor, Synribo®; Teva Pharmaceuticals); asparaginase Erwinia chrysanthemi (enzyme for depletion of asparagine, Elspar®, Lundbeck; Erwinaze®, EUSA Pharma); eribulin mesylate (microtubule inhibitor, tubulin-based antimitotic, Halaven®, Eisai); cabazitaxel (microtubule inhibitor, tubulin-based antimitotic, Jevtana®, Sanofi -Aventis); capacetrine (thymidylate synthase inhibitor, Xeloda®, Genentech); bendamustine (bifunctional mechlorethamine derivative, believed to form interstrand DNA cross-links, Treanda®, Cephalon/Teva); ixabepilone (semi-synthetic analog of epothilone B, microtubule inhibitor, tubulin-based antimitotic, Ixempra®, Bristol-Myers Squibb); nelarabine (prodrug of deoxyguanosine analog, nucleoside metabolic inhibitor, Arranon®, Novartis); clorafabine (prodrug of ribonucleotide reductase inhibitor, competitive inhibitor of deoxycytidine, Clolar®, Sanofi-Aventis); and trifluridine and tipiracil (thymidine-based nucleoside analog and thymidine phosphorylase inhibitor, Lonsurf®, Taiho Oncology).
[0184] In certain embodiments, the second therapeutic agent is a platinum-based therapeutic, also referred to as platins. Platins cause cross-linking of DNA, such that they inhibit DNA repair and/or DNA synthesis, mostly in rapidly reproducing cells, such as cancer cells. Approved platinum-based therapeutics which may be used in the present invention include cisplatin (Platinol®, Bristol-Myers Squibb); carboplatin (Paraplatin®, Bristol-Myers Squibb; also, Teva; Pfizer); oxaliplatin (Eloxitin® Sanofi-Aventis); and nedaplatin (Aqupla®, Shionogi). Other platinum-based therapeutics which have undergone clinical testing and may be used in the present invention include picoplatin (Poniard Pharmaceuticals); and satraplatin (IM-216, Agennix).
[0185] In certain embodiments, the second therapeutic agent is a taxane compound, which causes disruption of microtubules, which are essential for cell division. Approved taxane compounds which may be used in the present invention include paclitaxel (Taxol®, Bristol-Myers Squibb), docetaxel (Taxotere®, Sanofi-Aventis; Docefrez®, Sun Pharmaceutical), albumin-bound paclitaxel (Abraxane®; Abraxis/Celgene), and cabazitaxel (Jevtana®, Sanofi -Aventis). Other taxane compounds which have undergone clinical testing and may be used in the present invention include SID530 (SK Chemicals, Co.) (NCT00931008).
[0186] In certain embodiments, the second therapeutic agent is an inhibitor of anti-apoptotic proteins, such as BCL-2. Approved anti-apoptotics which may be used in the present invention include venetoclax (Venclexta®, AbbVie/Genentech); and blinatumomab (Blincyto®, Amgen). Other therapeutic agents targeting apoptotic proteins which have undergone clinical testing and may be used in the present invention include navitoclax (ABT-263, Abbott), a BCL-2 inhibitor (NCT02079740).
[0187] In certain embodiments, the second therapeutic agent is a selective estrogen receptor modulator (SERM), which interferes with the synthesis or activity of estrogens. Approved SERMs useful in the present invention include raloxifene (Evista®, Eh Lilly). [0188] In certain embodiments, the second therapeutic agent is an inhibitor of interaction between the two primary p53 suppressor proteins, MDMX and MDM2. Inhibitors of p53 suppression proteins being studied which may be used in the present invention include ALRN- 6924 (Aileron), a stapled peptide that equipotently binds to and disrupts the interaction of MDMX and MDM2 with p53. ALRN-6924 is currently being evaluated in clinical trials for the treatment of AML, advanced myelodysplastic syndrome (MDS) and peripheral T-cell lymphoma (PTCL) (NCT02909972; NCT02264613).
[0189] In certain embodiments, the second therapeutic agent is an inhibitor of transforming growth factor-beta (TGF-beta or TGF0). Inhibitors of TGF-beta proteins being studied which may be used in the present invention include NIS793 (Novartis), an anti-TGF-beta antibody being tested in the clinic for treatment of various cancers, including breast, lung, hepatocellular, colorectal, pancreatic, prostate and renal cancer (NCT 02947165). In some embodiments, the inhibitor of TGF-beta proteins is fresolimumab (GC1008; Sanofi-Genzyme), which is being studied for melanoma (NCT00923169); renal cell carcinoma (NCT00356460); and non-small cell lung cancer (NCT02581787). Additionally, in some embodiments, the additional therapeutic agent is a TGF-beta trap, such as described in Connolly et al. (2012) Int'l J. Biological Sciences 8:964-978. One therapeutic compound currently in clinical trials for treatment of solid tumors is M7824 (Merck KgaA — formerly MSB0011459X), which is a bispecific, anti-PD-Ll/TGFP trap compound (NCT02699515); and (NCT02517398). M7824 is comprised of a fully human IgGl antibody against PD-L1 fused to the extracellular domain of human TGF-beta receptor n, which functions as a TGFP “trap.”
[0190] In certain embodiments, the second therapeutic agent is a cancer vaccine. In some embodiments, the cancer vaccine is selected from sipuleucel-T (Provenge®, Dendreon/Valeant Pharmaceuticals), which has been approved for treatment of asymptomatic, or minimally symptomatic metastatic castrate-resistant (hormone-refractory) prostate cancer; and talimogene laherparepvec (Imlygic®, BioVex/ Amgen, previously known as T-VEC), a genetically modified oncolytic viral therapy approved for treatment of unresectable cutaneous, subcutaneous and nodal lesions in melanoma. In some embodiments, the additional therapeutic agent is selected from an oncolytic viral therapy such as pexastimogene devacirepvec (PexaVec/JX-594, SillaJen/formerly Jennerex Biotherapeutics), a thymidine kinase- (TK-) deficient vaccinia virus engineered to express GM-CSF, for hepatocellular carcinoma (NCT02562755) and melanoma (NCT00429312); pelareorep (Reolysin®, Oncolytics Biotech), a variant of respiratory enteric orphan virus (reovirus) which does not replicate in cells that are not RAS -activated, in numerous cancers, including colorectal cancer (NCT01622543); prostate cancer (NCT01619813); head and neck squamous cell cancer (NCT01166542); pancreatic adenocarcinoma (NCT00998322); and non- small cell lung cancer (NSCLC) (NCT 00861627); enadenotucirev (NG-348, PsiOxus, formerly known as Colo Adi), an adenovirus engineered to express a full length CD80 and an antibody fragment specific for the T-cell receptor CD3 protein, in ovarian cancer (NCT02028117); metastatic or advanced epithelial tumors such as in colorectal cancer, bladder cancer, head and neck squamous cell carcinoma and salivary gland cancer (NCT02636036); ONCOS-102 (Targovax/formerly Oncos), an adenovirus engineered to express GM-CSF, in melanoma (NCT03003676); and peritoneal disease, colorectal cancer or ovarian cancer (NCT02963831); GL-ONC1 (GLV-lh68/GLV-lhl53, Genelux GmbH), vaccinia viruses engineered to express beta-galactosidase (beta-gal)/beta-glucoronidase or beta-gal/human sodium iodide symporter (hNIS), respectively, were studied in peritoneal carcinomatosis (NCT01443260); fallopian tube cancer, ovarian cancer (NCT 02759588); or CG0070 (Cold Genesys), an adenovirus engineered to express GM-CSF, in bladder cancer (NCT02365818).
[0191] In certain embodiments, the second therapeutic agent is an immune checkpoint inhibitor selected from a PD-1 antagonist, a PD-L1 antagonist, or a CTLA-4 antagonist. In some embodiments, a compound disclosed herein or a pharmaceutically acceptable salt thereof is administered in combination with nivolumab (anti -PD-1 antibody, Opdivo®, Bristol-Myers Squibb); pembrolizumab (anti -PD-1 antibody, Keytruda®, Merck); ipilimumab (anti-CTLA-4 antibody, Yervoy®, Bristol-Myers Squibb); durvalumab (anti-PD-Ll antibody, Imfinzi®, AstraZeneca); or atezolizumab (anti-PD-Ll antibody, Tecentriq®, Genentech). Other immune checkpoint inhibitors suitable for use in the present invention include REGN2810 (Regeneron), an anti-PD-1 antibody tested in patients with basal cell carcinoma (NCT03132636); NSCLC (NCT03088540); cutaneous squamous cell carcinoma (NCT02760498); lymphoma (NCT02651662); and melanoma (NCT03002376); pidilizumab (CureTech), also known as CT- 011, an antibody that binds to PD-1, in clinical trials for diffuse large B-cell lymphoma and multiple myeloma; avelumab (Bavencio®, Pfizer/Merck KGaA), also known as MSB0010718C), a fully human IgGl anti-PD-Ll antibody, in clinical trials for non-small cell lung cancer, Merkel cell carcinoma, mesothelioma, solid tumors, renal cancer, ovarian cancer, bladder cancer, head and neck cancer, and gastric cancer; and PDR001 (Novartis), an inhibitory antibody that binds to PD-1, in clinical trials for non-small cell lung cancer, melanoma, triple negative breast cancer and advanced or metastatic solid tumors. Tremelimumab (CP-675,206; Astrazeneca) is a fully human monoclonal antibody against CTLA-4 that has been in studied in clinical trials for a number of indications, including: mesothelioma, colorectal cancer, kidney cancer, breast cancer, lung cancer and non-small cell lung cancer, pancreatic ductal adenocarcinoma, pancreatic cancer, germ cell cancer, squamous cell cancer of the head and neck, hepatocellular carcinoma, prostate cancer, endometrial cancer, metastatic cancer in the liver, liver cancer, large B-cell lymphoma, ovarian cancer, cervical cancer, metastatic anaplastic thyroid cancer, urothelial cancer, fallopian tube cancer, multiple myeloma, bladder cancer, soft tissue sarcoma, and melanoma. AGEN-1884 (Agenus) is an anti-CTLA4 antibody that is being studied in Phase 1 clinical trials for advanced solid tumors (NCT02694822).
VI. Definitions
[0192] Unless defined otherwise, all terms of art, notations and other technical and scientific terms or terminology used herein are intended to have the same meaning as is commonly understood by one of ordinary skill in the art to which the claimed subject matter pertains. In some cases, terms with commonly understood meanings are defined herein for clarity or ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art.
[0193] Throughout this application, various embodiments may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the disclosure.
Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range. As used herein, “between” is a range inclusive of the ends of the range. For example, a number between x and y explicitly includes the numbers x and y, and any numbers that fall within x and y.
[0194] The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.
[0195] As used in the specification and appended claims, unless specified to the contrary, the following terms have the meaning indicated below.
[0196] As used in the specification and claims, the singular forms “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a sample” includes a plurality of samples, including mixtures thereof.
[0197] As used herein, the term “about” a number refers to that number plus or minus 15% of that number. The term “about” a range refers to that range minus 15% of its lowest value and plus 15% of its greatest value.
[0198] As used herein, the terms “comprising” (and any variant or form of comprising, such as “comprise” and “comprises”), “having” (and any variant or form of having, such as “have” and “has”), “including” (and any variant or form of including, such as “includes” and “include”) or “containing” (and any variant or form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited, elements or method steps. It is contemplated that any embodiment discussed in this specification can be implemented with respect to any compound, protein, and/or method of the present disclosure.
[0199] The terms “determining,” “measuring,” “evaluating,” “assessing,” “assaying,” and “analyzing” are often used interchangeably herein to refer to forms of measurement. The terms include determining if an element is present or not (for example, detection). These terms can include quantitative, qualitative or quantitative and qualitative determinations. Assessing can be relative or absolute. “Detecting the presence of’ can include determining the amount of something present in addition to determining whether it is present or absent depending on the context.
[0200] The terms “subject,” “individual,” or “patient” are often used interchangeably herein. A “subject” can be a biological entity containing expressed genetic materials. The biological entity can be a plant, animal, or microorganism, including, for example, bacteria, viruses, fungi, and protozoa. The subject can be tissues, cells and their progeny of a biological entity obtained in vivo or cultured in vitro. The subject can be a mammal. The mammal can be a human. The subject may be diagnosed or suspected of being at high risk for a disease. In some cases, the subject is not necessarily diagnosed or suspected of being at high risk for the disease.
[0201] The term “protein” may include a polypeptide. A protein may include a eukaryotic protein, or a protein in a cell or subject.
[0202] As used herein, the terms “treatment” or “treating” are used in reference to a pharmaceutical or other intervention regimen for obtaining beneficial or desired results in the recipient. Beneficial or desired results include but are not limited to a therapeutic benefit or a prophylactic benefit. A therapeutic benefit may refer to eradication or amelioration of symptoms or of an underlying disorder being treated. Also, a therapeutic benefit can be achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder. A prophylactic effect includes delaying, preventing, or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof. For prophylactic benefit, a subject at risk of developing a particular disease, or to a subject reporting one or more of the physiological symptoms of a disease may undergo treatment, even though a diagnosis of this disease may not have been made. [0203] "Amino" refers to the -NH2 radical.
[0204] "Cyano" refers to the -CN radical.
[0205] "Nitro" refers to the -NO2 radical. [0206] "Oxa" refers to the -O- radical.
[0207] "Oxo" refers to the =0 radical.
[0208] "Thioxo" refers to the =S radical.
[0209] Imino" refers to the =N-H radical. [0210] "Oximo" refers to the =N-0H radical. [0211] "Hydrazino" refers to the =N-NH2 radical.
[0212] "Alkyl" refers to a straight or branched hydrocarbon chain radical consisting solely of carbon and hydrogen atoms, containing no unsaturation, having from one to fifteen carbon atoms (e.g., C1-C15 alkyl). In certain embodiments, an alkyl comprises one to thirteen carbon atoms (e.g., C1-C13 alkyl). In certain embodiments, an alkyl comprises one to eight carbon atoms (e.g., Ci-Cs alkyl). In other embodiments, an alkyl comprises one to five carbon atoms (e.g., C1-C5 alkyl). In other embodiments, an alkyl comprises one to four carbon atoms (e.g., C1-C4 alkyl). In other embodiments, an alkyl comprises one to three carbon atoms (e.g., C1-C3 alkyl). In other embodiments, an alkyl comprises one to two carbon atoms (e.g., C1-C2 alkyl). In other embodiments, an alkyl comprises one carbon atom (e.g., Ci alkyl). In other embodiments, an alkyl comprises five to fifteen carbon atoms (e.g., C5-C15 alkyl). In other embodiments, an alkyl comprises five to eight carbon atoms (e.g., Cs-Cs alkyl). In other embodiments, an alkyl comprises two to five carbon atoms (e.g., C2-C5 alkyl). In other embodiments, an alkyl comprises three to five carbon atoms (e.g., C3-C5 alkyl). In other embodiments, the alkyl group is selected from methyl, ethyl, 1 -propyl (w-propyl), 1 -methylethyl (Ao-propyl), 1 -butyl (w-butyl), 1- methylpropyl (sec-butyl), 2 -methylpropyl (Ao-butyl), 1,1 -dimethyl ethyl (ze/7-butyl), 1 -pentyl (n- pentyl). The alkyl is attached to the rest of the molecule by a single bond. Unless stated otherwise specifically in the specification, an alkyl group is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo, trimethylsilanyl, -ORa, - SRa, -OC(O)-Ra, -N(Ra)2, -C(O)Ra, -C(O)ORa, -C(O)N(Ra)2, -N(Ra)C(O)ORa, -OC(O)-N(Ra)2, - N(Ra)C(O)Ra, -N(Ra)S(O)tRa (where t is 1 or 2), -S(O)tORa (where t is 1 or 2), -S(O)tRa (where t is 1 or 2) and -S(O)tN(Ra)2 (where t is 1 or 2) where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, carbocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), carbocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl).
[0213] "Alkoxy" refers to a radical bonded through an oxygen atom of the formula -O-alkyl, where alkyl is an alkyl chain as defined above.
[0214] "Alkenyl" refers to a straight or branched hydrocarbon chain radical group consisting solely of carbon and hydrogen atoms, containing at least one carbon-carbon double bond, and having from two to twelve carbon atoms. In certain embodiments, an alkenyl comprises two to eight carbon atoms. In other embodiments, an alkenyl comprises two to four carbon atoms. The alkenyl is attached to the rest of the molecule by a single bond, for example, ethenyl (i.e., vinyl), prop-l-enyl (i.e., allyl), but-l-enyl, pent-l-enyl, penta- 1,4-dienyl, and the like. Unless stated otherwise specifically in the specification, an alkenyl group is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo, tnmethylsilanyl, -ORa, -SRa, -OC(O)-Ra, -N(Ra)2, -C(O)Ra, -C(O)ORa, -C(O)N(Ra)2, - N(Ra)C(O)ORa, -OC(O)-N(Ra)2, -N(Ra)C(O)Ra, -N(Ra)S(O)tRa (where t is 1 or 2), -S(O)tORa (where t is 1 or 2), -S(O)tRa (where t is 1 or 2) and -S(O)tN(Ra)2 (where t is 1 or 2) where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, carbocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), carbocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl).
[0215] "Alkynyl" refers to a straight or branched hydrocarbon chain radical group consisting solely of carbon and hydrogen atoms, containing at least one carbon-carbon triple bond, having from two to twelve carbon atoms. In certain embodiments, an alkynyl comprises two to eight carbon atoms. In other embodiments, an alkynyl comprises two to six carbon atoms. In other embodiments, an alkynyl comprises two to four carbon atoms. The alkynyl is attached to the rest of the molecule by a single bond, for example, ethynyl, propynyl, butynyl, pentynyl, hexynyl, and the like. Unless stated otherwise specifically in the specification, an alkynyl group is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo, trimethylsilanyl, -ORa, -SRa, -OC(O)-Ra, -N(Ra)2, -C(O)Ra, -C(O)ORa, -C(O)N(Ra)2, - N(Ra)C(O)ORa, -OC(O)-N(Ra)2, -N(Ra)C(O)Ra, -N(Ra)S(O)tRa (where t is 1 or 2), -S(O)tORa (where t is 1 or 2), -S(O)tRa (where t is 1 or 2) and -S(O)tN(Ra)2 (where t is 1 or 2) where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, carbocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), carbocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl).
[0216] "Alkylene" or "alkylene chain" refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group, consisting solely of carbon and hydrogen, containing no unsaturation and having from one to twelve carbon atoms, for example, methylene, ethylene, propylene, n-butylene, and the like. The alkylene chain is attached to the rest of the molecule through a single bond and to the radical group through a single bond. The points of attachment of the alkylene chain to the rest of the molecule and to the radical group are through one carbon in the alkylene chain or through any two carbons within the chain. In certain embodiments, an alkylene comprises one to eight carbon atoms (e.g., Ci-Cs alkylene). In other embodiments, an alkylene comprises one to five carbon atoms (e.g., C1-C5 alkylene). In other embodiments, an alkylene comprises one to four carbon atoms (e.g., C1-C4 alkylene). In other embodiments, an alkylene comprises one to three carbon atoms (e.g., C1-C3 alkylene). In other embodiments, an alkylene comprises one to two carbon atoms (e.g., Ci-C2 alkylene). In other embodiments, an alkylene comprises one carbon atom (e.g., Ci alkylene). In other embodiments, an alkylene comprises five to eight carbon atoms (e.g., Cs-Cs alkylene). In other embodiments, an alkylene comprises two to five carbon atoms (e.g., C2-C5 alkylene). In other embodiments, an alkylene comprises three to five carbon atoms (e.g., C3-C5 alkylene). Unless stated otherwise specifically in the specification, an alkylene chain is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo, trimethylsilanyl, -ORa, - SRa, -OC(O)-Ra, -N(Ra)2, -C(O)Ra, -C(O)ORa, -C(O)N(Ra)2, -N(Ra)C(O)ORa, -OC(O)- N(Ra)2, - N(Ra)C(O)Ra, -N(Ra)S(O)tRa (where t is 1 or 2), -S(O)tORa (where t is 1 or 2), -S(O)tRa (where t is 1 or 2) and -S(O)tN(Ra)2 (where t is 1 or 2) where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, carbocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), carbocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl).
[0217] "Aryl" refers to a radical derived from an aromatic monocyclic or multicyclic hydrocarbon ring system by removing a hydrogen atom from a ring carbon atom. The aromatic monocyclic or multicyclic hydrocarbon ring system contains only hydrogen and carbon from five to eighteen carbon atoms, where at least one of the rings in the ring system is fully unsaturated, i.e., it contains a cyclic, delocalized (4n+2) p-electron system in accordance with the Hiickel theory. The ring system from which aryl groups are derived include, but are not limited to, groups such as benzene, fluorene, indane, indene, tetralin and naphthalene. Unless stated otherwise specifically in the specification, the term "aryl" or the prefix "ar-" (such as in "aralkyl") is meant to include aryl radicals optionally substituted by one or more substituents independently selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -Rb-0Ra, -Rb-OC(O)-Ra, -Rb-OC(O)-ORa, -Rb-OC(O)- N(Ra)2, -Rb-N(Ra)2, -Rb-C(O)Ra, -Rb-C(O)ORa, -Rb-C(O)N(Ra)2, -Rb-O-Rc-C(O)N(Ra)2, -Rb- N(Ra)C(O)ORa, -Rb-N(Ra)C(O)Ra, -Rb-N(Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb-S(O)tORa (where t is 1 or 2) and -Rb-S(O)tN(Ra)2 (where t is 1 or 2), where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, cycloalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), cycloalkylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), each Rb is independently a direct bond or a straight or branched alkylene or alkenylene chain, and Rc is a straight or branched alkylene or alkenylene chain, and where each of the above substituents is unsubstituted unless otherwise indicated.
[0218] "Aralkyl" refers to a radical of the formula -Rc-aryl where Rc is an alkylene chain as defined above, for example, methylene, ethylene, and the like. The alkylene chain part of the aralkyl radical is optionally substituted as described above for an alkylene chain. The aryl part of the aralkyl radical is optionally substituted as described above for an aryl group.
[0219] "Carbocyclyl" or “cycloalkyl” refers to a stable non-aromatic monocyclic or polycyclic hydrocarbon radical consisting solely of carbon and hydrogen atoms, which includes fused or bridged ring systems, having from three to fifteen carbon atoms. In certain embodiments, a carbocyclyl comprises three to ten carbon atoms. In other embodiments, a carbocyclyl comprises five to seven carbon atoms. The carbocyclyl is attached to the rest of the molecule by a single bond. Carbocyclyl is saturated (i.e., containing single C-C bonds only) or unsaturated (i.e., containing one or more double bonds or triple bonds). A fully saturated carbocyclyl radical is also referred to as "cycloalkyl." Examples of monocyclic cycloalkyls include, e.g., cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. An unsaturated carbocyclyl is also referred to as "cycloalkenyl." Examples of monocyclic cycloalkenyls include, e.g., cyclopentenyl, cyclohexenyl, cycloheptenyl, and cyclooctenyl. Polycyclic carbocyclyl radicals include, for example, adamantyl, norbomyl (i.e., bicyclo[2.2.1]heptanyl), norbomenyl, decalinyl, 7,7-dimethyl-bicyclo[2.2.1]heptanyl, and the like. Unless otherwise stated specifically in the specification, the term "carbocyclyl" is meant to include carbocyclyl radicals that are optionally substituted by one or more substituents independently selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, oxo, thioxo, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -Rb-0Ra, -Rb-OC(O)-Ra, -Rb-OC(O)-ORa, -Rb-OC(O)-N(Ra)2, -Rb-N(Ra)2, -Rb- C(O)Ra, -Rb-C(O)ORa, -Rb-C(O)N(Ra)2, -Rb-O-Rc-C(O)N(Ra)2, -Rb-N(Ra)C(O)ORa, -Rb- N(Ra)C(O)Ra, -Rb-N(Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb-S(O)tORa (where t is 1 or 2) and -Rb-S(O)tN(Ra)2 (where t is 1 or 2), where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, cycloalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), cycloalkylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), each Rb is independently a direct bond or a straight or branched alkylene or alkenylene chain, and Rc is a straight or branched alkylene or alkenylene chain, and where each of the above substituents is unsubstituted unless otherwise indicated.
[0220] "Carbocyclylalkyl" refers to a radical of the formula -Rc-carbocyclyl where Rc is an alkylene chain as defined above. The alkylene chain and the carbocyclyl radical are optionally substituted as defined above.
[0221] "Halo" or "halogen" refers to bromo, chloro, fluoro or iodo substituents.
[0222] "Fluoroalkyl" refers to an alkyl radical, as defined above, that is substituted by one or more fluoro radicals, as defined above, for example, trifluoromethyl, difluoromethyl, fluoromethyl, 2,2,2-trifluoroethyl, l-fluoromethyl-2-fluoroethyl, and the like. In some embodiments, the alkyl part of the fluoroalkyl radical is optionally substituted as defined above for an alkyl group.
[0223] "Heterocyclyl" or “heterocycloalkyl” refers to a stable 3- to 18-membered nonaromatic ring radical that comprises two to twelve carbon atoms and from one to six heteroatoms selected from nitrogen, oxygen and sulfur. Unless stated otherwise specifically in the specification, the heterocyclyl radical is a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which optionally includes fused or bridged ring systems. The heteroatoms in the heterocyclyl radical are optionally oxidized. One or more nitrogen atoms, if present, are optionally quatemized. The heterocyclyl radical is partially or fully saturated. The heterocyclyl is attached to the rest of the molecule through any atom of the ring(s). Examples of such heterocyclyl radicals include, but are not limited to, dioxolanyl, thienyl[l,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2-oxopiperazinyl, 2-oxopiperidinyl, 2-oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4-piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl, 1-oxo-thiomorpholinyl, and 1,1-dioxo-thiomorpholinyl. Unless stated otherwise specifically in the specification, the term "heterocyclyl" is meant to include heterocyclyl radicals as defined above that are optionally substituted by one or more substituents selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, thioxo, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -Rb-ORa, -Rb-OC(O)-Ra, -Rb-OC(O)-ORa, -Rb-OC(O)-N(Ra)2, -Rb-N(Ra)2, -Rb- C(O)Ra, -Rb-C(O)ORa, -Rb-C(O)N(Ra)2, -Rb-O-Rc-C(O)N(Ra)2, -Rb-N(Ra)C(O)ORa, -Rb- N(Ra)C(O)Ra, -Rb-N(Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb-S(O)tORa (where t is 1 or 2) and -Rb-S(O)tN(Ra)2 (where t is 1 or 2), where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, cycloalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), cycloalkylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), each Rb is independently a direct bond or a straight or branched alkylene or alkenylene chain, and Rc is a straight or branched alkylene or alkenylene chain, and where each of the above substituents is unsubstituted unless otherwise indicated.
[0224] "A-heterocyclyl" or “N-attached heterocyclyl” refers to a heterocyclyl radical as defined above containing at least one nitrogen and where the point of attachment of the heterocyclyl radical to the rest of the molecule is through a nitrogen atom in the heterocyclyl radical. An A-heterocyclyl radical is optionally substituted as described above for heterocyclyl radicals. Examples of such A-heterocyclyl radicals include, but are not limited to, 1-morpholinyl,
1-piperidinyl, 1-piperazinyl, 1-pyrrolidinyl, pyrazolidinyl, imidazolinyl, and imidazolidinyl. [0225] "C-heterocyclyl" or “C-attached heterocyclyl” refers to a heterocyclyl radical as defined above containing at least one heteroatom and where the point of attachment of the heterocyclyl radical to the rest of the molecule is through a carbon atom in the heterocyclyl radical. A C-heterocyclyl radical is optionally substituted as described above for heterocyclyl radicals. Examples of such C-heterocyclyl radicals include, but are not limited to, 2-morpholinyl,
2- or 3- or 4-piperidinyl, 2-piperazinyl, 2- or 3-pyrrolidinyl, and the like.
[0226] "Heteroaryl" refers to a radical derived from a 3 - to 18- membered aromatic ring radical that comprises two to seventeen carbon atoms and from one to six heteroatoms selected from nitrogen, oxygen and sulfur. As used herein, the heteroaryl radical is a monocyclic, bicyclic, tricyclic or tetracyclic ring system, wherein at least one of the rings in the ring system is fully unsaturated, i.e., it contains a cyclic, delocalized (4n+2) p-electron system in accordance with the Hiickel theory. Heteroaryl includes fused or bridged ring systems. The heteroatom(s) in the heteroaryl radical is optionally oxidized. One or more nitrogen atoms, if present, are optionally quatemized. The heteroaryl is attached to the rest of the molecule through any atom of the ring(s). Examples of heteroaryls include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzindolyl, 1,3-benzodioxolyl, benzofuranyl, benzooxazolyl, benzo[d]thiazolyl, benzothiadiazolyl, benzo[/?][ l ,4]dioxepinyl, benzo[b][l,4]oxazinyl, 1 ,4-benzodioxanyl, benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl, benzopyranyl, benzopyranonyl, benzofuranyl, benzofuranonyl, benzothienyl (benzothiophenyl), benzothieno[3,2-d]pyrimidinyl, benzotriazolyl, benzo[4,6]imidazo[l,2-a]pyridinyl, carbazolyl, cinnolinyl, cyclopenta[d]pyrimidinyl, 6,7-dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidinyl,
5.6-dihydrobenzo[h]quinazolinyl, 5,6-dihydrobenzo[h]cinnolinyl, 6,7-dihydro-5H- benzo[6,7]cyclohepta[l,2-c]pyridazinyl, dibenzofuranyl, dibenzothiophenyl, furanyl, furanonyl, furo[3,2-c]pyridinyl, 5,6,7,8,9,10-hexahydrocycloocta[d]pyrimidinyl, 5,6,7,8,9,10-hexahydrocycloocta[d]pyridazinyl, 5,6,7,8,9,10-hexahydrocycloocta[d]pyridinyl, isothiazolyl, imidazolyl, indazolyl, indolyl, indazolyl, isoindolyl, indolinyl, isoindolinyl, isoquinolyl, indolizinyl, isoxazolyl, 5,8-methano-5,6,7,8-tetrahydroquinazolinyl, naphthyridinyl,
1.6-naphthyri dinonyl, oxadiazolyl, 2-oxoazepinyl, oxazolyl, oxiranyl,
5, 6, 6a, 7, 8, 9, 10, 10a-octahydrobenzo[h]quinazolinyl, 1 -phenyl- 1 /7-pyrrolyl, phenazinyl, phenothiazinyl, phenoxazinyl, phthalazinyl, pteridinyl, purinyl, pyrrolyl, pyrazolyl, pyrazolo[3,4-d]pyrimidinyl, pyridinyl, pyrido[3,2-d]pyrimidinyl, pyrido[3,4-d]pyrimidinyl, pyrazinyl, pyrimidinyl, pyridazinyl, pyrrolyl, quinazolinyl, quinoxalinyl, quinolinyl, isoquinolinyl, tetrahydroquinolinyl, 5,6,7,8-tetrahydroquinazolinyl,
5.6.7.8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidinyl,
6.7.8.9-tetrahydro-5H-cyclohepta[4,5]thieno[2,3-d]pyrimidinyl, 5,6,7,8-tetrahydropyrido[4,5-c]pyridazinyl, thiazolyl, thiadiazolyl, triazolyl, tetrazolyl, triazinyl, thieno[2,3-d]pyrimidinyl, thieno[3,2-d]pyrimidinyl, thieno[2,3-c]pridinyl, and thiophenyl (i.e. thienyl). Unless stated otherwise specifically in the specification, the term "heteroaryl" is meant to include heteroaryl radicals as defined above which are optionally substituted by one or more substituents selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, haloalkenyl, haloalkynyl, oxo, thioxo, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -Rb- 0Ra, -Rb-0C(0)-Ra, -Rb-0C(0)-0Ra, -Rb-0C(0)-N(Ra)2, -Rb-N(Ra)2, -Rb-C(0)Ra, -Rb-C(0)0Ra, -Rb-C(0)N(Ra)2, -Rb-0-Rc-C(0)N(Ra)2, -Rb-N(Ra)C(0)0Ra, -Rb-N(Ra)C(0)Ra, -Rb-N(Ra)S(0)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb-S(O)tORa (where t is 1 or 2) and -Rb- S(O)tN(Ra)2 (where t is 1 or 2), where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, cycloalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), cycloalkylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), each Rb is independently a direct bond or a straight or branched alkylene or alkenylene chain, and Rc is a straight or branched alkylene or alkenylene chain, and where each of the above substituents is unsubstituted unless otherwise indicated.
[0227] "A-heteroaryl" refers to a heteroaryl radical as defined above containing at least one nitrogen and where the point of attachment of the heteroaryl radical to the rest of the molecule is through a nitrogen atom in the heteroaryl radical. An A-heteroaryl radical is optionally substituted as described above for heteroaryl radicals.
[0228] "C-heteroaryl" refers to a heteroaryl radical as defined above and where the point of attachment of the heteroaryl radical to the rest of the molecule is through a carbon atom in the heteroaryl radical. A C-heteroaryl radical is optionally substituted as described above for heteroaryl radicals.
[0229] “Attachment point” or “AP” refers to an atom or molecule that connects the linker to the target ligand and/or the recruiting ligand. The attachment point can be covalently bonded to the linker, target ligand, and the recruiting ligand.
[0230] The compounds disclosed herein, in some embodiments, contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric forms that are defined, in terms of absolute stereochemistry, as (R)- or (5)-. Unless stated otherwise, it is intended that all stereoisomeric forms of the compounds disclosed herein are contemplated by this disclosure. When the compounds described herein contain alkene double bonds, and unless specified otherwise, it is intended that this disclosure includes both E and Z geometric isomers (e.g., cis or trans.} Likewise, all possible isomers, as well as their racemic and optically pure forms, and all tautomeric forms are also intended to be included. The term “geometric isomer” refers to E or Z geometric isomers (e.g., cis or trans) of an alkene double bond. The term “positional isomer” refers to structural isomers around a central ring, such as ortho-, meta-, and para- isomers around a benzene ring.
[0231] A "tautomer" refers to a molecule wherein a proton shift from one atom of a molecule to another atom of the same molecule is possible. The compounds presented herein, in certain embodiments, exist as tautomers. In circumstances where tautomerization is possible, a chemical equilibrium of the tautomers will exist. The exact ratio of the tautomers depends on several factors, including physical state, temperature, solvent, and pH. Some examples of tautomeric equilibrium include:
[0232] The compounds disclosed herein, in some embodiments, are used in different enriched isotopic forms, e.g., enriched in the content of 2H, 3H, nC, 13C or 14C. In one particular embodiment, the compound is deuterated in at least one position. Such deuterated forms can be made by the procedure described in U.S. Patent Nos. 5,846,514 and 6,334,997. As described in U.S. Patent Nos. 5,846,514 and 6,334,997, deuteration can improve the metabolic stability and or efficacy, thus increasing the duration of action of drugs.
[0233] Unless otherwise stated, structures depicted herein are intended to include compounds which differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of a hydrogen by a deuterium or tritium, or the replacement of a carbon by 13C- or 14C-enriched carbon are within the scope of the present disclosure.
[0234] The compounds of the present disclosure optionally contain unnatural proportions of atomic isotopes at one or more atoms that constitute such compounds. For example, the compounds may be labeled with isotopes, such as for example, deuterium (2H), tritium (3H), iodine- 125 (125I) or carbon- 14 (14C). Isotopic substitution with 2H, "C, 13C, 14C, 15C, 12N, 13N, 15N, 16N, 16O, 17O, 14F, 15F, 16F, 17F, 18F, 33S, 34S, 35S, 36S, 35C1, 37C1, 79Br, 81Br, 125I are all contemplated. All isotopic variations of the compounds of the present invention, whether radioactive or not, are encompassed within the scope of the present invention.
[0235] In certain embodiments, the compounds disclosed herein have some or all of the 1 H atoms replaced with 2H atoms. The methods of synthesis for deuterium-containing compounds are known in the art and include, by way of non-limiting example only, the following synthetic methods.
[0236] Deuterium substituted compounds are synthesized using various methods such as described in: Dean, Dennis C.; Editor. Recent Advances in the Synthesis and Applications of Radiolabeled Compounds for Drug Discovery and Development. [In: Curr., Pharm. Des., 2000; 6(10)] 2000, 110 pp; George W.; Varma, Rajender S. The Synthesis of Radiolabeled Compounds via Organometallic Intermediates, Tetrahedron, 1989, 45(21), 6601-21; and Evans, E. Anthony. Synthesis of radiolabeled compounds, J. Radioanal. Chem., 1981, 64(1-2), 9-32.
[0237] Isotopic labeling can be performed using a variety of readily available reagents not limited to: isotopically -enriched carbon dioxide, dimethylformamide, cyanide salts, acetylenes, ammonium salts, other small organic and inorganic sources. Various methods are employed such as described in: Neumann, K. T. et al. Synthesis and Selective 2H-, 13C-, and 15N-Labehng of the Tau Protein Binder THK-523. J. Labelled Compd. Radiopharm. 2017, 60, 30-35; Baldwin, M. A.; Langley, G. J. Synthesis of [2-I3C]Quinoline and [3-13C] Quinolone. J. Labelled Compd. Radiopharm. 1985, 22, 1233-1238; Wang, T. S. T. et al. Preparation of l-Methyl-4-[4-(7-chloro- 4-quinolyl-[3-14C]-amino)benzoyl]piperazme. J. Labelled Compd. Radiopharm 1995, 36, 313- 320; Saemian, N. et al. Synthesis of 14C .Analogue of l,2-Diaryl-[2-14C]-pyrroles. J. Radioanal. NucL Chem. 2007, 274, 631-634; Czeskis, B. A. et al. Synthesis of 14C-Labeled 4- Hydroxyindole as an Intermediate for the Preparation of (S)-2-[4-[2-[3 -(Indol-2- [14C]-4-yloxy)- 2 -hy droxypropylammo] -2-methy Ipropyl] -phenoxy ]py ri dine-5 -carboxamide (LY368842- [Indole- 14C]) Glycolate. J. Labelled Compd. Radiopharm. 2002, 45, 1143-1152; Latli, B., et al. Synthesis of Two Potent Glucocoticoid Receptor Agonists Labeled with Carbon-14 and Stable Isotopes. J. Labelled Compd. Radiopharm. 2015, 58, 445-452, Cappon, J. J., et al. Synthesis of L-Histidine Specfically Labelled with Stable Isotopes. Reel. I'rav. Clnm. Pays-Bas 1994, 113, 318-328;
Guillame, M., et al. Unexpected Trifluoromethylated Pyrazoles From Ethyl 2-Diazo~4,4,4~ trifluoroacetoacetate and 1-Diethylamino-prop-l-yne. J. Fluorine Chem. 1994, 69, 253-256; Hickey, M. I, et al. Syntheses of a Radiolabelled CXCR2 Antagonist AZD5069 and Its Major Human Metabolite. J. Labelled Compd. Radiopharm. 2016, 59, 432-438.
[0238] Deuterated starting materials are readily available and are subjected to the synthetic methods described herein to provide for the synthesis of deuterium-containing compounds. Large numbers of deuterium-containing reagents and building blocks are available commercially from chemical vendors, such as Aldrich Chemical Co.
[0239] "Pharmaceutically acceptable salt" includes both acid and base addition salts. A pharmaceutically acceptable salt of any one of the compounds described herein is intended to encompass any and all pharmaceutically suitable salt forms. Preferred pharmaceutically acceptable salts of the compounds described herein are pharmaceutically acceptable acid addition salts and pharmaceutically acceptable base addition salts.
[0240] "Pharmaceutically acceptable acid addition salt" refers to those salts which retain the biological effectiveness and properties of the free bases, which are not biologically or otherwise undesirable, and which are formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, hydroiodic acid, hydrofluoric acid, phosphorous acid, and the like. Also included are salts that are formed with organic acids such as aliphatic mono- and di carboxylic acids, phenyl-substituted alkanoic acids, hydroxy alkanoic acids, alkanedioic acids, aromatic acids, aliphatic and. aromatic sulfonic acids, etc. and include, for example, acetic acid, trifluoroacetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like. Exemplary salts thus include sulfates, pyrosulfates, bisulfates, sulfites, bisulfites, nitrates, phosphates, monohydrogenphosphates, dihydrogenphosphates, metaphosphates, pyrophosphates, chlorides, bromides, iodides, acetates, trifluoroacetates, propionates, caprylates, isobutyrates, oxalates, malonates, succinate suberates, sebacates, fumarates, maleates, mandelates, benzoates, chlorobenzoates, methylbenzoates, dinitrobenzoates, phthalates, benzenesulfonates, toluenesulfonates, phenylacetates, citrates, lactates, malates, tartrates, methanesulfonates, and the like. Also contemplated are salts of amino acids, such as arginates, gluconates, and galacturonates (see, for example, Berge S.M. et al., "Pharmaceutical Salts," Journal of Pharmaceutical Science, 66:1-19 (1997); Gould, P. L. “Salt Selection for basic drugs” International Journal of Pharmaceutics, 33:201-217 (1986)). Acid addition salts ofbasic compounds are, in some embodiments, prepared by contacting the free base forms with a sufficient amount of the desired acid to produce the salt according to methods and techniques with which a skilled artisan is familiar.
[0241] "Pharmaceutically acceptable base addition salt" refers to those salts that retain the biological effectiveness and properties of the free acids, which are not biologically or otherwise undesirable. These salts are prepared from addition of an inorganic base or an organic base to the free acid. Pharmaceutically acceptable base addition salts are, in some embodiments, formed with metals or amines, such as alkali and alkaline earth metals or organic amines. Salts derived from inorganic bases include, but are not limited to, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Salts derived from organic bases include, but are not limited to, salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, for example, isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, ethanolamine, diethanolamine, 2-dimethylaminoethanol, 2-diethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, N, A-dibenzylethylenedi amine, chloroprocaine, hydrabamine, choline, betaine, ethylenediamine, ethylenedianiline, A-methylglucamine, glucosamine, methylglucamine, theobromine, purines, piperazine, piperidine, A-ethylpiperidine, polyamine resins and the like. See Berge et al., supra.
[0242] The publications, patents, and patent applications referenced herein are hereby incorporated by reference.
EXAMPLES
Example 1: Synthetic general procedures
General Procedure 1: Synthesis of Key Iodo
[0243] Step 1: The synthesis of l-(4-methylbenzenesulfonyl)-4-nitro-lH-indole. To a solution of 4-nitro-lH-indole (50.0 g, 308.56 mmol) in anhydrous DMF (400 ml) under inert atmosphere sodium hydride (18.5 g, 770.92 mmol) was added in portions while stirring at 0°C. After the addition was completed, the resulting solution was allowed to warm up to room temperature and left while stirring at room temperature for 2 hrs. After that period the reaction mixture was cooled down again and 4-methylbenzene-l -sulfonyl chloride (88.18 g, 464.16 mmol) was added in portions at 0°C. Then the mixture was stirred for 18 hours at room temperature. The reaction mixture was diluted with saturated solution of NH4CI (2000 ml), stirred for 1 h, then filtered. The collected precipitate was washed with water (3 x 500 ml), hexane (2 x 500 ml) and dried under reduced pressure to afford the desired 1 -(4-methylbenzenesulfonyl)-4- nitro-lH-indole (95.0 g, 87.7% yield).
[0244] Step 2 : The synthesis of 2-iodo-l-(4-methylbenzenesulfonyl)-4-nitro-lH-indole. To bis(propan-2-yl)amine (5.12 g, 50.62 mmol, 7.16 mL, 3.2 eq) in dry THF (25 mL) at -78°C n- butyllithium (3.04 g, 47.46 mmol, 19.45 mL, 3.0 eq) was added and the mixture was stirred for 10 min at -78°C. The resulting solution was added via cannula needle to the drip funnel and then dropwise to the solution of l-(4-methylbenzenesulfonyl)-4-nitro-lH-indole (5.0 g, 15.82 mmol) in dry THF (50 ml) at -78°C. The mixture was left while stirring at -78 °C for 15 min. After that the solution of iodine (6.02 g, 23.73 mmol) in dry THF (25 mL) was added to the reaction mixture at -78°C. After the addition was completed the reaction mixture was allowed to warm to 0°C. Then the mixture was quenched with saturated aqueous solution of NH4CI (200 mL) and diluted with ethyl acetate (200 mL). The organic layer was separated, washed with 10% aqueous solution of Na2S2O3 (150 mL), brine (150 mL), dried over anhydrous Na2SC>4 and fdtered. The fdtrate collected was concentrated under reduced pressure and the obtained crude residue was subjected for flash chromatography purification (Interchim, 220 g SiO2, petroleum ether/EtOAc with EtOAc from 10-45%, flow rate = 100 mL/min, Rf = 3.4-5 CV) to result in the desired 2- iodo-l-(4-methylbenzenesulfonyl)-4-nitro-lH-indole (1.53 g, 95.0% purity, 3.29 mmol, 20.8% yield) with the following spectra data: LCMS (2 min, 91.8% by UV 215 nm, RT 1.566, M+l = 443.0). The product obtained was of sufficient purity, so it was used in further experiments without any additional purification.
[0245] Step 3: The synthesis of 2-iodo-4-nitro-lH-indole. To a starting 2-iodo-l-(4- methylbenzenesulfonyl)-4-nitro-lH-indole (9.6 g, 21.72 mmol) in dioxane (250 mL) powdered sodium hydroxide (4.34 g, 108.56 mmol) was added, and the reaction mixture was vigorously stirred at 60° C overnight. The resulting suspension was then concentrated under reduced pressure, the obtained residue was diluted with water (150 mL) and extracted with ethyl acetate (3 x 100 mL). The organic layers were combined, dried over anhydrous Na2SC>4 and filtered. The collected filtrate was concentrated under reduced pressure to afford the desired 2-iodo-4-nitro- IH-indole (5.0 g, 72% yield) with the following spectra data: LCMS (2 min, 97.9% by UV 215 nm, RT 1.321, M+l = 289.0).
[0246] Step 4: The synthesis of 2-iodo-4-nitro-l-(2,2,2-trifluoroethyl)-lH-indole. To a solution of 2-iodo-4-nitro-lH-indole (23.0 g, 79.88 mmol) in anhydrous DMF (250 mL) sodium hydride (4.15 g, 173.01 mmol) was added in portions at 0°C under inert atmosphere. After the addition was completed, the resulting solution was allowed to warm up to room temperature and left to stir at room temperature for 1 hour. After that period the reaction mixture was cooled down again and 2,2,2-trifluoroethyl trifluoromethanesulfonate (37.07 g, 159.8 mmol, 23.0 mL, 2.0 eq) was added dropwise at 0°C. Then the mixture was stirred for 18 hours at room temperature. The reaction mixture was diluted with saturated solution of NH4CI (1000 ml), stirred for 1 hour and fdtered. The collected precipitate was washed with water (200 mL), hexane (2 x 200 mL) and dried under reduced pressure to afford the desired 2-iodo-4-nitro-l -(2,2,2-trifluoroethyl)- 1 flindole (25.0 g, 76.1% yield) with the following spectra data: LCMS (2 min, 92.5% by UV 215 nm, RT 1.290, M+l = 370.8).
[0247] Step 5: The synthesis of 2-iodo-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine. To a solution of 2-iodo-4-nitro-l-(2,2,2-trifluoroethyl)-lH-indole (15.0 g, 40.55 mmol, 231.7 mL, 1.0 eq) and 4-(pyridin-4-yl)pyridine (316.54 mg, 2.03 mmol) in anhydrous DMF (250 mL) (dihydroxyboranyl)boronic acid (10.9 g, 121.09 mmol) was added in portions at 5°C under inert atmosphere. The resulting reaction mixture solution was allowed to warm up to room temperature and stirred for 1 h. After that period the mixture was quenched by 10% aqueous solution of K2CO3 (1 L) and stirred for 1 h. Then the mixture was extracted with ethyl acetate (3 x 200 mL). The organic layers were combined, washed with water (3 x 150 ml), brine (200 mL), dried over anhydrous ISfeSCL and filtered. The collected filtrate was concentrated under reduced pressure to result in the desired 2-iodo-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine (14.0 g, 90.0% purity, 91.4% yield) with the following spectra data: LCMS (2 min, 98.8% by UV 215 nm, RT 1.022, M+l = 341.0). The product obtained was used in further experiments without any additional purification.
General Procedure 2. Synthesis of Key Chiral Iodo.
[0248] Step 1: To a mixture of iodo indole 1 (leq) and preferred Boc-piperidine 2a-2d (2.1 eq) in AcOH (0.2 M) was added NaBH(OAc)3 (2.5 eq) in portions at 25 °C under N2. The mixture was stirred at 40 °C for 2 hr. LCMS and HPLC showed that the reactant was consumed completely and 50% of desired mass was detected. The reaction mixture was quenched by addition of ice water at 0 °C. The mixture was adjusted with saturated NaHCCh to pH=8. The mixture was extracted with EtOAc (2x). The organic phase was washed with brine (2x). The organic phase was dried over anhydrous Na2SO4 and concentrated in vacuo. The residue was purified by p/ep-HPLC (FA column: Phenomenex luna C18 (250*70mm, 10 pm); mobile phase: [water(FA)-ACN]; gradient:55%-85% B over 20 min) to give single peakl (S,R), desired indole 3 (54% yield) as a brown solid. [0249] Step 2: The product indole 3 was subjected to TFA/DCM (0.5M, 5: 1) for 2 hours at 25 °C. Crude reaction was adjusted with saturated NaHCO? to pH=8. The aqueous phase was extracted with EtOAc (3x). The organic phase was dried over anhydrous Na2SO4 and concentrated in vacuo to give deprotected piperidine 4 which was used as is in the next step.
[0250] Step 3: To (S,R), desired indole 4 (1 eq) in MeOH (0.2M) was added HCHO (1.1 eq), AcOH (1.5 eq) and NaBH(OAc)3 (2.5 eq). The mixture was stirred at 25 °C for 1 hr. LCMS showed starting material was consumed completely and 96.5% of desired mass was detected. The mixture was adjusted with saturated NaHCO3 to pH=8. The aqueous phase was extracted with EtOAc (3x). The organic phase was dried over anhydrous Na2SO4 and concentrated in vacuo. The residue was purified by resolution (column: DAICEL CEURALPAK AD(250mm*50mm, 10 pm);mobile phase: [CO2-ACN/MeOH(0.1% NH3.H2O)];B%:54%, isocratic elution mode) to give N-methylated piperidine 5 as a mixture of stereoisomers (79% yield) as gray solid.
[0251] Step 4: Recrystallization was performed on the stereoisomers mixture by adding 1 eq of chiral acid N-Acetyl-L-Leucine, stirred for 1 hour at room temperature then heat to 70 °C for 1 hour followed by overnight stirring at room temperature using MeoH/H2O (6:1) solvent ratio. The solid was isolated and further purified by SFC to obtain desired pure enantiomer.
[0252] The following illustrative examples are representative of embodiments of the stimulation, systems, and methods described herein and are not meant to be limiting in any way.
General Procedure 3. Assembly of BFM through amide coupling.
[0253] Step 1: A solution of amine 1 (1 eq), [(dimethylamino)(3H-[l,2,3]triazolo[4,5- b]pyridin-3-yloxy)methylidene]dimethylazanium; hexafluoro-lambda5-phosphanuide (1.3 eq), acid 2 (1 eq), and ethylbis(propan-2-yl)amine (5 eq) in DMF (0.2 M) was stirred overnight at room temperature. Solvent was evaporated from mixture and re-dissolved in water-acetonitrile for HPLC purification to obtain the amide. General procedure 4. Assembly of BFM through Click coupling.
[0254] Step 1: To a solution of alkyne 2 (1 eq) in the mixture of t-BuOFLTbO (2:1, 0.2 M) at 0°C was added sodium (2R)-2-[(lS)-l,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3- olate (1 eq), followed by the addition of copper (II) sulfate pentahydrate (0.5 eq). After 5 min of stirring, the solution of azide 1 (1 eq) in THF (0.1 M) was added to the reaction mixture, which was then heated up to 50°C and left while stirring overnight. After the reaction was completed (monitored by LCMS), the mixture was concentrated under reduced pressure and the residue was diluted with minimal DMSO and subjected for prep HPLC without any further work-up to obtain BFM 3.
General procedure 5. Synthesis of amide-containing Rl-L scaffolds.
[0255] Step 1 : To a solution of aniline 1 (1.2 eq) in anhydrous DMF (1 M) dipotassium carbonate (1.5 eq) was added. The reaction mixture was cooled to 0°C and 3 -bromoprop- 1-yne (1 eq) dropwise was added dropwise under an inert atmosphere. The resulting solution was then allowed to warm up to room temperature and left to stir for 18 hrs. The reaction mixture was diluted with saturated solution of NH4CI and extracted with ethyl acetate (3x). The organic layers were combined, washed with water (3x), brine, dried over anhydrous Na2SO4 and filtered. The collected filtrate was concentrated under reduced pressure and the obtained crude was subjected for flash chromatography to afford the desired benzoate 2.
[0256] Step 2 : To a solution of key aryl iodide 3 (1 eq), benzoate 2 (1.2 eq), copper (I) iodide (0.5 eq) and tri ethylamine (3.0 eq) in DMSO (0.1 M) under inert atmosphere Palladium- tetrakis(triphenylphosphine) (10 wt. %) was added. The resulting solution was stirred at room temperature for 18 hours. After that period the reaction mixture was diluted with distilled water, the mixture was stirred for 1 hour. The formed precipitate was collected by filtration, washed with water, dried and subjected for flash chromatography purification to afford the desired alkyne 4.
[0257] Step 3: To a solution of alkyne 4 (1 eq) in THF/MeOH (1: 1, 0.25M) the solution of lithium hydroxide hydrate (15 eq) in water (0.25 M) was added. The resulting solution was stirred at room temperature for 48 hours. The reaction mixture was then concentrated under reduced pressure, diluted with water and acidified with sodium hydrogen sulfate (15 eq). The mixture was extracted with ethyl acetate/acetonitrile, dried over anhydrous Na2SO4 and filtered. The collected filtrate was concentrated under reduced pressure to afford the desired acid 5.
[0258] Step 4: To a solution of acid 5 (1 eq) in DMF (0.1 M) was added 3H- [l,2,3]triazolo[4,5-b]pyridin-3-ol (1.5 eq), (3- [(ethylimino)methylidene]aminopropyl)dimethylamine hydrochloride (1.5 eq), and after 5 min, amine linker 6 (1.1 eq). The resulting mixture was stirred at room temperature overnight. The reaction mixture was diluted by water, extracted with ethyl acetate (3x). The organic layers were combined, washed with water (3x), brine, dried over anhydrous Na2SO4 and filtered. The filtrate collected was concentrated under reduced pressure and the residue obtained was subjected to prep HPLC purification to result in the desired amide 7.
[0259] Step 5: To solution of amide 7 (1 eq) in MeOH (0.1 M) 10% HC1 in dioxane was added. The reaction mixture was stirred at room temperature for 18 hours. After that period the mixture was concentrated under reduced pressure to afford the desired amine 8. General procedure 6. Synthesis of sulfonamide containing Rl-L scaffolds.
[0260] Step 1 : To a solution of amine 1, (1 eq) and triethylamine (1.5 eq) in DCM (0.35 M), solution of sulfonyl chloride (1 eq) in THF (1 M) was added at 0°C under nitrogen atmosphere. The mixture was warmed to room temperature and stirred for 12 hours. Reaction was monitored until completion via LCMS analysis. The mixture was concentrated, diluted with EtOAc and washed with 1 M solution of NaHSO4 in water, saturated solution of NaHCCE, brine, dried over anhydrous Na2SO4 and concentrated under reduced pressure to afford sulfonamide 3 that was used in the next step without further purification.
[0261] Step 2A: To a solution of nitro arene 3 (1 eq) and 4,4’-bipyridine (0.05 eq) in anhydrous DMF (0.15 M), (dihydroxyboranyl)boronic acid (3 eq) was added portion wise under inert atmosphere at 5°C. The resulting solution was warmed up and stirred at room temperature for 1 hour. The reaction mixture was quenched by 10% solution of K2CO3, stirred for 1 hour, and extracted by EtOAc. The organic layer was washed by water (3x), brine, dried over Na2SO4 and concentrated under reduced pressure to afford amine 4 that was used in the next step without purification.
[0262] Step 2B: To a suspension of Pd/C (10 wt. %) in MeOH (0.2 M) under nitrogen atmosphere nitro-containing sulfonamide linker 3 (1 eq) was added. The mixture was degassed and purged with H2 3 times, and then the mixture was stirred under H2 (15 Psi) atmosphere at 25 °C for 12 hrs. When the starting material disappeared by LCMS, the reaction was filtered, and the solid residue was washed by THF (3x). The filtrate was concentrated in vacuo to give desired aniline. [0263] Step 3 : To a solution of amine 4, (1 eq) in DMF (0.13 M), was added 3 -bromoprop- 1- yne, (1 eq) and dipotassium carbonate (3 eq) at room temperature under nitrogen atmosphere. The mixture was stirred at 60°C for 12 hours. After that another portion of 3 -bromoprop- l-yne (1 eq) was added and the reaction was stirred at 60°C for 8 hours. The addition was continued until 80% conversion by LCMS was achieved. Then the mixture diluted with EtOAc and washed with water (3x), brine, dried over anhydrous Na2SO4 and concentrated under reduced pressure to afford crude compound that was sent to flash chromatography/ISCO (petroleum ether/THF with acetonitrile solvent system) to afford alkyne 5.
[0264] Step 4 : solution of Aryl iodide 6, (1 eq), alkyne 5, (2 eq), DiPA, (0.4 eq), and dry DMSO (0.15 M) was degassed by bubbling argon for 2 min. Palladium- tetrakis(triphenylphosphine) (30 wt. %) and Cui (lOwt. %) were added and the mixture was again degassed by bubbling argon and was stirred under argon at room temperature for 12 hours.
LCMS analysis of the reaction mixture showed full conversion to the desired product. The mixture was diluted by saturated solution of EDTA in water, extracted by EtOAc (3x). The combined organic layers were washed with water, brine, dried over anhydrous Na2SO4 and concentrated under reduced pressure to afford crude compound that was sent to flash chromatography/ISCO (Acetonitrile /Methanol with Methanol solvent system) to afford 7.
General procedure 7. Synthesis of carbamate -containing Rl-L scaffolds.
[0265] Step 1: Mono-Boc diamine 1 (1 eq) and pyridine (2.0 eq) were mixed in DCM (0.2M) and mixture was cooled to 0°C. Ditrichloromethyl carbonate (0.4 eq) was added portion wise, mixture was left to stir at 0°C for Ihour and then was stirred overnight at rt. The solution was washed with H2O (lx) and saturated aq solution of NaHSO4 (2x), organic layer dried over Na2SO4, and concentrated under reduced pressure to obtain acid chloride 2 (63.4% yield) which was used in the next step without further purification.
[0266] Step 2 : Under Ar in DMF (0.2 M) nitro phenol (1.2 eq) was mixed with sodium hydride (l.leq). After 30 min at room temperature the suspension was cooled to 0°C and acid chloride (1 eq) was added drop wise in DMF (1.5 M) and the reaction mixture was stirred at room temperature for 12 hours. The resulting mixture was diluted with water and extracted with ethyl acetate (3x). The organic layer was washed with brine, dried overNa2SO4, and concentrated under reduced pressure to obtain carbamate 4 (65.9% yield) after FCInterchim; 120g SiCL, CH2C12-THF% 0-20-100, flow rate = 40 mL/min. Rv=3,8-4,8, column equilibration with CH2CI2. Step 3: At 0°C carbamate 4 (1 eq), (dihydroxyboranyl)boronic acid (4 eq) were mixed in DMF, after 10 min (dihydroxyboranyl)boronic acid (4 eq) was added portionwise and the mixture was left to stir at room temperature overnight. The reaction mixture was diluted with distilled water and extracted with DCM (3x). The organic layers were combined, washed with water (3x), brine, dried over anhydrous Na2SO4 and filtered. The filtrate collected was concentrated under reduced pressure to result in the desired aniline 5 (76% yield) which was used in the next step without purification.
[0267] Step 4 : At 0°C aniline 5 (1 eq) and dipotassium carbonate (1.5 eq) were mixed in DMF (0.2 M) after 3 min 3 -bromoprop- l-yne (1.3 eq) was added dropwise and the mixture was left to stir at room temperature overnight. The resulting mixture was extracted with ethyl acetate. The organic layer was washed with water, dried overNa2SO4, and concentrated under reduced pressure to obtain product 6 (33% yield) after FC and HPLC (30-55% 0-5min H2O/ACN, flow: 30ml/min (loading pump 4ml/min ACN) target mass 509.60, column: Chromatorex 18 SMB100- 5T 100x19mm).
[0268] Step 5 : Under argon, iodo 7 (1 eq), carbamate 6 (1.2) copper(I) iodide (10 mol %) tetrakis(triphenylphosphine)palladium (10 mol %) were mixed in DMSO/(i-Pr)2NH (5M, 3:1) and the mixture was left to stir at room temperature overnight. Alkyne 8 (93.4% yield) was obtained after HPLC (40-65% 0-5min H2O/ACN/0.1%NH4OH, flow: 30ml/min (loading pump 4ml/min ACN) target mass 818.94, column: XBridge C18 100x19 mm). General procedure 8. Synthesis of ether-containing Rl-L scaffolds.
[0269] Step 1: Dipotassium carbonate (1.5 eq) was added to a solution of alkyl halide 1 (1 eq) in DMF (0.35 M). The resulting mixture was stirred at room temperature for 30 min and phenol 2 (1.2 eq), was added in one portion. The reaction was stirred at 50°C for 24 hours (monitored by LCMS). The resulting mixture was diluted with EtOAc then washed with H2O, brine (3x), dried overNa2SO4, and concentrated under reduced pressure to dryness to afford ether 3.
[0270] Step 2 : A solution of ether 3 (1 eq), in methanol (0.15 M) was treated with Pd/C (5 wt. %). The resulting mixture was hydrogenated at 2 atm and ambient temperature until spectral data of an aliquot revealed completion of the reaction (by LCMS). Then the catalyst was fdtered off and the filtrate was concentrated to afford aniline 4. The product was used in further experiments without any additional purification.
[0271] Step 3: 3 -Bromoprop- l-yne (1.05 eq), was added portion wise to the solution of aniline 4 (1 eq) and dipotassium carbonate (1.5 eq) in DMF (0.2 M) and the mixture was stirred at rt for 24 hrs. The resulting mixture was diluted with EtOAc, washed with H2O and aq NaHSOs. The combined organics were then washed with brine (5x), dried over Na2SO4, and concentrated to afford 9 g of crude oil. The crude product obtained was purified by flash chromatography (ISCO® Interchim). As a result, propargyl aniline 5 was obtained.
[0272] Step 4 : A mixture of propargyl aniline 5 (1.2 eq), key intermediate 7 (1 eq), copper iodide (10 wt. %) and palladium-tetrakis(triphenylphosphine) (20 wt. %) was stirred in DMSO:TEA (3:1, 0.1 M) under argon atmosphere at room temperature for 4 hrs. Then the mixture was purified by HPLC to obtain di-substituted alkyne 8. General procedure 9. Synthesis of sulfone-containing Rl-L scaffolds.
[0273] Step 1 : To a stirred heated solution of sodium sulfide nonahydrate (1 eq) and sulfur (1 eq) in i-PrOH (0.3 M) aryl fluoride 1 (1 eq) in i-PrOH (1.5 M) was added dropwise over 20 min. Reaction mixture was and stirred for another 3 hours, then cooled to room temperature. The mixture was acidified to pH=3 with HC1. The resulting mixture was concentrated under vacuum, diluted with water and then extracted with ethyl acetate (2x). The combined organic layers were washed with brine (2x) and dried over anhydrous Na2SO4 to obtain thiol 2 after flash chromatography.
[0274] Step 2 : A solution of thiol 2 (1 eq), alkyl halide 3 (1.8 eq), sodium hydroxymethanesulfinate (2.7 eq), and dipotassium carbonate (1.8 eq) in DMF (0.24 M) was stirred overnight at room temperature. The resulting mixture was concentrated under vacuum, diluted with water and then extracted with ethyl acetate (2x). The combined organic layers were washed with brine (4x) and dried over anhydrous Na2SO4, to obtain sulfide 4.
[0275] Step 3: To cooled to 0°C solution of sulfide 4 (1 eq) in DCM (0.15 M) 3- chlorobenzene-l-carboperoxoic acid (3 eq) was added. The mixture was stirred overnight at room temperature then diluted with water and extracted with DCM. The combined organic layers were washed with 20% K2CO3 (2x), brine (4x), dried over anhydrous Na2SO4, and concentrated under reduced pressure to obtain sulfonyl 5.
[0276] Step 4 : A stirred solution of sulfonyl 5 (leq) and 4-(pyridin-4-yl)pyridine (0.05 eq) in DMF (0.15 M) was cooled to 0 °C and (dihydroxyboranyl)boronic acid (3 eq) was added dropwise at the temperature not exceeding 5 °C. The reaction mixture was allowed to warm up to room temperature and stirred for another 12 hours. Then 20% K2CO3 and ethyl acetate were added, organic layers separated, washed with H2O (2x) and brine (3x), dried overNa2SO4 and concentrated in vacuo to obtain aniline 6. [0277] Step 5 : A stirred solution of aniline 6 (1 eq), potassium iodide (1.3 eq) and 3- bromoprop-l-yne (1.3 eq) in DMF (0.2 M) dipotassium carbonate (2 eq) was added portion wise at the room temperature. The reaction mixture was stirred at 75 °C for another 48 hours. Then ethyl acetate was added, organic layers separated, washed with H2O (2x) and brine (3x), dried over Na2SO4 and concentrated in vacuo to obtain propargyl aniline 7 after flash chromatography.
[0278] Step 6 : To a stirred solution of propargyl aniline 7 (1.2 eq), iodo indole 8 (1 eq) in THF/EhN (1: 1, 0.1M) palladium-tetrakis(triphenylphosphine) (20 wt. %) and copper iodide (10 wt. %) were added portion wise at the room temperature under Argon atmosphere. Reaction mixture was stirred at room temperature for another 12 hours. Then the mixture was purified by flash chromatography to obtain di-substituted alkyne 9.
General procedure 10. Synthesis of methyl sulfone- with meta-ether-containing Rl-L scaffolds.
[0279] Step 1: Dipotassium carbonate (1.5 eq) was added to a solution nitrophenol 2 (1 eq) in DMF (0.5 M). The resulting mixture was stirred at room temperature for 30 min then linker intermediate 1 (1.2 eq) and potassium iodide (0.1 eq) were added in one portion. The reaction was stirred at 40 °C for 24 hours (monitored by LCMS). The resulting mixture was diluted with ethyl acetate then washed with H2O, brine (4x), dried overNa2SO4, and concentrated under reduced pressure to dryness to afford 3.
[0280] Step 2: Copper (I) iodide (10 wt. %) was added to a round bottom flask charged with aryl bromide 3 (1 eq), sodium methanesulfmate (1.2 eq) and (2S)-pyrrolidine-2-carboxylic acid (2 wt. %) in DMSO (0.5 M) at room temperature. The resulting mixture was sparged with argon for 10 minutes, then the reaction mixture was stirred at 100 °C for 12 hours. The mixture was diluted with ethyl acetate, organic layers were separated, washed with H2O, aqua NH3 (2x), brine (3x), dried overNa2SO4, and concentrated under reduced pressure to dryness to afford 4 as a crude oil. The crude product obtained was purified by flash chromatography to obtain pure aryl sulfone 4.
[0281] Step 3 : A solution of aryl sulfone 4 (1 eq) in methanol (5 M) was treated with Pd/C (5 wt. %). The resulting mixture was hydrogenated at 2 atm and ambient temperature until spectral data of an aliquot revealed completion of the reaction (by LCMS). Then the catalyst was filtered off and the filtrate was concentrated to afford aniline 5. The product was used in further experiments without any additional purification.
[0282] Step 4: 3 -Bromoprop- 1-yne (1.2 eq) was added portion wise to the solution of aniline 5 (1 eq), dipotassium carbonate (1.5 eq) and potassium iodide (10 wt. %) in DMF (2 M) and the mixture was stirred at 90°C for 4 days. The resulting mixture was diluted with ethyl acetate, washed with H2O and aq NaHSCh. The combined organic layers were then washed with brine (3x), dried overNa2SO4, and concentrated to afford 6 as a crude oil. The crude product obtained was purified by flash chromatography to obtain alkylated arene 6.
[0283] Step 5: Key intermediate 7 (1 eq), palladium-tetrakis(triphenylphosphine) (20 wt. %), aryl sulfone 6 (1.2 eq) and copper (I) iodide (10 wt. %) in DMSO/z-Pr2NH (3:1, 0.08 M) were added to round bottom flask at room temperature. The resulting mixture was sparged with argon for 10 minutes and was left to stir at room temperature for 12 hours. The mixture was diluted with ethyl acetate, washed with H2O, aqua NH3 (2x), brine, dried overNa2SO4, and concentrated under reduced pressure to dryness to afford 8 as crude brown oil. The crude product obtained was purified by flash chromatography to obtain alkyne 8.
[0284] Step 6: Alkyne 8 (1 eq) was dissolved in MeOH (0.02 M). Hydrogen chloride (10.0 eq) was added and the mixture was stirred at room temperature overnight. After consumption of the starting material (monitored by LCMS) the resulting mixture was concentrated under reduced pressure to dryness (<40°C). The obtained residue was quenched with NaHCO? and extracted with dichloromethane (3x). The combined organic extracts were washed with brine, dried over Na2SO4, and concentrated under reduced pressure to afford amine 9. General procedure 11. Synthesis of propargylated aniline-containing NH-sulfonamide linker.
[0285] Step 1 : A mixture of 3 -methoxy-4-nitro-benzenesulfonyl chloride (1.2 eq) and mono- Boc protected diamine linker (1.0 eq) in pyridine (0.68 M) was degassed, purged with N2 3 times, and then stirred at 25 °C for 1 hour under N2 atmosphere. LCMS showed complete consumption of starting 1 and formation of desired product 3. The mixture was concentrated in vacuo to give an oil residue that was purified by flash column chromatography to provide nitro-containing intermediate 2.
[0286] Step 2: To a solution of NH-sulfonamide containing intermediate 3 (1.0 eq) in DCM (0.18 M) DMAP (0.1 eq) and EtsN (3 eq) were added followed by (Boc)2O (1.4 eq). The mixture was stirred at 25 °C for 12 hours. LCMS showed complete consumption of starting material 3 and formation of the desired Boc-protected sulfonamide product 4. The mixture was concentrated in vacuo to give an oil residue that was further purified by flash column chromatography.
[0287] Step 3: To a suspension of Pd/C (75 mg/mmol, 10% purity) in MeOH (0.26 M) under nitrogen atmosphere nitro -containing intermediate 4 was added. The mixture was degassed, purged with H23 times, and stirred under H2 (15 Psi) atmosphere at 25°C for 12 hours. LCMS showed complete consumption of starting material and formation of the desired product. The reaction was filtered, solid residue was washed by THF (3x), and collected filtrate was concentrated in vacuo to give the desired aniline intermediate 5.
[0288] Step 4 : A mixture of aniline intermediate 5 (1 eq), 3 -bromoprop- l-yne (1.3 eq), K2CO3 (2 eq), and KI (0.2 eq) in DMF (0.45 M) was degassed, purged with N2 3 times, and stirred under nitrogen atmosphere at 80 °C for 12 hours. LCMS showed complete consumption of starting materials and formation of the desired product. Ethyl acetate and water were added and then layers were separated. The aqueous phase was extracted with ethyl acetate (3x). The combined organic layers were washed with brine, dried over Na2SO4, filtered and concentrated in vacuo to give an oil residue. The residue was purified by prep-WLC to give the propargylated aniline-containing NBoc-sulfonamide linker 6.
[0289] Step 5 : To a solution of the propargylated aniline-containing NBoc-sulfonamide linker 6 (1 eq) in MeOH (1 M), K2CO3 (2 eq) was added. The mixture was stirred at 50 °C for 12 hours. LCMS showed complete consumption of starting material and formation of the desired product. The reaction mixture was concentrated in vacuo to give an oil residue. The residue was purified by flash silica gel chromatography to give the desired propargylated aniline-containing NH sulfonamide linker 7.
General procedure 12. Synthesis of amino benzimidazole-containing R2 acids.
[0290] Step 1 : To a stirred suspension of 2,6-dinitroaniline 1 (1 eq) in glacial acetic acid (4 M) was added bromine (1.1 eq) dropwise and heated at 120° C for 2 hours. After cooling to ambient temperature, the resultant mixture was poured into water. The precipitate solid was collected by filtration, washed with water, and then dried in-air to obtain aryl bromide 2.
[0291] Step 2 : A mixture of aryl bromide 2 (1 eq) and diammonium sulfide (1 eq) in ethanol
(0.25 M) was heated at 90 °C for 12 hours. Then the mixture was concentrated and purified on silica gel to give di aniline 3.
[0292] Step 3 : To a suspension of dianiline 3 (1 eq) in 4M HC1 (0.3 M) was added formic acid (2.5 eq). The mixture was heated at 100°C for 1.5 hours, and then cooled to room temperature. Water was added and neutralization with concentrated NH4OH gave a precipitate which was collected, washed with water, and dried to give benzimidazole 4.
[0293] Step 4 : A suspension of benzimidazole 4 (1 eq), key intermediate benzyl bromide (1 eq) and dipotassium carbonate (3 eq) in dioxane (0.1 M) was stirred at 75°C for 12 hours, filtered and evaporated to obtain alkylated benzimidazole 5 which was used without further purification. [0294] Step 5 : A suspension of tricyclic intermediate 5 (1 eq), 3,5-dimethyl-4-(tetramethyl- l,3,2-dioxaborolan-2-yl)-l,2-oxazole 6 (1.2), dipotassium carbonate (3 eq), and palladium- tetrakis(triphenylphosphine) (lOwt. %) in degassed dioxane/H2O (10: 1, 0.05 M) was stirred under argon at 100°C overnight. After cooling to room temperature, the mixture was evaporated, then water and EtOAc were added, and the mixture was filtered to obtain acid 7.
[0295] Step 6: To a solution of acid 7 (1 eq) in THF/DMF (4: 1, 0.1 M), Pd/C (5wt. %) was added. The resulting mixture was hydrogenated at ambient pressure and ambient temperature until 1 H NMR of an aliquot revealed completion of reaction. The catalyst was filtered off and the filtrate evaporated in vacuo. Then water was added, and the solids were collected and dried to afford benzimidazole 8.
General procedure 13. Synthesis of Benzimidazole-containing R2 acids.
[0296] Step 1 : A suspension of aryl bromide 1 (1 eq), ester 2 (1.2 eq) and dipotassium carbonate (2 eq) in dioxane (2M) was stirred at 100°C for 12 hours, filtered and evaporated to obtain alkylated product 3 (90.8% yield) (1: 1 mixture of isomers) which was used without further purification but later separated and confirmed by 2D-NMR/nOe.
[0297] Step 2 : A suspension of aryl bromide 3 (1 eq), boronic ester 4 (1.5 eq), tetrakis(triphenylphosphine)palladium (10 mol %), and dipotassium carbonate (2.2 eq) in degassed dioxane/H^O (3M, 10: 1) was stirred under argon at 100°C overnight. After cooling to room temperature, the mixture was filtered, evaporated and purified by FC (Interchim; 120g Si O2, hexane/MTBE/methanol with methanol from 0~9%, flow rate =40 mL/min, Rv = 22 - 25min) to obtain ester 5 (37.2% yield) (1 : 1 mixture of isomers).
[0298] Step 3: A solution of ester 5 (1 eq) and sodium hydroxide (10 eq) in Me0H:H20 (0.5M, 10:1) was stirred at room temperature for 12 hours, acidified with TFA to pH ~3 and purified by HPLC (5-12% 0-7 min H2O/ACN/0.1% FA, flow: 30ml/min (loading pump 4ml/min ACN) target mass 347.88 column: Chromatorex 18 SMB100-5T 100x19mm 5 pm) to obtain free acid 6 (14.2% yield) as a white solid. The regioisomers were separated by prep HPLC, the structure was confirmed by 2D NMR. General procedure 14. Synthesis of imidazo[4,5-b]pyridin containing RL acids.
[0299] Step 1 : A mixture of aldehyde 1 (1 eq), tert-butyl 2-bromoacetate (1.1 eq) and dipotassium carbonate (2.1 eq) in acetonitrile (0.2 M) was stirred overnight at 78°C. Then the mixture was filtered and evaporated to obtain tert butyl ester 2 (91.2% yield) as a yellow oil which was used without further purification.
[0300] Step 2 : A mixture of dianiline 3 (1 eq), boronic ester 4 (1.2 eq), tetrakis(triphenylphosphine)palladium (9 mol %) and dipotassium carbonate (2 eq) in dioxane/H2O (5M, 10: 1) was degassed and purged with Ar for 3x, and then the mixture was stirred at 90 °C for 12 hours under Ar atmosphere. The mixture was diluted with EtOAc and water, separated. The aqueous phase was extracted with EtOAc (3x). The organic phase was washed with brine. The organic phase was dried over anhydrous Na2SO4 and concentrated in vacuum. The residue was triturated with EtOAc. The mixture was filtered. The filter cake was dried in vacuum to afford bi-aryl 5 (49.4% yield) as a brown solid.
[0301] Step 3 : To a mixture of bi-aryl 5 (2.94 mmol) and aldehyde 2 (2.94 mmol) in DCM/MeOH (2M, 1: 1), acetic acid (0.85 equiv) was added. The mixture was stirred at 25 °C for 12 hours. LCMS showed that about 35% of desired mass was detected. The mixture adjusted with saturated NaHCO3 to pH = 8. The aqueous phase was extracted with DCM (3x). The organic phase was dried over anhydrous Na2SO4 and concentrated in vacuum to afford imine 6 (33.8% yield) as a brown oil. [0302] Step 4 : To a solution of imine 6 (1 eq) in DCM/MeOH (2M, 1:1) sodium borohydride
(5 eq) was added at 5~10°C under N2. The mixture was stirred at 25 °C for 1 hour, then diluted with water. The mixture was extracted with ethyl acetate (3x). The combined organic phase was dried over anhydrous Na2SO4, filtered and concentrated in vacuo. The residue was purified by silica gel chromatography (Interchim; 40g SiCh, chloroform/ ACN with ACN from 0-75%, flow rate = 40mL/min, Rv =15.8-20.5CV) to afford amine 7 (23.3% yield) as ayellow oil. The product was confirmed by 2D NMR.
[0303] Step 5 : To a solution of amine 7 (1 eq) in dioxane (4M) l-(lH-imidazole-l- carbonyl)-lH-imidazole (4.5 eq) was added. The mixture was stirred at 80 °C for 12 hours, diluted with EtOAc and water, separated. The aqueous phase was extracted with EtOAc (lx), The organic phase was washed with brine (2x). The organic phase was dried over anhydrous ISfeSCE and concentrated in vacuum to obtain urea 8 (78.7% yield) as a yellow solid.
[0304] Step 6 : A solution of urea 8 (1 eq) in POCI3 (5 eq) was stirred at 110°C for 36 hours, diluted with water, extracted with EtOAc (2x), washed with brine, dried under Na2SO4 and evaporated to obtain chloride 9 (53% yield) as a brown oil.
[0305] Step 7 : A solution of chloride 9 (1 eq) in MeNEE in MeOH (excess eq) was stirred at
80 °C overnight and purified by HPLC (5-5-25% 0-l-5min H2O/ACN/0.1% FA, flow: 30ml/min (loading pump 4ml/min ACN) target mass 407.43 column: Chromatorex 18 SMB100-5T 100x19mm 5 pm) to obtain aryl amine 10 (90% yield) as a beige solid.
General procedure 15. Synthesis of Methoxypyridine-containing R2 acids.
[0306] Step 1: To a solution of CD3OH (9.17 g, 254.34 mmol, 10.33 ml, 1.2 equiv) in THF (500ml) sodium hydride (10.6 g, 60.0% purity, 264.94 mmol) was added portion wise at 0-°C under inert atmosphere. After 30min of stirring 5 -bromo-2-chloro-3 -nitropyridine (50.0 g, 211.96 mmol) was added to this mixture at room temperature. After 12 hours solvent was evaporated under reduced pressure and water (500ml) was added. Precipitated solids were collected by fdtration, washed with water and purified by FC (Ok. Interchim, 330 g SiO2, hexane /EtOAc with EtOAc from 0~100%, flow rate = 100 mL/min, Rv=4.3-7 cv) to obtain 5-bromo-2- (2H3)methoxy-3 -nitropyridine (15.0 g, 63.55 mmol, 30% yield) as an orange solid. [0307] Step 2 : A suspension of 5-bromo-2-(2H3)methoxy-3-nitropyridine (15.0 g, 63.84 mmol), 3,5-dimethyl-4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)-l,2-oxazole (17.09 g, 76.61 mmol), dipotassium carbonate (17.61 g, 127.68 mmol) and tetrakis(triphenylphosphine)palladium (3.7 g, 3.19 mmol) in dioxane:H2O (10: 1, 300ml) was stirred at 100°C under inert atmosphere overnight. Then the mixture was fdtered, evaporated and purified by FC (Interchim; 330g SiCh, petroleum ether/ethyl acetate with ethyl acetate from 0-100%, flow rate = lOOmL/min, Rv =6- 11CV) to obtain 5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-(2H3)methoxy-3-nitropyridine (13.4 g, 53.12 mmol, 83.2% yield) as a yellow solid.
[0308] Step 3: To a solution of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-(2H3)methoxy-3- nitropyridine (13.4 g, 53.15 mmol) and 4,4'-bipyridine (829.57 mg, 5.32 mmol) in DMF (200ml) (dihydroxyboranyl)boronic acid (14.36 g, 159.46 mmol) was added portion wise at temperature below 50°C (exoterm observed). The mixture was stirred for 30 min at room temperature, then the solvent was distilled under high vacuum. The crude residue was purified by FC (Ok. Interchim, 330 g SiO2, hexane / EtOAc with EtOAc from 0~100%, flow rate = 100 mL/min, Rv=2.9-10cv) to obtain 5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-(2H3)methoxypyridin-3-amine (11.5 g, 51.74 mmol, 97.3% yield) as a yellow solid.
[0309] Step 4 : A mixture of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-(2H3)methoxypyridin-3- amine (75.0 mg, 337.45 pmol), 2-(3-formylphenoxy)acetic acid (60.57 mg, 336.42 pmol) and sodium bis(acetyloxy)boranuidyl acetate (214.01 mg, 1.01 mmol) in 1,2-di chloroethane (20ml) was stirred overnight at room temperature. Then the mixture was evaporated and purified by HPLC (20-20-60% 0-l-6min H2O/ACN/FA flow: 60ml/min (loading pump 4ml/min ACN) target mass 387 column: Xbridge C18 OBD 30x100mm 5 pm) to obtain 2-[3-([5-(3,5-dimethyl-l,2- oxazol-4-yl)-2-(2H3)methoxypyridin-3-yl]aminomethyl)phenoxy]acetic acid (38.0 mg, 98.34 pmol, 29.2% yield) as a white solid.
General procedure 16. Synthesis of pyridone-containing R2 acids. [0310] Step 1 : To a solution of aldehyde 1, (1 eq) in MeOH (0.5 M) sodium borohydride (1 eq) was added in portions at 0°C. Then the solution was stirred at room temperature for 2 hours, diluted with 10% HC1, extracted with methyl tert-butyl ether (2x), washed with brine, dried over anhydrous sodium sulfate and filtered. The collected filtrate was concentrated under reduced pressure to obtain the desired alcohol 2, which was used without further purification.
[0311] Step 2a: To a solution of alcohol 2 (1.0 eq) and triethylamine (1.5 eq) in ethyl acetate (0.35 M) methanesulfonyl chloride (1.0 eq) was added at 0°C. The mixture was stirred for 30 min at 0°C, then diluted with distilled water. The organic layer was separated, washed with water and brine, dried over magnesium sulfate, filtered, and concentrated in vacuo to produce the desired mesylate 3, which was immediately used as crude in the next step.
[0312] Step 2b: benzylic bromide 3 (X= Br) was prepared from alcohol using Appel reaction conditions or was purchased from commercial sources.
[0313] Step 3 : A suspension of aryl bromide 4 (1 eq), (dimethyl-l,2-oxazol-4-yl)boronic acid (1.3 eq), dipotassium carbonate (2 eq) and [1,1'- bis(diphenylphosphino)ferrocene]dichloropalladium (II) dichloromethane complex (5 wt. %) in a degassed mixture of dioxane and water (10:1, 0.3 M) was stirred under argon at 90°C overnight. After cooling to room temperature, the mixture was diluted with water and extracted with ethyl acetate (2x). The organic layers were combined, washed with water and brine, dried over magnesium sulfate, filtered, and concentrated in vacuo to afford the desired bi-aryl 5.
[0314] Step 4 : To a magnetically stirred solution of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-2- methoxypyridine (1 eq) in EtOH (0.1 M) hydrogen bromide (35 eq) was added. The resulting mixture was heated at 90°C for 4 hours. Then the reaction mixture was cooled down to room temperature and concentrated under reduced pressure. The residue obtained was diluted with brine and the precipitate formed was collected by filtration and washed with small amount of water to result in the desired pyridone 6.
[0315] Step 5 : A solution of pyridone 6 (1 eq), mesylate or bromide 3 (1.7 eq) and dipotassium carbonate (3 eq) in acetonitrile (0.2 M) was heated at 70°C for 2 hours. Then the mixture was filtered, evaporated to dryness and the residue obtained was purified by flash chromatography to obtain the desired ester 7.
[0316] Step 6: To a solution of methyl ester 7 (1 eq) in Me0H/H20 (6:1, 0.7 M) sodium hydroxide (3 eq) was added at room temperature. The reaction mixture was stirred for 12 hours, then evaporated to dryness, dissolved in water and acidified to pH 2 with NaHSCU The formed precipitate was collected by filtration, washed with water and purified by prep HPLC to provide the desired acid 8.
General procedure 17. Synthesis of pyridone-containing R2 acids.
[0317] Step 1 : A mixture of bromide 1 (1 eq), (dimethyl- l,2-oxazol-4-yl)boronic acid (1.3 eq), dipotassium carbonate (2 eq) Pd(PPhs)4 (0.1 eq) in a degassed mixture of dioxane and water (10: 1, 0.3 M) was stirred under argon at 90°C overnight. TLC (silica gel plate, petroleum ether: ethyl acetate = 1: 1) showed starting material was consumed completely and several new spots were observed. The reaction mixture was diluted with ethyl acetate (100 mL) and water (50 mL). The mixture was separated and extracted with ethyl acetate (50 mL*3). The combined organic layer was washed with brine (100 mL*3), dried with anhydrous Na2SO4, fdtered and concentrated in vacuo. The residue was purified by column chromatography (SiCh, petroleum ether: ethyl acetate = 10:1 to 1:1) to afford bi-aryl 3.
[0318] Step 2 : To a solution of bi-aryl 3 in dioxane was added HBr/HOAc (IM). The mixture was stirred at 90 °C for 12 hours. LCMS showed compound 2 was consumed completely and 63% of desired mass was detected. The mixture was cooled to 0 °C and quenched by adding water. The resulting reaction mixture was extracted with ethyl acetate (3x). Ethyl acetate layer was washed with water (2x), dried over anhydrous Na2SO4 and evaporated under reduced pressure. The residue was purified by p/ep-HPLC (column: Phenomenex luna Cl 8 (250*70mm, 10 pm); mobile phase: [water (FA)-ACN]; gradient: l%-30% B over 22 min) to afford compound 4 (52% yield) as a white solid.
[0319] Step 3 : To a solution of aniline 4 (1 eq) and 3-amino-5-(3,5-dimethylisoxazol-4-yl)- l/f-pyridin-2-one (1 eq) in MeOH was added NaBFLCN and AcOH. LCMS showed compound 4 was consumed completely and 82% of desired mass was detected. TLC (silica gel plate, petroleum ether: ethyl acetate = 0: 1) showed reactants was consumed completely and one major spot was observed. The reaction mixture was diluted with H2O and extracted with ethyl acetate (3x). The combined organic layers were washed with saturated brine, dried over Na2SO4, filtered and 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 50-75% Ethyl acetate/Petroleum ether gradient at 60 mL/min) to afford benzyl amine product 6 (45% yield) as a yellow solid.
[0320] Step 4: To a solution of tBu ester 6 (1 eq) was added DCM/TFA (0.2 M, 1:1). The mixture was stirred at 25 °C for 12 hours. LCMS showed 13% compound 8 remained and 78% of desired mass was detected. The reaction mixture was fdtered and concentrated under reduced pressure to remove solvent and give a residue. The residue was purified by prep-WVC (column: Phenomenex luna C18 150*40mm* 15um; mobile phase: [water (FA)-ACN]; gradient: 33%-63% B over 15 min) to afford free acid 7 blue solid.
Final Target Synthesis Examples
Example 2: Synthesis of2-{3-[(4-{2-[2-(2-aminoethoxy)ethoxy]ethoxy}phenyl)amino]prop-l- yn-l-yl}-N-(l-methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine.
[0321] Step 1: The synthesis of tert-butyl N-(2-{2-[2-(4- nitrophenoxy)ethoxy]ethoxy}ethyl)carbamate. Dipotassium carbonate (6.65 g, 48.22 mmol) was added to a solution of tert-butyl N-2-[2-(2-bromoethoxy)ethoxy]ethylcarbamate (10.0 g, 32.15 mmol) in DMF (50 mL). The resulting mixture was stirred at room temperature for 30 min and 4- nitrophenol (5.36 g, 38.58 mmol) was added in one portion. The reaction was stirred at 50 °C for 24 hrs and monitored by LCMS. The resulting mixture was diluted with EtOAc (250 mL), then washed with H2O (80 mL), brine (4 x 40 mL), dried over Na2SO4, and concentrated under reduced pressure to dryness to afford tert-butyl N-(2-2-[2-(4- nitrophenoxy)ethoxy]ethoxyethyl)carbamate (9.5 g, 67.8% yield) as yellow solid.
[0322] Step 2: The synthesis of tert-butyl N-(2-{2-[2-(4- aminophenoxy)ethoxy]ethoxy}ethyl)carbamate. A solution of tert-butyl N-(2-2-[2-(4- nitrophenoxy)ethoxy]ethoxyethyl)carbamate (9.5 g, 25.65 mmol) in methanol (150 ml) was treated with Pd/C (0.95 g, 5 wt. %). The resulting mixture was hydrogenated at 2 atm and ambient temperature until spectral data of an aliquot revealed completion of the reaction (by LCMS). Then the catalyst was filtered off and the filtrate was concentrated to afford tert -butyl N- (2-2- [2-(4-aminophenoxy)ethoxy] ethoxy ethyl)carbamate (8.2 g, 79.8% yield) as yellow solid. The product was used in further experiments without any additional purification.
[0323] Step 3: The synthesis of zc/7-butyl N-{2-[2-(2-{4-[(prop-2-yn-l yl)amino]phenoxy}ethoxy)ethoxy] ethyl (carbamate. 3 -Bromoprop- 1-yne (3.41 g, 28.92 mmol, 2.17 ml) was added portionwise to the solution of tert-butyl N-(2-2-[2-(4- aminophenoxy)ethoxy]ethoxyethyl)carbamate (8.2 g, 24.1 mmol) and dipotassium carbonate (4.99 g, 36.15 mmol) in DMF (60 mL) and the mixture was stirred at room temperature for 24 hrs. The resulting mixture was diluted with EtOAc (300 mL), washed with H2O (80 mL) and aq NaHSCh (50 mL). The combined organics were then washed with brine (5*50 mL), dried over Na2SO4, and concentrated to afford 9 g of crude oil (50-60% purity). The crude product obtained was purified by flash chromatography (ISCO® Interchim; 220g SiO2, chloroform/acetonitrile with acetonitrile from 90-30%; flow rate: 60 mL/min, Rf = 3.6-6CV). As a result, ze/7-butyl N-2- [2-(2-4-[(prop-2-yn-l-yl)amino]phenoxyethoxy)ethoxy]ethylcarbamate (4.6 g, 45.4% yield) was obtained as yellow oil.
[0324] Step 4: The synthesis of zcrz-butyl N-{2-[2-(2-{4-[(3-{4-[(l-methylpiperidin-4- yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]phenoxy(ethoxy)ethoxy] ethyl (carbamate. 2-Iodo-N-(l-methylpiperidin-4-yl)-l-(2,2,2- trifluoroethyl)-lH-indol-4-amine (531.87 mg, 1.22 mmol) (see procedure Z7163717351) and palladium-tetrakis(triphenylphosphine) (281.92 mg, 243.39 pmol) were added to a round bottom flask charged with 2-iodo-N-(l-methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine (531.87 mg, 1.22 mmol), zcrz-butyl N-2-[2-(2-4-[(prop-2-yn-l- yl)amino]phenoxyethoxy)ethoxy]ethylcarbamate (650.0 mg, 85.0% purity, 1.46 mmol) and copper iodide (23.1 mg, 121.69 pmol) in DMSO/z-Pr2NH(3 : 1 , 16 mL) at room temperature. The resulting mixture was sparged with argon for 10 min and stirred at room temperature for 12 hrs. The mixture was diluted with EtOAc (100 mL), washed with H2O (30 mL), aq. NH3 (2 x 30 mL), brine (20 mL), dried over Na2SO4, and concentrated under reduced pressure to dryness to afford 1.1 g of crude brown oil. The crude product obtained was purified by flash chromatography (ISCO® Interchim; 40g SiO2, acetonitrile/methanol 40 to 100% gradient; flow rate: 60 mL/min; Rf =6-11 CV). As a result, tert-butyl N-2-[2-(2-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2- trifluoroethyl)-lH-indol-2-ylprop-2-yn-l-yl)amino]phenoxyethoxy)ethoxy]ethylcarbamate (500.0 mg, 53.8% yield) was obtained as brown oil. [0325] Step 5: The synthesis of 2-{3-[(4-{2-[2-(2- aminoethoxy)ethoxy]ethoxy}phenyl)amino]prop-l-yn-l-yl}-N-(l-methylpiperidin-4-yl)-l-(2,2,2- trifluoroethyl)- lH-indol-4-amine. Tert-butyl N-2-[2-(2-4-[(3-4-[(l-methylpiperidin-4-yl)amino]- l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l- yl)amino]phenoxyethoxy)ethoxy]ethylcarbamate (500.0 mg, 80.0% purity, 581.57 pmol) was dissolved in 12 mL of MeOH. Hydrogen chloride (209.37 mg, 5.82 mmol, 2.91 ml) was added and the resulting mixture was stirred at room temperature overnight. After consumption of the starting material (observed by LCMS) the resulting mixture was concentrated under reduced pressure to dryness (<40°C). The residue obtained was quenched with NaHCCh (20 mL) and extracted with DCM (3x20 mL). The combined organic extracts were washed with brine (10 mL), dried overNa2SO4, and concentrated to afford 2-3-[(4-2-[2-(2- aminoethoxy)ethoxy]ethoxyphenyl)amino]prop- 1 -yn- 1 -yl-N-(l -methylpiperidin-4-yl)- 1 -(2,2,2- trifhroroethyl)-lH-indol-4-amine (370.0 mg, 81.1% yield, 75.0% purity) as brown oil. The product was used in further experiments without any additional purification.
Example 3: Synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-({3-[(6-{4-[(3-{4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifluoroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino] phenoxy} hexyl)oxy] phenyl}methyl)-l,2-dihydropyridin-2-one. [0326] Step 1 : The synthesis of 6-(4-nitrophenoxy)hexan-l-ol. A mixture of 4-nitrophenol (5.0 g, 35.96 mmol), 6-bromohexan-l-ol (6.8 g, 37.76 mmol) and dipotassium carbonate (9.92 g, 71.93 mmol) in acetonitrile (100 mL) was stirred overnight at 75°C. Then the mixture was cooled, filtered and evaporated to obtain 6-(4-nitrophenoxy)hexan-l-ol (5 g, 86% yield) which was used without further purification to the next step.
[0327] Step 2 : The synthesis of 6-(4-nitrophenoxy)hexyl methanesulfonate. To a solution of 6-(4-nitrophenoxy)hexan-l-ol (1.0 g, 4.19 mmol) and ethylbis(propan-2-yl)amine (1.08 g, 8.39 mmol, 1.46 ml) in ethyl acetate (20 mL) methanesulfonyl chloride (525.72 mg, 4.61 mmol, 360.0 pl) was added at 0°C. The mixture was stirred 30 min at 0°C, then diluted with water (20 mL). The organic layer was separated, washed with water and brine, dried over magnesium sulfate, filtered, and concentrated in vacuo to afford 6-(4-nitrophenoxy)hexyl methanesulfonate (1.2 g, 92% yield) which was immediately used in the next step.
[0328] Step 3: The synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-[(3-{[6-(4- nitrophenoxy)hexyl]oxy}phenyl)methyl]-l,2-dihydropyridin-2-one. A mixture of 5-(3,5- dimethyl- 1 ,2-oxazol-4-yl)- 1 - [(3 -hy droxyphenyl)methyl] - 1 ,2-dihy dropyridin-2-one (649.81 mg, 2.19 mmol), 6-(4-nitrophenoxy)hexyl methanesulfonate (800.0 mg, 2.52 mmol) and dipotassium carbonate (907.29 mg, 6.58 mmol) in MeCN (50 mL) was stirred for 48 hrs at 78°C. Then the mixture was cooled, filtered, and filtrate evaporated to obtain 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l- [(3-[6-(4-nitrophenoxy)hexyl]oxyphenyl)methyl]-l,2-dihydropyridin-2-one (1g, 88% yield) which was used directly in the next step.
[0329] Step 4 : The synthesis of l-[(3-{[6-(4-aminophenoxy)hexyl]oxy}phenyl)methyl]-5- (3,5-dimethyl-l,2-oxazol-4-yl)-l,2-dihydropyridin-2-one. A mixture of 5-(3,5-dimethyl-l,2- oxazol-4-yl)-l-[(3-[6-(4-nitrophenoxy)hexyl]oxyphenyl)methyl]-l,2-dihydropyridin-2-one (500.0 mg, 966.7 pmol), dichlorostannane dihydrate (880.49 mg, 3.86 mmol) and acetic acid (579.79 mg, 9.66 mmol) was stirred at reflux in THF (50 mL) for 12 hrs. Then the mixture was cooled to room temperature and poured into water (100 mL), neutralized to pH = 7 with ISfeCCh, extracted twice with ethyl acetate (2 x 50 mL), dried under ISfeSCL and evaporated to obtain l-[(3-[6-(4- aminophenoxy)hexyl]oxyphenyl)methyl]-5-(3,5-dimethyl-l,2-oxazol-4-yl)-l,2-dihydropyri din-2- one (0.4g, 85% yield) which was used without further purification.
[0330] Step 5: The synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-({3-[(6-{4-[(prop-2-yn- l-yl)amino]phenoxy}hexyl)oxy]phenyl}methyl)-l,2-dihydropyridin-2-one. A mixture of l-[(3- [6-(4-aminophenoxy)hexyl]oxyphenyl)methyl]-5-(3,5-dimethyl-l,2-oxazol-4-yl)-l,2- dihydropyridin-2-one (400.0 mg, 820.36 pmol) , 3 -bromoprop- l-yne (96.71 mg, 819.96 pmol) and dipotassium carbonate (226.16 mg, 1.64 mmol) in MeCN (10 mL) was stirred at room temperature overnight. The same portion of l-[(3-[6-(4-aminophenoxy)hexyl]oxyphenyl)methyl]- 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l,2-dihydropyridin-2-one (400.0 mg, 820.36 pmol) was added twice during this time. Then the mixture was fdtered and purified by HPLC (40-40-90% 0-1- 6min H2O/MeCN/NH4OH; flow: 60 mL/min; loading pump: 4 mL/min MeCN; target mass: 525; column: XBridge C18 OBD 100x30mm 5 pm) to obtain 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-(3- [(6-4-[(prop-2-yn-l-yl)amino]phenoxyhexyl)oxy]phenylmethyl)-l,2-dihydropyridin-2-one (57 mg, 13% yield).
[0331] Step 6: The synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-({3-[(6-{4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]phenoxy}hexyl)oxy]phenyl}methyl)-l,2-dihydropyridin-2-one. A mixture of 5-(3,5- dimethyl-l,2-oxazol-4-yl)-l-(3-[(6-4-[(prop-2-yn-l-yl)amino]phenoxyhexyl)oxy]phenylmethyl)-
1.2-dihydropyridin-2-one (40.0 mg, 76.1 pmol) , 2-iodo-N-( 1 -methylpiperi din-4-yl)-l -(2,2,2- trifluoroethyl)-lH-indol-4-amine (39.89 mg, 91.26 pmol), copper iodide (721.9 pg, 3.8 pmol) and palladium-tetrakis(triphenylphosphine) (35.24 mg, 30.42 pmol) was stirred in DMSO:iPr2NH (2 mL, 2:1) under argon atmosphere at room temperature for 4 hrs. Then the mixture was purified by HPLC (13-50-75-100% 0-2-7-7.1min; 30 mL/min HiO/MeCN/NlLOH; loading pump: 4 mL/min; target mass: 835; column: Xbridge C18 19*100mm 5 pM) to obtain 5-(3,5-dimethyl-
1.2-oxazol-4-yl)-l-(3-[(6-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH- indol-2-ylprop-2-yn-l-yl)amino]phenoxyhexyl)oxy]phenylmethyl)-l,2-dihydropyridin-2-one (0.5mg, 8% yield, 95.5% purity) as orange solid.
Example 4: Synthesis ofN-(2-{2-[2-(2-aminoethoxy)ethoxy]ethoxy}ethyl)-3-methoxy-N- methyl-4-[(3-{4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2- yl}prop-2-yn-l-yl)amino]benzene-l-sulfonamide.
[0332] Step 1: The synthesis of tert-butyl N-[2-(2-{2-[2-(N-methyl-3-methoxy-4 nitrobenzenesulfonamido)ethoxy]ethoxy}ethoxy)ethyl]carbamate. To a solution of tert-butyl N- (5,8,1 l-trioxa-2-azatridecan-13-yl)carbamate (3.66 g, 11.95 mmol) and tri ethyl amine (1.81 g, 17.93 mmol, 2.5 mL) in DCM (30 mL), was added solution of 3-methoxy-4-nitrobenzene-l- sulfonyl chloride (3.0 g, 11.95 mmol) in THF(10 mL) at 0°C under nitrogen atmosphere. The mixture was warmed to room temperature and stirred for 12 hrs. LCMS analysis of the reaction mixture showed full conversion to the desired product .Then the mixture was concentrated under reduced pressure, diluted with EtOAc (60 mL) and washed with 1 M solution of NaHSCL (10 mL), saturated solution of NaHCCh (10 mL), brine, dried over anhydrous Na2SO4 and concentrated under reduced pressure to afford tert-butyl N-[2-(2-2-[2-(N-methyl-3-methoxy-4- nitrobenzenesulfonamido)ethoxy]ethoxyethoxy)ethyl]carbamate (5.0 g, 76.2% yield) that was used in next step without purification.
[0333] Step 2: The synthesis of tert-butyl N-[2-(2-{2-[2-(N-methyl-4-amino-3- methoxybenzenesulfonamido)ethoxy]ethoxy}ethoxy)ethyl]carbamate. To a solution of tert-butyl N-[2-(2-2-[2-(N-methyl-3-methoxy-4- nitrobenzenesulfonamido)ethoxy]ethoxyethoxy)ethyl]carbamate (4.9 g, 9.39 mmol) and reagent 2 in anhydrous DMF (60 mL), under inert atmosphere was added (dihydroxyboranyl)boronic acid (2.54 g, 28.18 mmol) portion wise at 5 °C. The resulting solution was warmed up and stirred at room temperature for 1 hour. The reaction mixture was quenched by 10% solution of K2CO3 (240 mL), stirred up for 1 hour, extracted by EtOAc (3x100 mL). Organic phase washed by water (3x50 mL), brine, dried over Na2SO4 and concentrated under reduced pressure to afford /c/7-butyl N-[2-(2-2-[2-(N-methyl-4-amino-3- methoxybenzenesulfonamido)ethoxy]ethoxyethoxy)ethyl]carbamate (4.0 g, 73.6% yield) that was used in next step without purification.
[0334] Step 3: The synthesis oftert-butyl N-(2-{2-[2-(2-{N-methyl-3-methoxy-4-[(prop-2- yn-l-yl)amino]benzenesulfonamido}ethoxy)ethoxy]ethoxy}ethyl)carbamate. To a solution of /c/7-butyl N-[2-(2-2-[2-(N-methyl-4-amino-3- methoxybenzenesulfonamido)ethoxy] ethoxy ethoxy)ethyl] carbamate (4.6 g, 9.36 mmol) in DMF (75 mL), was added 3 -bromoprop- l-yne (1.1 g, 9.36 mmol, 700.0 pl) and dipotassium carbonate (3.87 g, 28.07 mmol) at room temperature under nitrogen atmosphere. The mixture was stirred at 60°C for 12 hrs. After that another portion of 3 -bromoprop- 1-yne (1.1 g, 9.36 mmol, 700.0 pl) was added and reaction was stirred at 60°C for 8 hrs. The addition was continued until 80% conversion by LCMS was achieved. Then the mixture diluted with EtOAc (150 mL) and washed with water (3x50 mL), brine, dried over anhydrous Na2SO4 and concentrated under reduced pressure to afford crude compound that was sent to flash column (ISCO® ® Interchim; 120g SiO2, petroleum ether/THF with acetonitrile from 10-60%; flow rate: 46 mL/min, Rf = 7.8-9.6 CV) to afford tert-butyl N-(2-2-[2-(2-N-methyl-3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)carbamate (2.5 g, 45.4% yield).
[0335] Step 4: The synthesis of tert-butyl N-(2-{2-[2-(2-{N-methyl-3-methoxy-4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonamido}ethoxy)ethoxy]ethoxy}ethyl)carbamate. A solution of the 2-iodo- N-(l-methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine (800.0 mg, 1.83 mmol), the tert-butyl N-(2-2-[2-(2-N-methyl-3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)carbamate (1.82 g, 80.0% purity, 2.75 mmol) , DiPA (5 mL), and dry DMSO (15 mL) was degassed by bubbling argon for 2 min. Palladium-tetrakis(triphenylphosphine) (636.19 mg, 549.24 pmol) and Cui (34.75 mg, 183.08 pmol) were added, and the mixture was again degassed by bubbling argon and was stirred under argon at room temperature for 12 hrs. LCMS analysis of the reaction mixture showed full conversion to the desired product. The mixture was diluted by saturated solution of EDTA in water (60 mL), extracted by EtOAc (3x50 mL). The combined organic layers were washed with water, brine, dried over anhydrous Na2SO4 and concentrated under reduced pressure to afford crude compound that was sent to flash column chromatography (ISCO® ® Interchim; 80g SiO2, acetonitrile /methanol with methanol from 0~95%; flow rate: 60 mL/min, Rf = 10-15CV) to affordtert-butyl N-(2-2-[2-(2-N-methyl-3-methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l- (2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l- yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)carbamate (800.0 mg, 51.6% yield).
[0336] Step 5 : The synthesis ofN-(2-{2-[2-(2-aminoethoxy)ethoxy]ethoxy}ethyl)-3- methoxy-N-methyl-4-[(3-{4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol- 2-yl}prop-2-yn-l-yl)amino]benzene-l -sulfonamide trihydrochloride. To a solution of /c/7-butyl N-(2-2-[2-(2-N-methyl-3-methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l -(2,2,2- trifluoroethyl)- lH-indol-2-ylprop-2-yn-l- yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)carbamate (32.0 mg, 38.14 pmol) in MeOH (1 mL), was added 1 mL of HC1 in Dioxane (2.2 M) at room temperature under nitrogen atmosphere. The mixture was stirred at room temperature for 1 h. LCMS analysis of the reaction mixture showed full conversion to the desired product. Then the mixture concentrated under reduced pressure to afford crude N-(2-2-[2-(2-aminoethoxy)ethoxy]ethoxyethyl)-3-methoxy-N- methyl-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn- l-yl)amino]benzene-l -sulfonamide trihydrochloride (28.0 mg, 63.9% yield, 73.0% purity) that was used in next step without purification.
Example 5: Synthesis of 4-(4-{[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l- yl] methyl} phenoxy)-N-(2- {2- [2-(2- {4- [(3- {4- [(l-methylpiperidin-4-yl)amino] - 1-(2,2,2- trifhioroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino]phenoxy}ethoxy)ethoxy]ethoxy}ethyl)butanamide.
[0337] Step 1 : The synthesis of 4-(4-{[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2- dihydropyridin-l-yl]methyl}phenoxy)-N-(2-{2-[2-(2-{4-[(3-{4-[(l-methylpiperidin-4-yl)amino]- 1 -(2,2,2-trifluoroethyl)- lH-indol-2-yl } prop-2-yn- 1 - yl)amino]phenoxy}ethoxy)ethoxy] ethoxy }ethyl)butanami de. Procedure as described in general procedure 3. 4-(4-[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l- yl]methylphenoxy)-N-(2-2-[2-(2-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2- trifluoroethyl)-lH-indol-2-ylprop-2-yn-l- yl)amino]phenoxyethoxy)ethoxy]ethoxyethyl)butanamide (11.7 mg, 28.8% yield, 97.0% purity) was obtained as yellow solid.
Example 6: Synthesis of 2-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl}phenoxy)-N-(2- {2- [2-(N-methyl-4- { [3-(4- { [(3S,4R)-3-fhioro-l- methylpiperidin-4-yl]amino}-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino}- 3-methoxybenzenesulfonamido)ethoxy]ethoxy}ethyl)acetamide.
[0338] Step 1: The synthesis of tert-butyl N-[2-(2-{2-[N-methyl-4-({3-[4-bromo-l-(2,2,2- trifluoroethyl)-lH-indol-2-yl]prop-2-yn-l-yl}amino)-3- methoxybenzenesulfonamido]ethoxy}ethoxy)ethyl]carbamate. To a stirred solution of /c/7-butyl N-2-[2-(2-N-methyl-3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonamidoethoxy)ethoxy]ethylcarbamate (450.0 mg, 926.7 pmol), 4-bromo- 2-iodo-l-(2,2,2-trifluoroethyl)-lH-indole (311.02 mg, 772.01 pmol) in THF (9 ml) and EtsN (9 ml), palladium-tetrakis(triphenylphosphine) (178.84 mg, 154.4 pmol) and copper iodide (14.66 mg, 77.2 pmol) were added dropwise at room temperature under argon atmosphere. The reaction mixture was stirred at room temperature for another 12 hrs. Then the mixture was purified by flash column chromatography to obtaintert-butyl N-[2-(2-2-[N-methyl-4-(3-[4-bromo-l-(2,2,2- trifluoroethyl)- 1 H-indol-2-yl]prop-2-yn- 1 -ylamino)-3 - methoxybenzenesulfonamido]ethoxyethoxy)ethyl]carbamate (350.0 mg, 53.6% yield) as yellow gum.
[0339] Step 2: The synthesis oftert-butyl N-(2-{2-[2-(N-methyl-4-{[3-(4-{[(3S,4R)-3- fluoro- 1 -methylpiperi din -4-yl] amino } - 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2-yn- 1 - yl]amino } -3-methoxybenzenesulfonamido)ethoxy]ethoxy } ethyl (carbamate. To a stirred solution oftert-butyl N-[2-(2-2-[N-methyl-4-(3-[4-bromo-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl]prop-2- yn-l-ylamino)-3-methoxybenzenesulfonamido]ethoxyethoxy)ethyl]carbamate (30.47 mg, 40.0 pmol), (3 S,4R)-3 -fluoro- l-methylpiperidin-4-amine (15.84 mg, 119.94 pmol), and sodium 2- methylpropan-2-olate (11.52 mg, 119.94 pmol) in toluene (1 mL), tris( 1,5 -diphenylpenta- 1,4- dien-3-one), Pd2(dba)s (7.31 mg, 8.0 pmol) and [l,l'-biphenyl]-2-yldi-tert-butyl)phosphane (4.77 mg, 15.99 pmol) were added at the room temperature under argon atmosphere. The reaction mixture was stirred at room temperature for another 12 hrs. Purification by HPLC (40-65% 0- 5min H2O/MeCN/0.1%NH4OH, flow: 30 mL/min; loading pump: 4 mL/min MeCN; target mass: 856.99; column: XBridge C18 100x19mm 5pm) affordedtert-butyl N-(2-2-[2-(N-methyl-4-[3-(4- [(3 S,4R)-3 -fluoro- 1 -methylpiperidin-4-yl] amino- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2- yn- 1 -yl] amino-3 -methoxybenzenesulfonamido)ethoxy ] ethoxy ethyl)carbamate (33.0 mg, quantitative yield).
[0340] Step 3: The synthesis of N-{2-[2-(2-aminoethoxy)ethoxy]ethyl}-4-{[3-(4-{[(3S,4R)- 3 -fluoro- 1 -methylpiperidin-4-yl] amino } - 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2-yn- 1 - yl]amino}-3-methoxy-N-methylbenzene-l-sulfonamide tetrahydrochloride. A stirred solution of /c/7-butyl N-(2-2-[2-(N-methyl-4-[3-(4-[(3 S,4R)-3-fluoro-l-methylpiperidin-4-yl]amino-l -(2,2,2- trifluoroethyl)- lH-indol-2-yl)prop-2-yn-l-yl] amino-3 - methoxybenzenesulfonamido)ethoxy]ethoxyethyl)carbamate (11.0 mg, 13.53 pmol) in MeOH (0.1 mL) and dioxane/HCl (0.1 mL) at the room temperature. Reaction mixture was stirred at room temperature for another 3 hrs and concentrated in vacuo to obtain N-2-[2-(2- aminoethoxy)ethoxy]ethyl-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]amino-l-(2,2,2- trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3-methoxy-N-methylbenzene-l -sulfonamide tetrahydrochloride (11.0 mg, 92.9% yield) as brown gum which was used directly in the next step.
[0341] Step 4: The synthesis of 2-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl}phenoxy)-N-(2-{2-[2-(N-methyl-4-{[3-(4-{[(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino}-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino}-3- methoxybenzenesulfonamido)ethoxy]ethoxy}ethyl)acetamide. A solution ofN-2-[2-(2- aminoethoxy)ethoxy]ethyl-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]amino-l-(2,2,2- trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3-methoxy-N-methylbenzene-l -sulfonamide tetrahydrochloride (11.6 mg, 13.51 pmol), [(dimethylamino)(3H-[l,2,3]triazolo[4,5-b]pyridin-3- yloxy)methylidene]dimethylazanium; hexafluoro-lambda5-phosphanuide (6.68 mg, 17.58 pmol), 2-(3-[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3-benzodiazol-l-yl]methylphenoxy)acetic acid (6.9 mg, 17.58 pmol), and ethylbis(propan-2-yl)amine (17.46 mg, 135.21 pmol) in DMF (0.2 mL) was stirred overnight at room temperature. Mixture was purified by HPLC (30-55% 0- 5min H2O/MeCN/0.1%NH4OH; flow: 30 mL/min; loading pump: 4 mL/min MeCN; target mass: 1131.2; column: XBridge C18 100x19mm, 5pm) to obtain 2-(3-[4-amino-6-(3,5-dimethyl-l,2- oxazol-4-yl)- 1 H- 1 ,3 -benzodi azol- 1 -yl]methylphenoxy)-N-(2-2- [2-(N-methyl-4- [3 -(4- [(3 S,4R)-3 - fluoro-1 -methylpiperi din -4-yl]amino-l -(2, 2, 2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l- yl]amino-3-methoxybenzenesulfonamido)ethoxy]ethoxyethyl)acetamide (5.0 mg, 34% yield, 99% purity).
Example 7: Synthesis of 2-[3-(3,5-dimethyl-l,2-oxazol-4-yl)-5-
[hydroxy(phenyl)methyl] phenoxy] -N- [2- (2- {2- [2-({3-methoxy-4- [(3- {4- [(1-methylpiperidin-
4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino]phenyl}formamido)ethoxy]ethoxy}ethoxy)ethyl]acetamide.
[0342] Step 1: The synthesis of 2-[3-(3,5-dimethyl-l,2-oxazol-4-yl)-5- [hydroxy(phenyl)methyl]phenoxy]-N-[2-(2-{2-[2-({3-methoxy-4-[(3-{4-[(l-methylpiperi din-4- yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]phenyl}formamido)ethoxy]ethoxy}ethoxy)ethyl] acetamide. A solution of the N-(2-2- [2-(2-aminoethoxy)ethoxy] ethoxy ethyl)-3 -methoxy -4-[(3-4-[(l -methylpiperi din-4-yl)amino]-l - (2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l-yl)amino]benzamide (24.95 mg, 36.23 pmol), the 2-[3-(3,5-dimethyl-l,2-oxazol-4-yl)-5-[hydroxy(phenyl)methyl]phenoxy]acetic acid (12.79 mg, 36.23 pmol) , l-[bis(dimethylamino)methylene]-lH-l,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (17.9 mg, 47.09 pmol) and the ethylbis(propan-2-yl)amine (46.75 mg, 361.95 pmol, 60.0 pl) in dry DMF (1 mL) was stirred under argon at room temperature for 12 hrs. LCMS analysis of the reaction mixture showed full conversion to the desired product. The mixture was sent to HPLC (30-30-70% 0-l-6min H2O/MeCN/NH4OH; flow: 60 mL/min; loading pump: 4 mL/min MeCN; target mass: 1025; column: Interchim XBridge C18 OBD 100x30mm 5 pm) to afford 2-[3-(3,5-dimethyl-l,2-oxazol-4-yl)-5-[hydroxy(phenyl)methyl]phenoxy]-N-[2-(2- 2-[2-(3-methoxy-4-[(3-4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2- ylprop-2-yn-l-yl)amino]phenylformamido)ethoxy]ethoxyethoxy)ethyl]acetamide (16.4 mg, 44.2% yield, 99% purity). Example 8: Synthesis of5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-({3-[4-(4-{4-[(3-{4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifluoroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino] phenoxy} butoxy) butoxy]phenyl}methyl)-l,2-dihydropyridin-2-one.
[0343] Step 1 : The synthesis of tert-butyl N-{4-[4-(4-hydroxybutoxy)butoxy]phenyl}-N- (prop-2-yn-l-yl)carbamate. Tert-butyl N-(4-hydroxyphenyl)-N-(prop-2-yn-l-yl)carbamate (1.02 g, 4.12 mmol), 4-(4-chlorobutoxy)butan-l-ol (891.49 mg, 4.95 mmol), dipotassium carbonate (853.36 mg, 6.19 mmol), potassium iodide (684.23 mg, 4.13 mmol) were mixed in MeCN (30 mL) and suspension was heated at 75°C for 3 days. Cooled mixture was poured on cold water (20 mL). EtOAc (40 ml) was added, and organic layer was separated after removal of insoluble inorganics by filtration. The resulting organic layer was dried overNa2SO4 and concentrated under reduced pressure to afford tert-butyl N-4-[4-(4-hydroxybutoxy)butoxy]phenyl-N-(prop-2- yn-l-yl)carbamate (1.4 g, 67.6% yield) which was used in the next step without any further purification.
[0344] Step 2: The synthesis of tert-butyl N-(4-{4-[4- (methanesulfonyloxy)butoxy]butoxy}phenyl)-N-(prop-2-yn-l-yl)carbamate. Tert-butyl N-4-[4- (4-hydroxybutoxy)butoxy]phenyl-N-(prop-2-yn-l-yl)carbamate (195.09 mg, 498.31 pmol) was dissolved in DCM (10 mL), ethylbis(propan-2-yl)amine (96.54 mg, 747.46 pmol, 130.0 pl) was added, the mixture was cooled to 0°C, and methanesulfonyl chloride (68.08 mg, 597.43 pmol, 50.0 pl) was added dropwise and mixture was stirred for 16 hrs. The mixture was extracted with DCM (3x20 mL). The combined organic layers were washed with saturated aqueous NaCl (3x20 mL), dried with Na2SO4, and concentrated in vacuo to give tert-butyl N-(4-4-[4- (methanesulfonyloxy)butoxy]butoxyphenyl)-N-(prop-2-yn-l-yl)carbamate (234.0 mg, 65% yield) which was used in the next step immediately without any purification.
[0345] Step 3: The synthesis oftert-butyl N-(4-{4-[4-(3-{[5-(3,5-dimethyl-l,2-oxazol-4-yl)- 2-oxo-l, 2-dihydropyri din-1 -yl] methyl} phenoxy )butoxy]butoxy}phenyl)-N-(prop-2-yn-l- yl)carbamate. 5-(3,5-Dimethyl-l,2-oxazol-4-yl)-l-[(3-hydroxyphenyl)methyl]-l,2- dihydropyridin-2-one (122.99 mg, 415.05 pmol), dipotassium carbonate (85.86 mg, 622.57 pmol)t,ert-butyl N-(4-4-[4-(methanesulfonyloxy)butoxy]butoxyphenyl)-N-(prop-2-yn-l- yl)carbamate (234.0 mg, 498.31 pmol) were mixed in MeCN (10 mL) and suspension was heated 75°C for 16 hrs. Cooled mixture was poured on cold water (20 mL), EtOAc (40 mL) was added and organic extract was separated after removal of insoluble inorganics by filtration. The resulting organic layer was dried over ISfeSCL and concentrated under reduced pressure to afford /c/7-butyl N-(4-4-[4-(3-[5-(3, 5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l, 2-dihydropyri din-1- yl]methylphenoxy)butoxy]butoxyphenyl)-N-(prop-2-yn-l-yl)carbamate (95.0 mg, 34.2% yield) after HPLC (50-100% 0-5min TEO/MeCN; flow: 30 mL/min; loading pump: 4 mL/min MeCM; target mass: 669.83; column: Chromatorex 18 SMB100-5T 100x19mm 5 pm).
[0346] Step 4: The synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-({3-[4-(4-{4-[(prop-2- yn-1 -yl)amino]phenoxy (butoxy )butoxy]phenyl } methyl)- l,2-dihydropyridin-2-one. 7c/7-butyl N- (4-4-[4-(3-[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l- yl]methylphenoxy)butoxy]butoxyphenyl)-N-(prop-2-yn-l-yl)carbamate (95.47 mg, 142.53 pmol) was dissolved in DCM (5 mL), trifluoroacetic acid (324.94 mg, 2.85 mmol, 220.0 pl) was added and the mixture was left to stir at room temperature for 13 hrs. After full evaporation 5 -(3,5- dimethyl- 1 ,2-oxazol-4-yl)- 1 -(3 - [4-(4-4- [(prop-2-yn- 1 - yl)amino]phenoxybutoxy)butoxy]phenylmethyl)-l,2-dihydropyridin-2-one (80.0 mg, 98.5% yield) was obtained.
[0347] Step 5: The synthesis of 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-({3-[4-(4-{4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]phenoxy}butoxy)butoxy]phenyl}methyl)-l,2-dihydropyridin-2-one. Under argon 2- iodo-N-(l-methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine (25.56 mg, 58.47 pmol), 5 -(3 , 5 -dimethyl- 1 ,2-oxazol-4-yl)- 1 -(3 - [4-(4-4- [(prop-2-yn- 1 - yl)amino]phenoxybutoxy)butoxy]phenylmethyl)-l,2-dihydropyridin-2-one (40.0 mg, 70.21 pmol), copper iodide (2.22 mg, 11.69 pmol), and palladium-tetrakis(triphenylphosphine) (13.55 mg, 11.69 pmol) were mixed in DMSO (2 mL) and di-isopropil-amine (1 mL) and the mixture was left to stir at room temperature for 13 hrs. After HPLC purification (40-40-90% 0-1-6 min H2O/MeCN; flow: 60 mL/min; loading pump: 4 mL/min MeCN; target mass: 880; column: XBridge C18 OBD 30x100mm 5pm) the desired 5-(3,5-dimethyl-l,2-oxazol-4-yl)-l-(3-[4-(4-4- [(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l- yl)amino]phenoxybutoxy)butoxy]phenylmethyl)-l,2-dihydropyridin-2-one (13.4 mg, 26.1% yield, 99% purity) was obtained.
Example 9: Synthesis of 2-(3-{[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l- yl] methyl} phenoxy)-N-(2- {2- [2- (4- { [3-(4- { [(3S,4R)-3-fhioro- l-methylpiperidin-4-yl] amino}- l-(2,2,2-trifhioroethyl)- lH-indol-2-yl)prop-2-yn- 1- yl]amino}phenoxy)ethoxy]ethoxy}ethyl)acetamide.
[0348] Step 1: 4-Bromo-2-iodo-l-(2,2,2-trifluoroethyl)-lH-indole (1.0 g, 2.48 mmol), tertbutyl N-2-[2-(2-4-[(prop-2-yn-l-yl)amino]phenoxyethoxy)ethoxy]ethylcarbamate (1.13 g, 2.98 mmol) see intermediate 5 from procedure Z8435419477, triphenyl[tris(triphenyl-lambda5- phosphanyl)palladio] -lambda5 -phosphane (575.15 mg, 496.55 pmol) was added to a RB flask charged with 4-bromo-2-iodo-l-(2,2,2-trifluoroethyl)-lH-indole (1.0 g, 2.48 mmol), tert-butyl N- 2-[2-(2-4-[(prop-2-yn-l-yl)amino]phenoxyethoxy)ethoxy]ethylcarbamate (1.13 g, 2.98 mmol) and copper iodide (47.13 mg, 248.28 pmol) in DMSO/z-Pr2NH(3/l, 16 ml) at room temperature. The resulting mixture was sparged with argon for 10 minutes, then the reaction mixture was stirred at room temperature for 12 hours. The mixture was diluted with EtOAc (100 ml), washed with H2O (30 ml), aqua NH3 (2*30 ml), brine (20 mL), dried overNa2SO4, and concentrated under reduced pressure to dryness to afford 2.3 g of crude brown oil. The crude product obtained was purified by flash chromatography (ISCO® Interchim; 80g SiO2, petroleum ether/MTBE with MTBE from 30-100%, flow rate = 60mL/min, Rf =7-12 CV). As a result, tert-butyl N-[2-(2-2-[4- (3 - [4-bromo- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl]prop-2-yn- 1 - ylamino)phenoxy]ethoxyethoxy)ethyl]carbamate (1.2 g, 66.5% yield) was obtained as brown oil. [0349] Step 2: To a RB flask charged with tert-butyl N-[2-(2-2-[4-(3-[4-bromo-l-(2,2,2- trifluoroethyl)-lH-indol-2-yl]prop-2-yn-l-ylamino)phenoxy]ethoxyethoxy)ethyl]carbamate (100.0 mg, 152.78 pmol) , (3 S,4R)-3 -fluoro- l-methylpiperidin-4-amine (60.65 mg, 459.07 pmol) , sodium 2-methylpropan-2-olate (44.1 mg, 459.06 pmol) , [l,l'-biphenyl]-2-yldi-tert- butyl)phosphane (18.25 mg, 61.21 pmol) and sodium 2-methylpropan-2-olate (44.1 mg, 459.06 pmol) was added Toluene (5 ml) at rt. The resulting mixture was sparged with argon for 10 minutes, then the reaction mixture was heated to 100°C and stirred at this temperature for 12 h. The mixture was then cooled to rt, diluted with EtOAc (40 ml) washed with H2O (2*8 ml), brine (5 ml), dried overNa2SO4, and concentrated under reduced pressure to dryness to afford 0.16 g of brown oil. The crude product obtained was subjected for prep HPLC purification (43-50-62- 100%0-2-5-5.1min; 30ml/min water- acn+nh3 (loading pump 4ml/min ACN); target mass 706; column Xbridge C18 5uM 19*100mm (L)) to afford tert-butyl N-(2-2-[2-(4-[3-(4-[(3S,4R)-3- fluoro-l-methylpiperidin-4-yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l- yl]aminophenoxy)ethoxy]ethoxyethyl)carbamate (14.7 mg, 10.6% yield) as yellow solid.
[0350] Step 3: Tert-butyl N-(2-2-[2-(4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4- yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l- yl]aminophenoxy)ethoxy]ethoxyethyl)carbamate (13.0 mg, 18.42 pmol) was dissolved in 0.9 ml of MeOH. Hydrogen chloride (6.65 mg, 184.92 pmol, 90.0 pl) was added and resulting mixture was stirred at room temperature overnight. After consumption of the starting material (LCMS control) the resulting mixture was concentrated under reduced pressure to dryness(<40°C) and immediately used in further experiment without any additional purification.
[0351] Step 4: following general procedure 3. The mixture obtained was subjected for prep HPLC purification (33-40-65% 0-2-7-7.1min; 30ml/min water-acn+nh3 (loading pump 4 ml/min acn+nh3); target mass 943 column Xbridge C18 5 uM 19*100mm) to afford 2-(3-[5-(3,5- dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l-yl]methylphenoxy)-N-(2-2-[2-(4-[3-(4- [(3 S,4R)-3 -fluoro- 1 -methylpiperidin-4-yl] amino- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2- yn-l-yl]aminophenoxy)ethoxy]ethoxyethyl)acetamide (2.1 mg, 12.7% yield, 95.0% purity) as yellow solid.
Example 10: Synthesis of 2-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl}phenoxy)-N- [2-(2- {2- [2-(N-methyl-4- { [3-(4- { [(3S,4R)-3-fhioro- 1- methylpiperidin-4-yl]amino}-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino}- 3-methoxybenzenesulfonamido)ethoxy]ethoxy}ethoxy)ethyl]acetamide.
[0352] Step 1: The synthesis of tert-butyl N-[2-(2-{2-[2-(N-methyl-3-methoxy-4- nitrobenzenesulfonamido)ethoxy]ethoxy}ethoxy)ethyl]carbamate. A stirred solution of tert-butyl N-(5,8,l l-trioxa-2-azatridecan-13-yl)carbamate (1.71 g, 5.58 mmol) and triethylamine (1.24 g, 12.28 mmol, 1.71 mL) in DCM (25 mL) was cooled to 0°C and 3-methoxy-4-nitrobenzene-l- sulfonyl chloride (1.4 g, 5.58 mmol) was added dropwise at the temperature not exceeding 50°C. Reaction mixture was allowed to warm to room temperature and stirred for another 3 hrs, then DCM (10 mL) was added. Organic layers were separated, washed with H2O (2x20 mL), dried over Na2SO4, and concentrated in vacuo to obtain tert-butyl N-[2-(2-2-[2-(N-methyl-3 -methoxy - 4-nitrobenzenesulfonamido)ethoxy] ethoxy ethoxy)ethyl] carbamate (2.8 g, 94.3% yield) as yellow oil.
[0353] Step 2: The synthesis of tert-butyl N-[2-(2-{2-[2-(N-methyl-4-amino-3- methoxybenzenesulfonamido)ethoxy]ethoxy}ethoxy)ethyl]carbamate. A stirred solution of tert- butyl N-[2-(2-2-[2-(N-methyl-3-methoxy-4- nitrobenzenesulfonamido)ethoxy]ethoxyethoxy)ethyl]carbamate (2.8 g, 5.37 mmol) and 4- (pyridin-4-yl)pyridine (41.89 mg, 268.41 pmol) in DMF (37 mL) was cooled to 0°C and (dihydroxyboranyl)boronic acid (1.45 g, 16.1 mmol) was added dropwise at the temperature not exceeding 5°C. Reaction mixture was allowed to warm to room temperature and stirred for another 12 hrs, then 20% K2CO3 (150 mL) and EtOAc (300 mL) were added. Organic layers were separated, washed with H2O (2x80 mL) and brine (3x80 mL), dried over Na2SO4 and concentrated in vacuo to obtain tert-butyl N-[2-(2-2-[2-(N-methyl-4-amino-3- methoxybenzenesulfonamido)ethoxy]ethoxyethoxy)ethyl]carbamate (2.2 g, 79.2% yield) as yellow gum.
[0354] Step 3: The synthesis of tert-butyl N-(2-{2-[2-(2-{N-methyl-3-methoxy-4-[(prop-2- yn-l-yl)amino]benzenesulfonamido}ethoxy)ethoxy]ethoxy}ethyl)carbamate. To a stirred solution of tert-butyl N-[2-(2-2-[2-(N-methyl-4-amino-3- methoxybenzenesulfonamido)ethoxy] ethoxy ethoxy)ethyl] carbamate (2.2 g, 4.48 mmol), dipotassium carbonate (925.67 mg, 6.71 mmol) and potassium iodide (816.43 mg, 4.92 mmol) in DMF (22 mL) 3 -bromoprop- l-yne (580.53 mg, 4.92 mmol, 370.0 pl) was added dropwise at the room temperature. Reaction mixture was stirred at 75°C for another 48 hrs, then EtOAc (220 mL) was added, organic layers were separated, washed with H2O (2x50 mL) and brine (3x60 mL), dried over Na2SO4 and concentrated in vacuo to obtain tert-butyl N-(2-2-[2-(2-N-methyl-3- methoxy-4-[(prop-2-yn-l-yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)carbamate (850.0 mg, 34.1% yield) after FC as yellow gum.
[0355] Step 4: The synthesis of tert-butyl N-{2-[2-(2-{2-[N-methyl-4-({3-[4-bromo-l- (2,2,2-trifluoroethyl)- 1 H-indol-2-yl]prop-2-yn- 1 -yl } amino)-3 - methoxybenzenesulfonamido] ethoxy} ethoxy)ethoxy] ethyl} carbamate. A stirred solution of tertbutyl N-(2-2-[2-(2-N-methyl-3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)carbamate (432.29 mg, 816.19 pmol), and 4-bromo-2-iodo-l-(2,2,2-trifluoroethyl)-lH-indole (274.0 mg, 680.12 pmol) in THF (9 mL) and EtsN (9 mL), palladium-tetrakis(triphenylphosphine) (157.56 mg, 136.03 pmol) and copper iodide (12.91 mg, 68.02 pmol) were added at the room temperature under argon atmosphere. Reaction mixture was stirred at room temperature for another 12 hrs. Then the mixture was concentrated and purified by flash column to obtain tert-butyl N-2-[2-(2-2-[N-methyl-4-(3-[4- bromo-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl]prop-2-yn-l-ylamino)-3- methoxybenzenesulfonamido] ethoxy ethoxy)ethoxy] ethylcarbamate (430.0 mg, 74.5% yield). [0356] Step 5: The synthesis of tert-butyl N-[2-(2-{2-[2-(N-methyl-4-{[3-(4-{[(3S,4R)-3- fluoro- 1 -methylpiperi din -4-yl] amino } - 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2-yn- 1 - yl]amino}-3-methoxybenzenesulfonamido)ethoxy]ethoxy}ethoxy)ethyl]carbamate. To a stirred solution of tert-butyl N-2-[2-(2-2-[N-methyl-4-(3-[4-bromo-l-(2,2,2-trifluoroethyl)-lH-indol-2- yl]prop-2-yn-l-ylamino)-3-methoxybenzenesulfonamido]ethoxyethoxy)ethoxy]ethylcarbamate (30.0 mg, 37.23 pmol), (3 S,4R)-3 -fluoro- 1 -methylpiperi din-4-amine (14.75 mg, 111.67 pmol), cesium (III) carbonate (36.38 mg, 111.67 pmol) in dioxane (1 mL), di cyclohexyl [2', 4', 6'- tris(propan-2-yl)-[ 1 , 1 '-biphenyl]-2-yl]phosphane; 2'-amino-[ 1 , 1 '-biphenyl]-2-ylpalladio methanesulfonate (6.29 mg, 7.44 pmol) was added at the room temperature under argon atmosphere. The reaction mixture was stirred at room temperature for another 12 hrs. Then the mixture was purified by HPLC (40-65% 0-5min H2O/MeCN/0.1%NH4OH; flow: 30 mL/min; loading pump: 4 mL/min MeCN; target mass: 856.99; column: XBridge C18 100x19 mm 5 pm) to obtain tert-butyl N-[2-(2-2-[2-(N-methyl-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4- yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3- methoxybenzenesulfonamido)ethoxy] ethoxy ethoxy)ethyl] carbamate (9.6 mg, 30.1% yield).
[0357] Step 6: The synthesis of N-(2-{2-[2-(2-aminoethoxy)ethoxy]ethoxy}ethyl)-4-{[3-(4- { [(3 S,4R)-3 -fluoro- 1 -methylpiperi din-4-yl]amino}-l -(2,2, 2-trifluoroethyl)-lH-indol-2-yl)prop-2- yn-l-yl]amino}-3-methoxy-N-methylbenzene-l-sulfonamide tetrahydrochloride. To a stirred solution of tert-butyl N-[2-(2-2-[2-(N-methyl-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4- yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3- methoxybenzenesulfonamido)ethoxy] ethoxy ethoxy)ethyl] carbamate (9.0 mg, 10.5 pmol) in MeOH (0.5 mL) dioxane/HCl (0.5 mL) was added dropwise at the room temperature. Reaction mixture was stirred at room temperature for another 3 hrs and concentrated in vacuo to obtain N- (2-2-[2-(2-aminoethoxy)ethoxy]ethoxyethyl)-4-[3-(4-[(3S,4R)-3-fluoro-l -methylpiperi din-4- yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3-methoxy-N- methylbenzene-1 -sulfonamide tetrahydrochloride (8.2 mg, 86.5% yield) as brown gum, which was used directly in the next step.
[0358] Step 7: The synthesis of 2-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl}phenoxy)-N-[2-(2-{2-[2-(N-methyl-4-{[3-(4-{[(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino}-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino}-3- methoxybenzenesulfonamido)ethoxy]ethoxy}ethoxy)ethyl]acetamide. A solution of N-(2-2-[2-(2- aminoethoxy)ethoxy ] ethoxy ethyl)-4- [3 -(4- [(3 S,4R)-3 -fluoro- l-methylpiperidin-4-yl] amino- 1- (2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3-methoxy-N-methylbenzene-l- sulfonamide tetrahydrochloride (9.0 mg, 9.97 pmol), l-[bis(dimethylamino)methylene]-lH-l,2,3- triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (4.94 mg, 12.99 pmol), 2-(3-[4-amino-6- (3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3-benzodiazol-l-yl]methylphenoxy)acetic acid (5.1 mg, 12.99 pmol), and ethylbis(propan-2-yl)amine (12.9 mg, 99.89 pmol) in DMF (0.5 mL) was stirred overnight at room temperature. Three exact batches (13 pmol scale) were set up in parallel and combined for purification by HPLC (30-55% 0-5min H2O/MeCN/0.1%NH4OH; flow: 30 mL/min; loading pump: 4 mL/min MeCN; target mass: 1131.27; column: XBridge C18 100x19mm 5 pm) to obtain 2-(3-[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3-benzodiazol- l-yl]methylphenoxy)-N-[2-(2-2-[2-(N-methyl-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperi din-4- yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3- methoxybenzenesulfonamido)ethoxy] ethoxy ethoxy)ethyl] acetamide (9.7 mg, 81.5% yield, 95.0% purity).
Example 11: Synthesis of 2-[(4-{[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin- 1 -y 1 ] methyl} pyridin-2-yl)oxy] -N-(2- {2- [2- (2- {N-methyl-3-methoxy-4- [(3- {4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino]benzenesulfonamido} ethoxy)ethoxy]ethoxy}ethyl)acetamide.
[0359] Step 1: The synthesis of 2-[(4-{[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2- dihydropyridin-l-yl]methyl}pyridin-2-yl)oxy]-N-(2-{2-[2-(2-{N-methyl- >xy-4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonamido}ethoxy)ethoxy]ethoxy}ethyl)acetamide. A solution of the N-(2-2- [2-(2-aminoethoxy)ethoxy]ethoxyethyl)-3-methoxy-N-methyl-4-[(3-4-[(l-methylpiperi din-4- yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l-yl)amino]benzene-l -sulfonamide (30.0 mg, 40.6 pmol)(see Example 4), the 2-[(4-[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2- dihydropyridin-l-yl]methylpyridin-2-yl)oxy]acetic acid (14.43 mg, 40.61 pmol), the 1- [bis(dimethylamino)methylene]-lH-l,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (23.15 mg, 60.91 pmol) and the ethylbis(propan-2-yl)amine (52.44 mg, 406.06 pmol) in dry DMF (1 mL) was stirred under argon at room temperature for 12 hrs. LCMS analysis of the reaction mixture showed full conversion to the desired product. The mixture was sent to HPLC (40-40-75% 0-l-6min ^O/MeCN/NFLOH; flow: 60 mL/min; loading pump: 4 mL/min MeCN; target mass: 1077; column: Xbridge C18 OBD 30 x 100 mm 5 pm) to afford 2-[(4-[5-(3,5- dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l-yl]methylpyridin-2-yl)oxy]-N-(2-2-[2-(2- N-methyl-3-methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol- 2-ylprop-2-yn-l -yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)acetamide (18.5 mg, 41.5% yield, 98.0% purity).
Example 12: Synthesis of 2-[(4-{[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin- 1 -y 1 ] methyl} pyridin-2-yl)oxy] -N- {2- [2- (2- {N-methyl-3-methoxy-4- [(3- {4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino]benzenesulfonamido} ethoxy)ethoxy]ethyl}acetamide.
[0360] Step 1: The synthesis of 2-[(4-{[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2- dihydropyridin-l-yl]methyl}pyridin-2-yl)oxy]-N-{2-[2-(2-{N-methyl-3-methoxy-4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonamido}ethoxy)ethoxy]ethyl} acetamide. A solution of the N-2-[2-(2- aminoethoxy)ethoxy]ethyl-3-methoxy-N-methyl-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l- (2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l-yl)amino]benzene-l -sulfonamide (30.0 mg, 43.18 pmol) (see Example 13), the 2-[(4-[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2- dihydropyridin-l-yl]methylpyridin-2-yl)oxy]acetic acid (15.35 mg, 43.21 pmol) , the 1- [Bis(dimethylamino)methylene]-lH-l,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (24.64 mg, 64.82 pmol) and the ethylbis(propan-2-yl)amine (55.81 mg, 432.11 pmol) in dry DMF (1 mL) was stirred under argon at room temperature for 12 hrs. LCMS analysis of the reaction mixture showed full conversion to the desired product. The mixture was sent to HPLC (35-35-75% 0-l-7min EEO/MeCN/NEUOH; 60 mL/min; loading pump: 4 mL/min MeCN; target mass: 1033; column: Xbridge C18 OBD 30x100mm 5 pm) to afford 2-[(4-[5-(3,5-dimethyl-l,2- oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l-yl]methylpyridin-2-yl)oxy]-N-2-[2-(2-N-methyl-3- methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2- yn-l-yl)amino]benzenesulfonamidoethoxy)ethoxy]ethylacetamide (12.8 mg, 28.1% yield, 98.0% purity). Example 13: Synthesis of 4-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl}phenoxy)-N- {2- [2-(2- {N-methyl-3-methoxy-4- [(3- {4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino]benzenesulfonamido}ethoxy) ethoxy]ethyl}butanamide (Z8772414956).
[0361] Step 1: The synthesis of tert-butyl N-(2-{2-[2- (methylamino)ethoxy]ethoxy}ethyl)carbamate. Tert-butyl N-2-[2-(2- bromoethoxy)ethoxy]ethylcarbamate (5.0 g, 16.07 mmol) was dissolved in MeOH (5 mL) and added dropwise to methanamine (49.9 g, 1.61 mol, 317.82 ml) over 30 min. Reaction mixture left stirring overnight. After that the solution was evaporated under reduced pressure to afford tertbutyl N-(2-2-[2-(methylamino)ethoxy]ethoxyethyl)carbamate (5.1 g, 96.8% yield) that was used in the next step without purification.
[0362] Step 2: The synthesis of tert-butyl N-(2-{2-[2-(N-methyl-3-methoxy-4- nitrobenzenesulfonamido)ethoxy]ethoxy}ethyl)carbamate. To a solution of tert-butyl N-(2-2-[2- (methylamino)ethoxy]ethoxyethyl)carbamate (4.2 g, 16.02 mmol) and triethylamine (2.43 g, 24.03 mmol, 3.35 ml) in DCM (30 mL), was added solution of 3-methoxy-4-nitrobenzene-l- sulfonyl chloride (4.02 g, 16.02 mmol) in THF(10 mL) at 0°C under nitrogen atmosphere. The mixture was warmed to room temperature and stirred for 12 hrs. LCMS analysis of the reaction mixture showed full conversion to the desired product. Then the mixture was concentrated, diluted with EtOAc (60 mL) and washed with 1 M solution of NaHSCL in water (10 mL), saturated solution of NaHCCh (10 mL), brine, dried over anhydrous Na2SO4, concentrated under reduced pressure and sent to flash column (ISCO® ® Interchim; 120g SiO2, chloroform/acetonitrile, gradient from 0 to 50%, flow rate: 60mL/min, Rf = 4.2-6.3 CV) to afford /c/7-butyl N-(2-2-[2-(N-methyl-3-methoxy-4- nitrobenzenesulfonamido)ethoxy]ethoxyethyl)carbamate (6.0 g, 70.6% yield).
[0363] Step 3: The synthesis of tert-butyl N-(2-{2-[2-(N-methyl-4-amino-3- methoxybenzenesulfonamido)ethoxy]ethoxy}ethyl)carbamate. To a solution of tert-butyl N-(2-2- [2-(N-methyl-3-methoxy-4-nitrobenzenesulfonamido)ethoxy]ethoxyethyl)carbamate (6.0 g, 12.56 mmol) and 4-(pyridin-4-yl)pyridine (98.04 mg, 628.2 pmol) in anhydrous DMF (60 mL), under inert atmosphere (dihydroxyboranyl)boronic acid (3.39 g, 37.69 mmol) was added by portions at 5°C . The resulting solution was warmed up and stirred at room temperature for 1 hour. The reaction mixture was quenched with 10% solution of K2CO3 (240 mL), stirred up for 1 hour, and extracted by EtOAc (3x100 mL). Organic phase washed by water (3x50 mL), brine, dried over Na2SO4 and concentrated under reduced pressure to afford tert-butyl N-(2-2-[2-(N-methyl-4- amino-3-methoxybenzenesulfonamido)ethoxy]ethoxyethyl)carbamate (4.2 g, 67.2% yield) that was used in next step without purification.
[0364] Step 4: The synthesis of tert-butyl N-{2-[2-(2-{N-methyl-3-methoxy-4-[(prop-2-yn- l-yl)amino]benzenesulfonamido}ethoxy)ethoxy]ethyl}carbamate. To a solution of tert-butyl N- (2-2-[2-(N-methyl-4-amino-3-methoxybenzenesulfonamido)ethoxy]ethoxyethyl)carbamate (4.17 g, 9.32 mmol) in DMF (40 mL), was added 3 -bromoprop- l-yne (1.1 g, 9.32 mmol, 700.0 pl) and dipotassium carbonate (3.86 g, 27.96 mmol) at room temperature under nitrogen atmosphere. The mixture was stirred at 60°C for 12 hrs. After that another portion of 3 -bromoprop- 1-yne (1.1 g, 9.32 mmol, 700.0 pl) was added and reaction was stirred at 60°C for 8 hrs. The addition was continued until 80% conversion by LCMS was achieved. Then the mixture diluted with EtOAc (150 mL) and washed with water (3x50 mL), brine, dried over anhydrous Na2SO4 and concentrated under reduced pressure to afford crude compound that was sent to flash column chromatography (ISCO® ® Interchim; 120g SiO2, petroleum ether/THF with acetonitrile, gradient from 10 to 60%, flow rate: 46mL/min, Rf = 7.8-9.6 CV) to afford tert-butyl N-2-[2-(2- N-methyl-3-methoxy-4-[(prop-2-yn- 1 - yl)amino]benzenesulfonamidoethoxy)ethoxy]ethylcarbamate (1.0 g, 19.9% yield).
[0365] Step 5: The synthesis of tert-butyl N-{2-[2-(2-{N-methyl-3-methoxy-4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonamido}ethoxy)ethoxy]ethyl} carbamate. A solution of the 2-iodo-N-(l- methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine (300.2 mg, 686.86 pmol), the tert-butyl N-2-[2-(2-N-methyl-3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonamidoethoxy)ethoxy]ethylcarbamate (500.0 mg, 1.03 mmol), DiPA (5 mL), and dry DMSO (15 mL) was degassed by bubbling argon for 2 min. Palladium- tetrakis(triphenylphosphine) (238.68 mg, 206.06 pmol) and copper iodide (13.04 mg, 68.69 pmol) were added, and the mixture was again degassed by bubbling argon and was stirred under argon at room temperature for 12 hrs. LCMS analysis of the reaction mixture showed full conversion to the desired product. The mixture was diluted by saturated solution of EDTA in water (60 mL), extracted by EtOAc (3x50 mL). The combined organic layers was washed with water, brine, dried over anhydrous Na2SO4 and concentrated under reduced pressure to afford crude compound that was sent to flash column (ISCO® Interchim; 40 g SiO2, acetonitrile/methanol with methanol from 0 to 100%, flow rate: 40 mL/min, Rf = 7-14 CV) to afford tert-butyl N-2-[2-(2-N-methyl-3-methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l- (2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l- yl)amino]benzenesulfonamidoethoxy)ethoxy]ethylcarbamate (250.0 mg, 38.9% yield).
[0366] Step 6 : The synthesis ofN-{2-[2-(2-aminoethoxy)ethoxy]ethyl}-3-methoxy-N- methyl-4-[(3-{4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2- yn-l-yl)amino]benzene-l -sulfonamide tetrahydrochloride. To a solution of N-2-[2-(2-tert-butyl N-methyl-3-methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol- 2-ylprop-2-yn-l-yl)amino]benzenesulfonamidoethoxy)ethoxy]ethylcarbamate (30.09 mg, 37.85 pmol) in MeOH (1 mL), 1 mL of HC1 in dioxane (2.2 M) was added at room temperature under nitrogen atmosphere. The mixture was stirred at room temperature for 1 h. LCMS analysis of the reaction mixture showed full conversion to the desired product. Then the mixture was concentrated under reduced pressure to afford crude N-2-[2-(2-aminoethoxy)ethoxy]ethyl-3- methoxy-N-methyl-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2- ylprop-2-yn-l-yl)amino]benzene-l -sulfonamide tetrahydrochloride (30.0 mg, 93.8% yield) that was used in next step without purification.
[0367] Step 7: The synthesis of 4-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl}phenoxy)-N-{2-[2-(2-{N-methyl-3-methoxy-4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonamido}ethoxy)ethoxy]ethyl}butanamide. A solution of the N-2-[2-(2- aminoethoxy)ethoxy]ethyl-3-methoxy-N-methyl-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l- (2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l-yl)amino]benzene-l -sulfonamide (30.0 mg, 43.18 pmol), the 4-(3-[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3-benzodiazol-l- yl]methylphenoxy)butanoic acid (18.16 mg, 43.2 pmol) , the l-[bis(dimethylamino)methylene]- lH-l,2,3-triazolo[4,5-b]pyridinium 3 -oxid hexafluorophosphate (24.63 mg, 64.8 pmol) and the ethylbis(propan-2-yl)amine (55.79 mg, 431.99 pmol) in dry DMF (1 mL) was stirred under argon at room temperature for 12 hrs. LCMS analysis of the reaction mixture showed full conversion to the desired product. The mixture was sent to HPLC(40-40-60% 0-l-8min; H2O/MeCN/NH4OH; flow: 60 mL/min; loading pump: 4 mL/min MeCN; target mass: 1098; column: XBridge C18 OBD 100x30mm 5 pm) to afford 4-(3-[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methylphenoxy)-N-2-[2-(2-N-methyl-3-methoxy-4-[(3-4-[(l-methylpiperidin- 4-yl)amino] - 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-ylprop-2-yn- 1 - yl)amino]benzenesulfonamidoethoxy)ethoxy]ethylbutanamide (13.8 mg, 29.1% yield, 95% purity).
Example 14: Synthesis of 2-(3-{[4-(2-{2-[2-(2-aminoethoxy)ethoxy]ethoxy}ethanesulfonyl)-2- methoxyphenyl] amino} prop- 1-yn- l-yl)-N-(l-methylpiperidin-4-yl)- l-(2,2,2-trifluoroethyl)- lH-indol-4-amine.
[0368] Step 1 : The synthesis of 3-methoxy-4-nitrobenzene-l-thiol. A stirred solution of sodium sulfide nonahydrate (21.23 g, 87.7 mmol) and sulfur (2.8 g, 87.7 mmol) in isopropanol (300 mL) was heated to 90°C and 4-fluoro-2-methoxy-l -nitrobenzene (15.0 g, 87.7 mmol) in isopropanol (60 mL) was added dropwise over 20 min. Reaction mixture was stirred for another 3 hrs, cooled to room temperature, and acidified to pH=3 with HCI (1 M). The resulting mixture was concentrated under vacuum, diluted with water (200 mL) and then extracted with ethyl acetate (2 x 200 mL). The combined organics were washed with brine (2 x 200 mL) and dried over anhydrous Na2SO4to obtain 3-methoxy-4-nitrobenzene-l-thiol (10.0 g, 58.5% yield) after flash column as yellow oil.
[0369] Step 2: The synthesis of tert-butyl N-{2-[2-(2-{2-[(3-methoxy-4- nitrophenyl)sulfanyl]ethoxy}ethoxy)ethoxy]ethyl}carbamate. A solution of 2-methoxy-4-[(3- methoxy-4-nitrophenyl)disulfanyl]-l -nitrobenzene (2.68 g, 7.28 mmol), tert-butyl N-(2-2-[2-(2- bromoethoxy)ethoxy]ethoxyethyl)carbamate (4.7 g, 13.24 mmol), sodium hydroxymethanesulfmate (2.34 g, 19.85 mmol), and dipotassium carbonate (1.83 g, 13.24 mmol) in DMF (30 mL) was stirred overnight at room temperature. The resulting mixture was concentrated under vacuum, diluted with water (70 mL) and then extracted with ethyl acetate (2x200 mL). The combined organics were washed with brine (4x50 mL) and dried over anhydrous Na2SO4, to obtain tert-butyl N-2-[2-(2-2-[(3-methoxy-4- nitrophenyl)sulfanyl]ethoxyethoxy)ethoxy]ethylcarbamate (6.0 g, quantitative yield) as yellow oil.
[0370] Step 3: The synthesis of tert-butyl N-[2-(2-{2-[2-(3-methoxy-4- nitrobenzenesulfonyl)ethoxy]ethoxy}ethoxy)ethyl]carbamate. To a solution of tert-butyl N-2-[2- (2-2-[(3-methoxy-4-nitrophenyl)sulfanyl]ethoxyethoxy)ethoxy]ethylcarbamate (5.9 g, 12.82 mmol) in DCM (100 mL), 3 -chlorobenzene- 1 -carboperoxoic acid (6.62 g, 38.46 mmol) was added at 0°C. The mixture was stirred overnight at room temperature. The resulting mixture was diluted with water (50 mL) and then extracted with DCM (100 mL). The combined organics were washed with 20% K2CO3 (2x30 mL) brine (4x40 mL) and dried over anhydrous Na2SO4, to obtain tert-butyl N-[2-(2-2-[2-(3-methoxy-4- nitrobenzenesulfonyl)ethoxy] ethoxy ethoxy)ethyl] carbamate (5.4 g, 75.2% yield) as yellow oil.
[0371] Step 4: The synthesis of tert-butyl N-[2-(2-{2-[2-(4-amino-3- methoxybenzenesulfonyl)ethoxy]ethoxy}ethoxy)ethyl]carbamate. A stirred solution of tert-butyl N-[2-(2-2-[2-(3-methoxy-4-nitrobenzenesulfonyl)ethoxy]ethoxyethoxy)ethyl]carbamate (5.35 g, 10.87 mmol) and 4-(pyridin-4-yl)pyridine (84.82 mg, 543.5 pmol) in DMF (80 mL) was cooled to 0°C and (dihydroxyboranyl)boronic acid (2.94 g, 32.61 mmol) was added dropwise at the temperature not exceeding 5°C. Reaction mixture was allowed to warm to room temperature and stirred for another 12 hrs, then 20% K2CO3 (150 mL) and EtOAc (400 mL) were added. Organic layers were washed with H2O (2x80 ml) and brine (3x80 ml), dried over Na2SO4 and concentrated in vacuo to obtain tert-butyl N-[2-(2-2-[2-(4-amino-3- methoxybenzenesulfonyl)ethoxy]ethoxyethoxy)ethyl]carbamate (3.6 g, 59.4% yield) as yellow gum. [0372] Step 5: The synthesis of tert-butyl N-(2-{2-[2-(2-{3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonyl}ethoxy)ethoxy]ethoxy}ethyl)carbamate. To a stirred solution of tertbutyl N-[2-(2-2-[2-(4-amino-3-methoxybenzenesulfonyl)ethoxy]ethoxyethoxy)ethyl]carbamate (2.6 g, 5.63 mmol), potassium iodide (1.21 g, 7.32 mmol) and 3 -bromoprop- 1-yne (863.5 mg, 7.32 mmol, 550.0 pl) in DMF (30 mL) dipotassium carbonate (1.55 g, 11.26 mmol) was added dropwise at the room temperature. Reaction mixture was stirred at 75°C for another 48 hrs, reaction mixture was cooled down and EtOAc (220 mL) was added. Organic layer was separated, washed with H2O (2x50 ml) and brine (3x60 mL), dried over Na2SO4 and concentrated in vacuo to obtain tert-butyl N-(2-2-[2-(2-3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonylethoxy)ethoxy]ethoxyethyl)carbamate (900.0 mg, 30.3% yield) after flash colum as a yellow gum.
[0373] Step 6: The synthesis of tert-butyl N-(2-{2-[2-(2-{3-methoxy-4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonyl}ethoxy)ethoxy]ethoxy}ethyl)carbamate. To a stirred solution of tertbutyl N-(2-2-[2-(2-3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonylethoxy)ethoxy]ethoxyethyl)carbamate (200.0 mg, 399.52 pmol) and 2- iodo-N-(l-methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine (145.7 mg, 333.36 pmol) in THF (4 mL) and Eh N (4 mL), palladium-tetrakis(triphenylphosphine) (77.23 mg, 66.67 pmol) and copper iodide (6.33 mg, 33.34 pmol) were added at the room temperature under argon atmosphere. The reaction mixture was stirred at room temperature for another 12 hrs. Then the mixture was purified by flash column to obtain tert-butyl N-(2-2-[2-(2-3-methoxy-4-[(3-4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l- yl)amino]benzenesulfonylethoxy)ethoxy]ethoxyethyl)carbamate (240.0 mg, 84.4% yield, 95.0% purity) as a yellow gum.
Example 15: Synthesis of 2- {3- [(4- {2- [2-(2-aminoethoxy)ethoxy] ethanesulfonyl} -2- methoxyphenyl)amino]prop-l-yn-l-yl}-N-(l-methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)- lH-indol-4-amine.
[0374] Step 1 : The synthesis of 3-methoxy-4-nitrobenzene-l-thiol. A stirred solution of sodium sulfide nonahydrate (21.23 g, 87.7 mmol) and sulfur (2.8 g, 87.7 mmol) in isopropanol (300 mL) was heated to 90°C and 4-fluoro-2-methoxy-l -nitrobenzene (15.0 g, 87.7 mmol) in isopropanol (60 mL) was added dropwise over 20 min. Reaction mixture was stirred for another 3 hrs and cooled to room temperature. The mixture was acidified to pH=3 with HCI (1 M). The resulting mixture was concentrated under vacuum, diluted with water (200 mL) and then extracted with ethyl acetate (2 x 200 mL). The combined organics were washed with brine (2 x 200 mL) and dried over anhydrous ISfeSCL to obtain 3-methoxy-4-nitrobenzene-l-thiol (10.0 g, 58.5% yield) after a flash column as a yellow oil.
[0375] Step 2: The synthesis of tert- Nb-u[t2y-l(2-{2-[(3-methoxy-4- nitrophenyl)sulfanyl]ethoxy}ethoxy)ethyl]carbamate. A solution of 2-methoxy-4-[(3-methoxy-4- nitrophenyl)disulfanyl]-l-nitrobenzene (3.06 g, 8.31 mmol), N-2-[2te-r(t2--butyl bromoethoxy)ethoxy]ethylcarbamate (4.7 g, 15.11 mmol), sodium hydroxymethanesulfinate (2.67 g, 22.66 mmol), and dipotassium carbonate (2.08 g, 15.11 mmol) in DMF (30 mL) was stirred overnight at room temperature. The resulting mixture was concentrated under vacuum, diluted with water (70 mL) and then extracted with ethyl acetate (2x200 mL). The combined organics were washed with brine (4x50 mL) and dried over anhydrous ISfeSCL, to obtain tert- butyl N-[2-(2-2-[(3-methoxy-4-nitrophenyl)sulfanyl]ethoxyethoxy)ethyl]carbamate (6.4 g, 158.7% yield) as yellow oil.
[0376] Step 3: The synthesis of tert- Nb-u(t2y-l{2-[2-(3-methoxy-4- nitrobenzenesulfonyl)ethoxy] ethoxy }ethyl)carbamate. A solution of N-[2-(2-2-[(t3er-t-butyl methoxy-4-nitrophenyl)sulfanyl] ethoxy ethoxy)ethyl] carbamate (6.3 g, 15.14 mmol) in DCM (100 mL) was cooled to 0°C and 3 -chlorobenzene- 1-carboperoxoic acid (7.81 g, 45.41 mmol) was added. The mixture was stirred overnight at room temperature. The resulting mixture was diluted with water (50 mL) and then extracted with DCM (100 mL). The combined organics were washed with 20% K2CO3 (2x30 mL), brine (4x40 mL) and dried over anhydrousNa2SO4, to obtain tert-butyl N-(2-2-[2-(3-methoxy-4-nitrobenzenesulfonyl)ethoxy]ethoxyethyl)carbamate (5.5 g, 68.9% yield) as a yellow oil.
[0377] Step 4: The synthesis of tert-butyl N-(2-{2-[2-(4-amino-3- methoxybenzenesulfonyl)ethoxy]ethoxy}ethyl)carbamate. A stirred solution of tert-butyl N-(2-2- [2-(3-methoxy-4-nitrobenzenesulfonyl)ethoxy]ethoxyethyl)carbamate (5.45 g, 12.16 mmol) and 4-(pyridin-4-yl)pyridine (94.89 mg, 608.0 pmol) in DMF (80 mL) was cooled to 0°C and (dihydroxyboranyl)boronic acid (3.28 g, 36.48 mmol) was added dropwise at the temperature not exceeding 5°C. Reaction mixture was allowed to warm to room temperature and stirred for another 12 hrs. Then 20% K2CO3 (150 mL) and EtOAc (400 mL) were added, organic layers separated, washed with H2O (2x80 mL) and brine (3x80 mL), dried overNa2SO4 and concentrated in vacuo to obtain tert-butyl N-(2-2-[2-(4-amino-3- methoxybenzenesulfonyl)ethoxy]ethoxyethyl)carbamate (3.9 g, 59% yield) as a yellow gum.
[0378] Step 5: The synthesis of tert-butyl N-{2-[2-(2-{3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonyl}ethoxy)ethoxy] ethyl (carbamate. To a stirred solution of tert-butyl N- (2-2- [2-(4-amino-3-methoxybenzenesulfonyl)ethoxy] ethoxy ethyl)carbamate (2.91 g, 6.96 mmol), potassium iodide (1.5 g, 9.05 mmol) and 3 -bromoprop- l-yne (1.07 g, 9.05 mmol, 680.0 pl) in DMF (30 mL) dipotassium carbonate (1.92 g, 13.93 mmol) was added by portions at the room temperature. Reaction mixture was stirred at 75°C for another 48 hrs and cooled down to room temperature. EtOAc (220 mL) was added, organic layer separated and washed with FLO (2x50 ml) and brine (3x60 ml), dried over Na2SO4 and concentrated in vacuo to obtain tert-butyl N-2- [2-(2-3-methoxy-4- [(prop-2 -yn-l-yl)amino]benzenesulfonylethoxy)ethoxy] ethylcarbamate (900.0 mg, 24.6% yield) after flash column as yellow gum.
[0379] Step 6: The synthesis of tert-butyl N-{2-[2-(2-{3-methoxy-4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonyl}ethoxy)ethoxy]ethyl} carbamate. To a stirred solution of tert-butyl N- 2- [2-(2-3-methoxy-4-[(prop-2-yn-l-yl)amino]benzenesulfonylethoxy)ethoxy] ethylcarbamate (200.0 mg, 438.07 pmol), 2-iodo-N-(l-methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4- amine (159.78 mg, 365.59 pmol) in THF (4 mL) and EtsN (4 mL), palladium- tetrakis(triphenylphosphine) (84.69 mg, 73.12 pmol) and copper iodide (6.94 mg, 36.56 pmol) were added at the room temperature under argon atmosphere. Reaction mixture was stirred at room temperature for another 12 hrs. Then the mixture was purified by flash column (Interchim, 40 g C18, water/acetonitrile (0-100%), flow rate: 70 ml/min, 20-25 CV) to obtain tert-butyl N-2- [2-(2-3-methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2- ylprop-2-yn-l-yl)amino]benzenesulfonylethoxy)ethoxy]ethylcarbamate (210.0 mg, 67.5% yield, 90.0% purity) as yellow gum.
Example 16: Synthesis of 2-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl}phenoxy)-N-(ll-{N-methyl-3-methoxy-4-[(3-{4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifluoroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino]benzenesulfonamido}undecyl)acetamide.
[0380] Step 1: The synthesis of tert-butyl N-(l l-{N-methyl-3-methoxy-4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonamido}undecyl)carbamate. To a solution of 2-iodo-N-(l- methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine (104.4 mg, 238.88 pmol), tertbutyl N-(l l-N-methyl-3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonamidoundecyl)carbamate (150.0 mg, 286.41 pmol), copper iodide (9.07 mg, 47.78 pmol) in DMSO and diisopropylamine (10 mL, 5:1) under inert atmosphere palladium- tetrakis(triphenylphosphine) (27.67 mg, 23.89 pmol) was added. The resulting solution was stirred at room temperature for 18 hrs. After that period the reaction mixture was poured onto water (50 ml) and extracted with ethyl acetate (3 x 50 ml). The organic layers were combined, washed with water (3 x 50 mL), brine (50 mL), dried over anhydrous Na2SO4 and fdtered. The fdtrate collected was concentrated under reduced pressure and the crude obtained was subjected for flash chromatography (ISCO®: Interchim; 40 g SiO2, MeCN/methanol with methanol gradient from 0 to 100%, flow rate: 40 mL/min, Rf = 10-15 CV) to afford the desired /e/7-butyl N-(l l-N-methyl-3-methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH- indol-2-ylprop-2-yn-l-yl)amino]benzenesulfonamidoundecyl)carbamate (80.0 mg, 39.8% yield) as yellow oil.
[0381] Step 2: The synthesis ofN-(l l-aminoundecyl)-3-methoxy-N-methyl-4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzene-l -sulfonamide hydrochloride. To solution of tert-butyl N-(l l-N-methyl-3- methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2- yn-l-yl)amino]benzenesulfonamidoundecyl)carbamate (80.12 mg, 96.18 pmol) in MeOH (2 mL) 10% HC1 in dioxane (0.3 mL) was added. The reaction mixture was stirred at room temperature for 18 hrs. After that period the mixture was concentrated under reduced pressure to afford the desired N-(l l-aminoundecyl)-3-methoxy-N-methyl-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l- (2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l-yl)amino]benzene-l -sulfonamide hydrochloride (60.0 mg, 77% yield) as yellow solid, and was used without any additional purification.
[0382] Step 3: The synthesis of 2-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl}phenoxy)-N-(l l-{N-methyl-3-methoxy-4-[(3-{4-[(l-methylpiperi din-4- yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonamido}undecyl)acetamide. To a solution of 2-(3-[4-amino-6-(3,5- dimethyl-l,2-oxazol-4-yl)-lH-l,3-benzodiazol-l-yl]methylphenoxy)acetic acid (38.27 mg, 97.53 pmol) in DMF (4 mL) at room temperature l-[bis(dimethylamino)methylene]-lH-l,2,3- triazolo[4,5-b]pyridinium 3 -oxid hexafluorophosphate (55.61 mg, 146.3 pmol) and ethylbis(propan-2-yl)amine (126.14 mg, 976.68 pmol, 170.0 pl) were added and after 5 min N- (1 l-aminoundecyl)-3-methoxy-N-methyl-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l -(2,2,2- trifluoroethyl)- 1 H-indol-2-ylprop-2-yn- 1 -yl)amino]benzene- 1 -sulfonamide hydrochloride (75.04 mg, 97.53 pmol) was introduced. The resulting mixture was stirred at room temperature overnight. After 15 hrs the reaction mixture was subjected for prep HPLC purification (53-60-85- 100% 0-2-7-7.1min; 30 mL/min; LLO/MeCN; loading pump: 4 mL/min MeCN; target mass: 1108; column SunFireC18 19* 100mm) to afford the desired 2-(3-[4-amino-6-(3,5-dimethyl-l,2- oxazol-4-yl)-lH-l,3-benzodiazol-l-yl]methylphenoxy)-N-(l l-N-methyl-3-methoxy-4-[(3-4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l- yl)amino]benzenesulfonamidoundecyl)acetamide (18.2 mg, 16.3% yield, 97.0% purity) as yellow solid. Example 17: Synthesis of 2-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl}phenoxy)-N- [ 1 l-(N-methyl-4- { [3-(4-{[(3S,4R)-3-fhioro-l- methylpiperidin-4-yl]amino}-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino}- 3-methoxybenzenesulfonamido) undecyl] acetamide.
[0383] Step 1 : The synthesis of tert-butyl N-(l l-hydroxyundecyl)carbamate. 11- Aminoundecan-l-ol (6.0 g, 32.05 mmol) was dissolved in methanol (100 mL), then di-tert-butyl dicarbonate (7.34 g, 33.65 mmol, 7.74 ml) and sodium hydroxide (1.35 g, 33.65 mmol) were added. The solution was stirred until the reaction was completed. Then solvent was evaporated under reduced pressure and the resulting oil dissolved in chloroform (100 mL) and washed with water (3 x 50 mL). The organic phase was dried over Na2SO4 and the solvent removed under reduced pressure to give tert-butyl N-(l l-hydroxyundecyl)carbamate (8.7 g, 80.3% yield).
[0384] Step 2 : The synthesis of tert-butyl N-[l l-(methanesulfonyloxy)undecyl]carbamate.
To a solution of tert-butyl N-(l l-hydroxyundecyl)carbamate (8.75 g, 30.46 mmol) in anhydrous EtOAc (100 mL) ethylbis(propan-2-yl)amine (7.87 g, 60.93 mmol, 10.6 ml) was added and then under inert atmosphere methanesulfonyl chloride (5.21 g, 45.69 mmol, 3.52 ml) was introduced dropwise at 0°C. The resulting solution was then allowed to warm up to room temperature and left to stir for 18 hrs. The reaction mixture was diluted with saturated solution of NaHCCh (50 mL) and extracted with ethyl acetate (3 x 50 mL). The organic layers were combined, washed with water (3 x 50 mL), brine (50 mL), dried over anhydrous Na2SO4, and fdtered. The collected fdtrate was concentrated under reduced pressure to afford the desired tert-butyl N-[l 1- (methanesulfonyloxy)undecyl]carbamate (10.0 g, 76.3% yield)
[0385] Step 3: The synthesis of tert-butyl N-[l l-(methylamino)undecyl]carbamate. To a solution of tert-butyl N-[ll-(methanesulfonyloxy)undecyl]carbamate (11.0 g, 30.12 mmol) in anhydrous MeOH (100 mL) methanamine (9.35 g, 301.18 mmol, 59.55 ml) was added at room temperature and the reaction mixture was left to stir at 60°C for 18 hrs. Then solvent was evaporated under reduced pressure, the resulting oil dissolved in EtOAc (100 mL) and washed with water (3 x 50 mL). The organic phase was dried overNa2SO4 and the solvent removed under reduced pressure to give tert-butyl N-[l l-(methylamino)undecyl] carbamate (9.0 g, 84.5% yield).
[0386] Step 4 : The synthesis of tert-butyl N-[l l-(N-methyl-3-methoxy-4- nitrobenzenesulfonamido)undecyl]carbamate. To a solution of tert-butyl N-[l l- (methylamino)undecyl]carbamate (5.0 g, 90.0% purity, 14.98 mmol) in anhydrous DCM (100 mL) under inert atmosphere triethylamine (2.27 g, 22.47 mmol, 3.13 ml) was added followed by 3 -methoxy-4-nitrobenzene-l -sulfonyl chloride (3.76 g, 14.98 mmol) at 0°C. The resulting solution was then allowed to warm up to room temperature and left to stir for 18 hrs. The reaction mixture was poured onto water (100 mL) and extracted with DCM (3 x 50 mL). The organic layers were combined, washed with water (3 x 50 mL), brine (50 mL), dried over anhydrous Na2SO4 and filtered. The collected filtrate was concentrated under reduced pressure to afford the desired tert-butyl N-[l l-(N-methyl-3-methoxy-4-nitrobenzenesulfonamido)undecyl]carbamate (7.0 g, 80.7% yield).
[0387] Step 5 : The synthesis of tert-butyl N-[l l-(N-methyl-4-amino-3- methoxybenzenesulfonamido)undecyl]carbamate. To a solution of tert-butyl N-[l l-(N-methyl-3- methoxy-4-nitrobenzenesulfonamido)undecyl]carbamate (7.0 g, 13.57 mmol, 77.57 ml) in anhydrous DMF (80 mL) under inert atmosphere at 0°C 4-(pyridin-4-yl)pyridine (105.93 mg, 678.74 pmol) was added followed by (dihydroxyboranyl)boronic acid (3.67 g, 40.72 mmol). The resulting solution was then allowed to warm up to room temperature and left to stir for 18 hrs. The reaction mixture was poured onto saturated solution of K2CO3 (300 mL) and extracted with EtOAc (3 x 150 mL). The organic layers were combined, washed with water (3 x 250 mL), brine (250 mL), dried over anhydrous Na2SO4 and filtered. The collected filtrate was concentrated under reduced pressure to obtain tert-butyl N-[l l-(N-methyl-4-amino-3- methoxybenzenesulfonamido)undecyl]carbamate (6.0 g, 82.8% yield).
[0388] Step 6 : The synthesis of tert-butyl N-(l l-{N-methyl-3-methoxy-4-[(prop-2-yn-l- yl)amino]benzenesulfonamido}undecyl)carbamate. To a solution of tert-butyl N-[l l-(N-methyl- 4-amino-3-methoxybenzenesulfonamido)undecyl]carbamate (6.0 g, 12.35 mmol) in anhydrous DMF (50 mL) dipotassium carbonate (3.41 g, 24.71 mmol) and potassium iodide (2.05 g, 12.35 mmol) were added followed by the addition of 3 -bromoprop- 1-yne (2.19 g, 18.53 mmol, 1.39 ml) under nitrogen atmosphere. The resulting solution was then allowed to warm up to 90°C and left while stirring for 18 hrs. The reaction mixture was diluted with saturated solution of NH4CI (250 mL) and extracted with ethyl acetate (3 x 150 mL). The organic layers were combined, washed with water (3 x 150 mL), brine (150 mL), dried over anhydrous ISfeSCL and filtered. The filtrate collected was concentrated under reduced pressure and the crude obtained was subjected for flash chromatography (ISCO® Interchim; 220g SiCL, petroleum ether/EtOAc with EtOAc gradient from 30 to 100%, flow rate: 60 mL/min, Rf = 3.1-3.9CV) to afford the desired tert-butyl N-(l l- N-methyl-3-methoxy-4-[(prop-2-yn-l-yl)amino]benzenesulfonamidoundecyl)carbamate (3.0 g, 41.7% yield).
[0389] Step 7: The synthesis of tert-butyl N-{1 l-[N-methyl-4-({3-[4-bromo-l-(2,2,2- trifluoroethyl)-lH-indol-2-yl]prop-2-yn-l-yl}amino)-3- methoxybenzenesulfonamido]undecyl}carbamate. To a solution of 4-bromo-2-iodo- 1 -(2,2,2- trifluoroethyl)-lH-indole (961.61 mg, 2.39 mmol), tert-butyl N-(l l-N-methyl-3-methoxy-4- [(prop-2-yn-l-yl)amino]benzenesulfonamidoundecyl)carbamate (1.5 g, 2.86 mmol) and copper iodide (90.62 mg, 477.38 pmol) in DMSO/diisopropylamine (40 mL, 5:1) under inert atmosphere, palladium-tetrakis(triphenylphosphine) (276.47 mg, 238.69 pmol) was added. The resulting solution was stirred at room temperature for 18 hrs. After that period the reaction mixture was poured onto water (150 mL) and extracted with ethyl acetate (3 x 100 mL). The organic layers were combined, washed with water (3 x 100 mL), brine (100 mL), dried over anhydrous ISfeSCL and filtered. The collected filtrate was concentrated under reduced pressure and the obtained crude was subjected for flash chromatography (ISCO® : Interchim; 40 g SiO2, MeCN/methanol with methanol gradient from 0 to 100%, flow rate: 40 mL/min, Rf = 10-15 CV) to afford the desired tert-butyl N-l l-[N-methyl-4-(3-[4-bromo-l-(2,2,2-trifluoroethyl)-lH-indol- 2-yl]prop-2-yn-l-ylamino)-3-methoxybenzenesulfonamido]undecylcarbamate (890.0 mg, 43.8% yield) .
[0390] Step 8: The synthesis of tert-butyl N-[l l-(N-methyl-4-{[3-(4-{[(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino}-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino}-3- methoxybenzenesulfonamido)undecyl]carbamate. To a solution of tert-butyl N-l l-[N-methyl-4- (3 - [4-bromo- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl]prop-2-yn- 1 -ylamino)-3 - methoxybenzenesulfonamido]undecylcarbamate (50.0 mg, 62.52 pmol), (3 S,4R)-3 -fluoro- 1- methylpiperidin-4-amine dihydrochloride (25.51 mg, 125.02 pmol), [l,l'-biphenyl]-2-yldi-tert- butyl)phosphane (7.46 mg, 25.0 pmol) and tris(l,5-diphenylpenta-l,4-dien-3-one) dipalladium (11.43 mg, 12.5 pmol) in toluene (6 mL) under inert atmosphere sodium 2-methylpropan-2-olate (18.01 mg, 187.53 pmol) was added. The resulting solution was stirred at 100°C for 12 hrs. After that period the reaction mixture was poured onto water (50 mL) and extracted with ethyl acetate (3 x 50 mL). The organic layers were combined, washed with water (3 x 50 mL), brine (50 mL), dried over anhydrous Na2SO4 and filtered. The collected filtrate was concentrated under reduced pressure and the obtained crude was subjected for HPLC (53-60-90-100% 0-2-7-7.1 min; 30 mL/min HiO/MeCN/NfLOH; loading pump: 4 mL/min MeCN/NILOH; target mass: 852; column Xbridge C18 19*100mm 5 pM) to afford the desired N-[l lt-e(rNt--bmuetythlyl-4-[3-(4- [(3 S,4R)-3 -fluoro- 1 -methylpiperidin-4-yl] amino- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2- yn-l-yl]amino-3-methoxybenzenesulfonamido)undecyl]carbamate (10.0 mg, 18.8% yield).
[0391] Step 9: The synthesis ofN-(l l-aminoundecyl)-4-{[3-(4-{[(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino}-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino}-3- methoxy-N-methylbenzene-1 -sulfonamide hydrochloride. To solution of N-[11-(N- tert-butyl methyl-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]amino-l-(2,2,2-trifluoroethyl)-lH- indol-2-yl)prop-2-yn-l-yl]amino-3-methoxybenzenesulfonamido)undecyl]carbamate (11.0 mg, 12.93 pmol) in MeOH (1 mL) 10% HC1 in dioxane (0.14 mL) was added. The reaction mixture was stirred at room temperature for 18 hrs. After that period the mixture was concentrated under reduced pressure to afford the desired N-(l l-aminoundecyl)-4-[3-(4-[(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3- methoxy-N-methylbenzene-1 -sulfonamide hydrochloride (11.0 mg, 62.5% yield) as dark solid, and was used without any additional purification.
[0392] Step 10: The synthesis of2-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl}phenoxy)-N-[l l-(N-methyl-4-{[3-(4-{[(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino}-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino}-3- methoxybenzenesulfonamido)undecyl]acetamide. To a solution of 2-(3-[4-amino-6-(3,5- dimethyl-l,2-oxazol-4-yl)-lH-l,3-benzodiazol-l-yl]methylphenoxy)acetic acid (9.55 mg, 24.35 pmol) in DMF (4 mL) at room temperature l-[bis(dimethylamino)methylene]-lH-l,2,3- triazolo[4,5-b]pyridinium 3 -oxid hexafluorophosphate (13.88 mg, 36.52 pmol) and ethylbis(propan-2-yl)amine (31.45 mg, 243.48 pmol, 40.0 pl) were added followed by N-(l l- aminoundecyl)-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]amino-l-(2,2,2-trifluoroethyl)- lH-indol-2-yl)prop-2-yn-l-yl]amino-3-methoxy-N-methylbenzene-l -sulfonamide dihydrochloride (20.0 mg, 24.32 pmol) after 5 min. The resulting mixture was stirred at room temperature overnight. After 15 hrs the reaction mixture was subjected for prep HPLC purification (53-60-90 -100% 0-2-7-7.1min; 30 mL/min HiO/MeCN/NH-iOH; loading pump: 4 mL/min MeCN/NH4OH; target mass: 1126; column XBridge C18 19*100mm) to result in the desired 2-(3 - [4-amino-6-(3 , 5 -dimethyl- 1 ,2-oxazol-4-yl)- 1 H- 1 ,3 -benzodi azol- 1 - yl]methylphenoxy)-N-[ll-(N-methyl-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]amino-l- (2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3- methoxybenzenesulfonamido)undecyl]acetamide (3.6 mg, 13.1% yield, 90% purity) as yellow gum.
Example 18: Synthesis of 2-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl}phenoxy)-N- {2- [2- (2- {3-methoxy-4- [(3- {4- [(l-methylpiperidin-4- yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino]benzenesulfonyl}ethoxy)ethoxy] ethyl} acetamide.
[0393] Step 1 : The synthesis of 2-{3-[(4-{2-[2-(2-aminoethoxy)ethoxy]ethanesulfonyl}-2- methoxyphenyl)amino]prop- 1 -yn- 1 -yl} -N-(l -methylpiperi din -4-yl)- 1 -(2,2, 2-tri fluoroethyl)- 1H- indol-4-amine tetrahydrochloride. To a stirred solution of N-2-[2t-e(r2t--3b-umtyelthoxy-4-[(3- 4-[(l -methylpiperi din-4-yl)amino]-l -(2, 2, 2-tri fluoroethyl)-lH-indol-2-ylprop-2-yn-l- yl)amino]benzenesulfonylethoxy)ethoxy]ethylcarbamate (30.0 mg, 39.17 pmol) from Example 15 in MeOH (0.5 ml) dioxane/HCl (0.5 ml) at the room temperature was added. Reaction mixture was stirred at room temperature for another 3 hrs and concentrated in vacuo to obtain 2-3-[(4-2- [2-(2-aminoethoxy)ethoxy]ethanesulfonyl-2-methoxyphenyl)amino]prop-l-yn-l-yl-N-(l- methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine tetrahydrochloride (31.0 mg, 74.1% yield) as brown gum which was used directly in the next step.
[0394] Step 2: The synthesis of 2-(3-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzo di azol-l-yl]methyl}phenoxy)-N-{2-[2-(2-{3-methoxy-4-[(3-{4-[(l-methylpiperi din-4- yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonyl}ethoxy)ethoxy]ethyl} acetamide. A solution of 2-3-[(4-2-[2-(2- aminoethoxy)ethoxy]ethanesulfonyl-2-methoxyphenyl)amino]prop-l-yn-l-yl-N-(l- methylpiperidin-4-yl)-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine (31.8 mg, 47.76 pmol), 1- [bis(dimethylamino)methylene]-lH-l,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (23.61 mg, 62.12 pmol), 2-(3-[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3-benzodiazol-l- yl]methylphenoxy)acetic acid (24.37 mg, 62.12 pmol), and ethylbis(propan-2-yl)amine (61.71 mg, 477.81 pmol) in DMF (0.5 mL) was stirred overnight at room temperature. Mixture was purified by HPLC(30-55% 0-5 min H2O/MeCN/0.1% NH4OH; flow: 30 mL/min; loading pump: 4 mL/min MeCN; target mass: 1131.27; column: XBridge C18 100x19mm 5 pm) to obtain 2-(3- [4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3-benzodiazol-l-yl]methylphenoxy)-N-2-[2-(2- 3-methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2- yn-l-yl)amino]benzenesulfonylethoxy)ethoxy]ethylacetamide (6.0 mg, 11.8% yield, 98.0% purity).
Example 19: Synthesis of rac-2-[3-(3,5-dimethyl-l,2-oxazol-4-yl)-5-[(R)-hydroxy (phenyl)methyl] phenoxy] -N-(2- {2- [2- (2- {N-methyl-3-methoxy-4- [(3- {4- [(1-methylpiperidin- 4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino]benzenesulfonamido} ethoxy)ethoxy]ethoxy}ethyl)acetamide.
[0395] Step 1: The synthesis of rac-2-[3-(3,5-dimethyl-l,2-oxazol-4-yl)-5-[(R)- hydroxy(phenyl)methyl]phenoxy]-N-(2-{2-[2-(2-{N-methyl-3-methoxy-4-[(3-{4-[(l- methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]benzenesulfonamido}ethoxy)ethoxy]ethoxy}ethyl)acetamide. A solution of the N-(2-2- [2-(2-aminoethoxy)ethoxy]ethoxyethyl)-3-methoxy-N-methyl-4-[(3-4-[(l-methylpiperi din-4- yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l-yl)amino]benzene-l -sulfonamide (30.0 mg, 40.6 pmol) (see Example 4), the rac-2-[3-(3,5-dimethyl-l,2-oxazol-4-yl)-5-[(R)- hydroxy(phenyl)methyl]phenoxy]acetic acid (14.33 mg, 40.59 pmol), 1- [bis(dimethylamino)methylene]-lH-l,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (23.14 mg, 60.88 pmol) and the ethylbis(propan-2-yl)amine (52.42 mg, 405.88 pmol) in dry DMF (1 mL) was stirred under argon at room temperature for 12 hrs. LCMS analysis of the reaction mixture showed full conversion to the desired product. The mixture was sent to HPLC (40-40-80% 0-l-7min EEO/MeCN/NEUOH; flow: 60 mL/min; loading pump: 4 mL/min MeCN; target mass: 1077; column: XBridge C18 OBD 30x100mm 5 pm) to afford rac-2-[3-(3,5- dimethyl-l,2-oxazol-4-yl)-5-[(R)-hydroxy(phenyl)methyl]phenoxy]-N-(2-2-[2-(2-N-methyl-3- methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2- yn-l-yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)acetamide (16.2 mg, 37.2% yield, 90% purity).
Example 20: Synthesis of 2-(4-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol- 1-yl] methyl}phenoxy)-N-(2- {2- [2-(2- {4- [(3- {4- [(l-methylpiperidin-4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino]phenoxy}ethoxy)ethoxy]ethoxy}ethyl)acetamide.
[0396] Step 1: The synthesis of 2-(4-{[4-amino-6-(3,5-dimethyl-l,2-oxazol-4-yl)-lH-l,3- benzodiazol-l-yl]methyl}phenoxy)-N-(2-{2-[2-(2-{4-[(3-{4-[(l-methylpiperidin-4-yl)amino]-l- (2,2,2-trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]phenoxy}ethoxy)ethoxy] ethoxy }ethyl)acetami de. Procedure described in WO 2024/112611 for 2-(3-{[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin-l- yl]methyl}phenoxy)-N-(2-{2-[2-(2-{4-[(3-{4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2- trifluoroethyl)-lH-indol-2-yl}prop-2-yn-l- yl)amino]phenoxy}ethoxy)ethoxy]ethoxy}ethyl)acetamide (see general procedure 3). 2-(4-[4- amino-6-(3 , 5 -dimethyl- 1 ,2-oxazol-4-yl)- 1 H- 1 ,3 -benzodi azol- 1 -yl]methylphenoxy)-N-(2-2-[2-(2- 4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2-yn-l- yl)amino]phenoxyethoxy)ethoxy]ethoxyethyl)acetamide (4.3 mg, 10.7% yield, 99% purity) was obtained as yellow oil with the following spectra data: LCMS: m/z [(M+2)/2]=503.8, purity 99.4%).
Example 21: Synthesis of 2-[3-({[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-methoxypyridin-3- yl] amino} methyl)phenoxy] -N- [2-(2- {2- [2-(N-methyl-4- { [3-(4-{ [(3S,4R)-3-fhioro- 1- methylpiperidin-4-yl]amino}-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino}- 3-methoxybenzenesulfonamido)ethoxy]ethoxy}ethoxy)ethyl]acetamide.
[0397] Step 1: A stirred solution of tert-butyl N-(2-2-[2-(2-N-methyl-3-methoxy-4-[(prop-2- yn-l-yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)carbamate (585.0 mg, 1.1 mmol) N- [(3 S,4R)-3 -fluoro- 1 -methylpiperi din-4-yl]-2-iodo- 1 -(2,2, 2-trifluoroethyl)- lH-indol-4- amine (419.13 mg, 920.69 pmol) in THF (9 mL), and EbN (9 mL) was prepared.
Tetrakis(triphenylphosphane) palladium (212.54 mg, 184.14 pmol) and copper(I) iodide (17.48 mg, 92.07 pmol) were added dropwise at room temperature under an argon atmosphere. The reaction mixture was stirred at room temperature for 12 hours. The mixture was then purified by flash chromatography (Interchim, 80 g Si O2, MTBE/MeOH gradient from 80-20%, flow rate: 60 mL/min, 8-14 CV) to obtain tert-butyl N-[2-(2-2-[2-(N-methyl-4-[3-(4-[(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3- methoxybenzenesulfonamido)ethoxy] ethoxy ethoxy)ethyl] carbamate (210.0 mg, 94.0% purity, 230.35 pmol, 25% yield) as a yellow gum.
[0398] Step 2: A stirred solution of tert-butyl N-[2-(2-2-[2-(N-methyl-4-[3-(4-[(3S,4R)-3- fluoro-1 -methylpiperi din -4-yl]amino-l -(2,2, 2-tri fluoroethyl)-lH-indol-2-yl)prop-2-yn-l - yl]amino-3-methoxybenzenesulfonamido)ethoxy]ethoxyethoxy)ethyl]carbamate (170.0 mg, 198.37 pmol) in MeOH (0.2 ml) and dioxane/hcl(0.2 ml) at the room temperature. Reaction mixture was stirred at room temperature for another 3h. Concentrated in vacuo to obtain N-(2-2- [2-(2-aminoethoxy)ethoxy]ethoxyethyl)-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]amino- l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3-methoxy-N-methylbenzene-l- sulfonamide (150.0 mg, 84.0% purity, 166.48 pmol, 84% yield) as brown gum which was used directly in the next step.
[0399] Step 3: A solution of N-(2-2-[2-(2-aminoethoxy)ethoxy]ethoxyethyl)-4-[3-(4- [(3 S,4R)-3 -fluoro- 1 -methylpiperidin-4-yl] amino- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2- yn-l-yl]amino-3-methoxy-N-methylbenzene-l-sulfonamide (88.3 mg, 116.67 pmol), [(dimethylamino)(3H-[l,2,3]triazolo[4,5-b]pyridin-3-yloxy)methylidene]dimethylazanium hexafhrorophosphamiide (57.68 mg, 151.75 pmol), 2-[3-([5-(3,5-dimethyl-l,2-oxazol-4-yl)-2- methoxypyridin-3-yl]aminomethyl)phenoxy] acetic acid (58.18 mg, 151.75 pmol) from mZ2 acid, and ethylbis(propan-2-yl)amine (150.76 mg, 1.17 mmol, 200.0 pl, 10.0 equiv) in DMF (0.5 mL) was stirred overnight at room temperature. The mixture was purified by HPLC (35-60% gradient over 0-5 min, H2O/ACN/0.1% NH4OH, flow rate: 30 mL/min, loading pump: 4 mL/min ACN, target mass: 1122.26, column: XBridge C18 OBD 100 x 19 mm, 5 pm) to obtain 2-[3-([5-(3,5- dimethyl-l,2-oxazol-4-yl)-2-methoxypyridin-3-yl]aminomethyl)phenoxy]-N-[2-(2-2-[2-(N- methyl-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]amino-l-(2,2,2-trifluoroethyl)-lH- indol-2-yl)prop-2-yn- 1 -yl] amino-3 - methoxybenzenesulfonamido)ethoxy]ethoxyethoxy)ethyl]acetamide (47.4 mg, 42.24 pmol, 36.2% yield).
Example 22: Synthesis of 2-{[6-({[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2- dihydropyridin-3-yl] amino} methyl)pyridin-2-yl] oxy}-N- [2-(2- {2- [2-(N-methyl-4- { [3- (4- { [(3S,4R)-3-fluoro- l-methylpiperidin-4-yl] amino}- l-(2,2,2-trifluoroethyl)- lH-indol-2- yl)prop-2-yn- 1-yl] amino}-3- methoxybenzenesulfonamido)ethoxy]ethoxy}ethoxy)ethyl]acetamide.
[0400] Step 1: A stirred solution of tert-butyl N-(2-2-[2-(2-N-methyl-3-methoxy-4-[(prop-2- yn-l-yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)carbamate (585.0 mg, 1.1 mmol), N-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]-2-iodo-l-(2,2,2-trifluoroethyl)-lH-indol-4-amine (419.13 mg, 920.69 pmol) in THF (9 mL), and EbN (9 mL) was prepared.
Tetrakis(triphenylphosphane) palladium (212.54 mg, 184.14 pmol) and copper(I) iodide (17.48 mg, 92.07 pmol) were added dropwise at room temperature under an argon atmosphere. The reaction mixture was stirred at room temperature for 12 hours. The mixture was then purified by flash chromatography (Interchim, 80 g Si O2, MTBE/MeOH gradient from 80-20%, flow rate: 60 mL/min, 8-14 CV) to obtain tert-butyl N-[2-(2-2-[2-(N-methyl-4-[3-(4-[(3S,4R)-3-fluoro-l- methylpiperidin-4-yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3- methoxybenzenesulfonamido)ethoxy] ethoxy ethoxy)ethyl] carbamate (210.0 mg, 94.0% purity, 230.35 pmol, 25% yield) as a yellow gum.
[0401] Step 2: A stirred solution of tert-butyl N-[2-(2-2-[2-(N-methyl-4-[3-(4-[(3S,4R)-3- fluoro-l-methylpiperidin-4-yl]amino-l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l- yl]amino-3-methoxybenzenesulfonamido)ethoxy]ethoxyethoxy)ethyl]carbamate (170.0 mg, 198.37 pmol) in MeOH (0.2 ml) and dioxane/HCL(0.2 ml) at the room temperature. Reaction mixture was stirred at room temperature for another 3h. Concentrated in vacuo to obtain N-(2-2- [2-(2-aminoethoxy)ethoxy]ethoxyethyl)-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]amino- l-(2,2,2-trifluoroethyl)-lH-indol-2-yl)prop-2-yn-l-yl]amino-3-methoxy-N-methylbenzene-l- sulfonamide (150.0 mg, 84.0% purity, 166.48 pmol, 84% yield) as brown gum which was used directly in the next step.
[0402] Step 3: A solution of N-(2-2-[2-(2-aminoethoxy)ethoxy]ethoxyethyl)-4-[3-(4- [(3 S,4R)-3 -fluoro- 1 -methylpiperidin-4-yl] amino- 1 -(2,2,2-trifluoroethyl)- 1 H-indol-2-yl)prop-2- yn-l-yl]amino-3-methoxy-N-methylbenzene-l-sulfonamide (48.0 mg, 63.42 pmol), [(dimethylamino)(3H-[l,2,3]triazolo[4,5-b]pyridin-3-yloxy)methylidene]dimethylazanium hexafluorophosphamiide (31.32 mg, 82.39 pmol), 2-[6-([5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo- l,2-dihydropyridin-3-yl]aminomethyl)pyridin-2-yl]oxyacetic acid (30.52 mg, 82.39 pmol) (mZ17 acid), and ethylbis(propan-2-yl)amine (81.86 mg, 633.79 pmol) in DMF (0.5 mL) was stirred overnight at room temperature. The mixture was then purified by HPLC (gradient: 20-50% over 0-6 min, H2O/ACN/0.1% NH4OH, flow rate: 30 mL/min, loading pump: 4 mL/min ACN, target mass: 1109.22, column: XBridge C18 100 x 19 mm, 5 pm) to obtain 2-[6-([5-(3,5-dimethyl-l,2- oxazol-4-yl)-2-oxo-l,2-dihydropyridin-3-yl]aminomethyl)pyridin-2-yl]oxy-N-[2-(2-2-[2-(N- methyl-4-[3-(4-[(3S,4R)-3-fluoro-l-methylpiperidin-4-yl]amino-l-(2,2,2-trifluoroethyl)-lH- indol-2-yl)prop-2-yn- 1 -yl] amino-3 - methoxybenzenesulfonamido)ethoxy] ethoxy ethoxy)ethyl] acetamide (19.5 mg, 97.0% purity, 17.05 pmol, 26.9% yield).
Example 23: Synthesis of 2-[3-({[5-(3,5-dimethyl-l,2-oxazol-4-yl)-2-oxo-l,2-dihydropyridin- 3-y 1 ] amino} methyl)phenoxy] -N-(2- {2- [2-(2-{N-methyl-3-methoxy-4- [(3- {4-[(l- methylpiperidin-4-yl)amino] - l-(2,2,2-trifhioroethyl)- lH-indol-2-yl} prop-2-yn- 1- yl)amino]benzenesulfonamido}ethoxy)ethoxy]ethoxy}ethyl)acetamide.
[0403] Step 1 : A solution of the N-(2-2-[2-(2-aminoethoxy)ethoxy]ethoxyethyl)-3-methoxy- N-methyl-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2- yn-l-yl)amino]benzene-l -sulfonamide (30.0 mg, 40.6 pmol), the 2-[3-([5-(3,5-dimethyl-l,2- oxazol-4-yl)-2-oxo-l,2-dihydropyridin-3-yl]aminomethyl)phenoxy]acetic acid (15.01 mg, 40.63 pmol), the [(dimethylamino)(3H-[l,2,3]triazolo[4,5-b]pyridin-3- yloxy)methylidene]dimethylazanium; hexafluoro-lambda5-phosphanuide (23.17 mg, 60.95 pmol) and the ethylbis(propan-2-yl)amine (52.48 mg, 406.34 pmol) in dry DMF (1 ml) was stirred under argon at RT for 12 h. LCMS analysis of the reaction mixture showed full conversion to the desired product. The mixture was purified by HPLC (Device (Mobile Phase, Column) : SYSTEM 40-40-80% 0-1-6 min H2O/ACN/NH4OH flow: 60ml/min (loading pump 4ml/min ACN target mass 1091 column: XBridge C18 OBD 30x100m 5 pm) to afford 2-[3-([5-(3,5-dimethyl-l,2- oxazol-4-yl)-2-oxo-l,2-dihydropyridin-3-yl]aminomethyl)phenoxy]-N-(2-2-[2-(2-N-methyl-3- methoxy-4-[(3-4-[(l-methylpiperidin-4-yl)amino]-l-(2,2,2-trifluoroethyl)-lH-indol-2-ylprop-2- yn-l-yl)amino]benzenesulfonamidoethoxy)ethoxy]ethoxyethyl)acetamide (13.4 mg, 12.29 pmol, 30.2% yield).
Example 24. Synthesis of tert- butyl 3-[2-[2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]propanoate.
[0404] Step 1 : The synthesis of 2-methoxy-4-[(4-methoxyphenyl)methylsulfanyl]-l-nitro- benzene. To a solution of 4-fluoro-2-methoxy-l -nitro-benzene (compound 1, 10.0 g, 58.4 mmol) and (4-methoxyphenyl)methanethiol (9.91 g, 64.3 mmol) in DMF (100 mL) K2CO3 (16.15 g, 116.9 mmol) was added . The mixture was stirred at 60 °C for 12 hrs. TLC (silica gel plate, petroleum ether: ethyl acetate= 5:1, Rf= 0.67) showed that compound 1 was consumed and a new spot formed. The mixture was poured into water (100 mL) and solid precipitation was observed. The precipitate was collected by filtration and then dried in vacuo to give 2-methoxy-4-[(4- methoxyphenyl)methylsulfanyl]-l-nitro-benzene (17.5 g, 98% yield) as a yellow solid.
[0405] Step 2 : The synthesis of 3-methoxy-4-nitro-benzenesulfonyl chloride. To a solution of 2-methoxy-4-[(4-methoxyphenyl)methylsulfanyl]-l-nitro-benzene (8 g, 26.2 mmol) in MeCN (72 mL), AcOH (6 mL) and H2O (2 mL) l,3-dichloro-5,5-dimethyl-imidazolidine-2, 4-dione (10.32 g, 52.4 mmol) was added. The mixture was stirred at 0 °C for Ih. TLC (silica gel plate, petroleum ether: ethyl acetate = 10: 1, Rf= 069) showed that reactant was consumed, and a new spot was formed. To the mixture ethyl acetate (100 mL) and water (15 mL) were added and then layers were separated. The aqueous phase was extracted with ethyl acetate (30 mL * 3). The combined organic layers were washed with brine (20 mL), dried over ISfeSCL, filtered, and concentrated in vacuo to give an oil residue. The residue was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of 0 to 20% ethyl acetate/petroleum ether gradient at 70 mL/min) to give the desired product 3 -methoxy-4-nitro- benzenesulfonyl chloride (4.5 g, 68% yield) as a yellow solid.
[0406] Step 3 : The synthesis of tert 3--b[u2t-y[2l -[2-[(3-methoxy-4-nitro-phenyl)sulfonyl- methylamino]ethoxy]ethoxy]ethoxy]propanoate. To a solution of 3-[2-[2-(2te-rt-butyl aminoethoxy)ethoxy]ethoxy]propanoate (2 g, 7.21 mmol) in DCM (10 mL) pyridine (1.14 g, 14.42 mmol) was added followed by 3-methoxy-4-nitro-benzenesulfonyl chloride 3 (2.18 g, 8.65 mmol). The reaction was stirred at 25 °C for 1 h. LCMS showed that 3 -methoxy-4-nitro- benzenesulfonyl chloride 3 was consumed completely and 39 % of desired mass was detected. The mixture was concentrated in vacuo to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash® Silica Flash Column, eluent of 0 to 50% ethyl acetate/petroleum ether gradient at 80 mL/min) to give the desired product /c/7-butyl 3-[2-[2-[2- [(3-methoxy-4-nitro-phenyl)sulfonylamino]ethoxy]ethoxy]ethoxy]propanoate (2.3 g, 65 % yield) as a yellow oil.
[0407] Step 4 : The synthesis of tert 3--b[u2t-y[2l -[2-[(3-methoxy-4-nitro-phenyl)sulfonyl- methylamino] ethoxy] ethoxy] ethoxy ]propanoate. To a solution of 3-[2-[2-[2-[(3te-rt-butyl methoxy-4-nitro-phenyl)sulfonylamino] ethoxy] ethoxy] ethoxy ]propanoate and K2CO3 (1.68 g, 12.18 mmol) in DMF (10 mL) Mel (1.30 g, 9.14 mmol) was added. The mixture was stirred at 25 °C for 3 hrs. LCMS showed that starting material was consumed completely and 95 % of desired mass was detected. To the mixture ethyl acetate (50 mL) and water (50 mL) were added and then layers were separated. The aqueous phase was extracted with ethyl acetate (30 mL x 3). The combined organic layers were washed with brine (20 mL), dried over ISfeSCL, fdtered and concentrated in vacuo to give te 3rt-[-2b-u[2ty-l[2-[(3-methoxy-4-nitro-phenyl)sulfonyl- methylamino] ethoxy] ethoxy] ethoxy ]propanoate (3.0 g, 97% yield) as yellow oil.
[0408] Step 5 : The synthesis of tert 3--b[u2t-y[2l -[2-[(4-amino-3-methoxy-phenyl)sulfonyl- methylamino] ethoxy] ethoxy] ethoxy ]propanoate. To a suspension of Pd/C (300 mg, 10% purity) in MeOH (20 mL), tert-but 3y-l [2-[2-[2-[(3-methoxy-4-nitro-phenyl)sulfonyl- methylamino] ethoxy] ethoxy] ethoxy ]propanoate (3 g, 5.92 mmol) was added under nitrogen atmosphere. The mixture was degassed and purged with H2 for 3 times, and then left to stir at 25°C for 12 hrs under H2 (50 Psi) atmosphere. LCMS showed compound 5 was consumed completely and 99 % of desired mass was detected. The reaction was fdtered off and the fdtrate was obtained then the fdter cake was washed by THF (30mLx3). The fdtrate was concentrated in vacuo to give tert-bu 3ty-[l2-[2-[2-[(4-amino-3-methoxy-phenyl)sulfonyl- methylamino] ethoxy] ethoxy] ethoxy ]propanoate (2.8 g, 5.88 mmol, 99% yield) as a colorless oil. [0409] Step 6: The synthesis of tert-butyl 3-[2-[2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]propanoate. To a solution of tert -butyl 3 - [2- [2- [2- [(4-amino-3 -methoxy -phenyl)sulfonyl- methylamino] ethoxy] ethoxy] ethoxy ]propanoate (2.8 g, 5.88 mmol) and 3 -bromoprop- l-yne (1.31 g, 8.81 mmol) in DMF (20 mL) KI (98 mg, 587 pmol) and K2CO3 (1.62 g, 11.75 mmol, 2 eq) were added. The mixture was stirred at 80 °C for 12 hrs. LCMS showed compound 6 was consumed completely and 77 % of desired mass was detected. To the mixture ethyl acetate (50 mL) and water (15 mL) were added and then layers were separated. The aqueous phase was extracted with ethyl acetate (30 mLx3). The combined organic layers were washed with brine (20 mL), dried over ISfeSCL, filtered and concentrated in vacuo to give an oil residue. The residue was purified by prep-HPLC (column: Phenomenex luna Cl 8 150 x 40mm 15 pm; mobile phase: water(FA)-MeCN; gradient: 53%-83% MeCN over 15 min) to give tert-butyl 3-[2-[2-[2-[[3- methoxy-4-(prop-2-ynylamino)phenyl]sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]propanoate (1.40 g, 2.59 mmol, 44% yield, 95% purity) as a yellow oil. JH NMR (400 MHz, DMSO-d6) δ 1.39 (9H, s), 2.40 (2H, t, J = 6.4 Hz), 2.67 (3H, s), 3.01-3.11 (3H, m), 3.48 (8H, d, J = 2.8 Hz), 3.50-3.54 (2H, m), 3.57 (2H, t, J = 6.4 Hz), 3.85 (3H, s), 3.94-4.02 (2H, m), 6.24 (1H, t, J = 6.0 Hz), 6.73 (1H, d, J = 8.4 Hz), 7.05 (1H, d, J = 2.0 Hz), 7.21-7.30 (1H, m).
Example 25. Synthesis of tert- butyl N-[2-[2-[2-[2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate.
[benzyl(methyl)amino]ethoxy]ethoxy]ethoxy] ethoxy] ethyl] carbamate. To a solution of tert-butyl N- [2- [2- [2- [2-(2-bromoethoxy)ethoxy] ethoxy] ethoxy] ethyl] carbamate (2 g, 5.00 mmol) and A- methyl-l-phenyl-methanamine (909 mg, 7.49 mmol) in MeCN (20 mL) K2CO3 (1.38 g, 9.99 mmol) was added. The mixture was stirred at 80 °C for 12 hrs. 70 % of desired mass was detected by LCMS. To the mixture ethyl acetate (100 mL) and water (50 mL) were added and then layers were separated. The aqueous phase was extracted with ethyl acetate (30 mLx3). The combined organic layers were washed with brine (50 mL), dried overNa2SO4, fdtered and concentrated in vacuo to give an oil residue. The residue was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, eluent of 0 to 80% ethyl acetate/petroleum ether gradient at 50 mL/min) to give tert-butyl /V- [2- [2- [2- [2- [2- [benzyl(methyl)amino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate (2.1 g, 95% yield) as a yellow oil.
[0411] Step 2: The synthesis of tert-butyl /V-[2-[2-[2-[2-[2- (methylamino)ethoxy] ethoxy] ethoxy] ethoxy]ethyl]carbamate. To a suspension of Pd/C (220 mg, 10% purity) in MeOH (20 mL) under nitrogen atmosphere tert-butyl N- [2- [2- [2- [2- [2- [benzyl(methyl)amino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate (2.1 g, 4.77 mmol) was added. The resulting mixture was degassed and purged with H2 3 times, and then the mixture was stirred at 25 °C for 12 hours under H2 (50 Psi) atmosphere. TLC (silica gel plate, petroleum ether: ethyl acetate = 1: 3, Rf= 0.33) showed that compound 2 was consumed and a new spot formed. The precipitate was filtered off, washed by THF (30mL*3) and collected filtrate was concentrated in vacuo to give tert-butyl N-[2-[2-[2-[2-[2-(methylamino)ethoxy]ethoxy]ethoxy] ethoxy]ethyl]carbamate (1.6 g, 4.57 mmol, 96% yield) as a colorless oil.
[0412] Step 3: The synthesis of tert-butyl N-[2-[2-[2-[2-[2-[(3-methoxy-4-nitro- phenyl)sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate. To a solution of tert-butyl N-[2-[2-[2-[2-[2-(methylamino)ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate (1.6 g, 4.57 mmol) in DCM (10 mL) pyridine (1.08 g, 13.70 mmol) was added. 3 -methoxy-4-nitro- benzenesulfonyl chloride (1.38 g, 5.48 mmol) was added to the mixture. The reaction was stirred at 25 °C for 1 h. 34 % of desired mass was detected by LC-MS. The mixture was concentrated in vacuo to give an oil residue. The residue was purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash® Silica Flash Column; Eluent: 0-50% Ethyl acetate/Petroleum ether gradient @ 70 mL/min) to give tert-butyl N-[2-[2-[2-[2-[2-[(3-methoxy-4-nitro-phenyl)sulfonyl- methylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate (1.6 g, 62% yield) as a colorless oil.
[0413] Step 4: The synthesis of tert-butyl JV-[2-[2-[2-[2-[2-[(4-amino-3-methoxy- phenyl)sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate. To a suspension of Pd/C (200 mg, 10% purity) in MeOH (20 mL) under nitrogen atmosphere tert-butyl 7V-[2-[2-[2- [2-[2-[(3-methoxy-4-nitro-phenyl)sulfonyl-methyl- amino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate (1.6 g, 2.83 mmol) was added. The resulting mixture was degassed and purged with H23 times, and then the mixture was stirred at 25 °C for 12 hours under H2 (15 Psi) atmosphere. LC-MS showed compound 4 was consumed completely and 96% of desired mass was detected. The precipitate was filtered off, washed by THF (30mL*3), and collected filtrate was concentrated in vacuo to give to give tert-butyl 7V-[2- [2-[2-[2-[2-[(4-amino-3-methoxy-phenyl)sulfonyl- methylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate (1.5 g, 99% yield) as a light red oil.
[0414] Step 5: The synthesis of tert-butyl N-[2-[2-[2-[2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonyl-methylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate. To a solution of tert-butyl N- [2- [2- [2- [2- [2- [(4-amino-3 -methoxy -phenyl )sulfonyl - methylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate (1.4 g, 2.61 mmol) and 3- bromoprop-l-yne (583 mg, 3.92 mmol) in DMF (4 mL) KI (44 mg, 261 pmol,) and K2CO3 (723 mg, 5.23 mmol) were added. The mixture was stirred at 80 °C for 12 hours. LC-MS showed compound 5 was consumed completely and 48 % of desired mass was detected. Ethyl acetate (50 mL) and water (15 mL) were added to the mixture, and then layers were separated. The aqueous phase was extracted with ethyl acetate (20 mL*3). The combined organic layers were washed with brine (20 mL), dried over ISfeSCL, filtered and concentrated in vacuo to give an oil residue. The residue was purified by prep-HPLC (column: Phenomenex luna Cl 8 150x40mm, 15pm; mobile phase: [water(FA)-MeCN]; gradient 50%-80% MeCN over 15 min) to give tert-butyl N- [2-[2-[2-[2-[2-[[3-methoxy-4-(prop-2-ynylamino)phenyl]sulfonyl- methylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]carbamate (855.82 mg, 54% yield, 95% purity) as a yellow oil. 1H NMR (400 MHz, DMSO-d6) δ 1.37 (9H, s), 2.67 (3H, s), 3.03-3.10 (5H, m), 3.36 (2H, t, J = 6.4 Hz), 3.47-3.51 (12H, m), 3.51-3.54 (2H, m), 3.85 (3H, s), 3.94-4.02 (2H, m), 6.24 (1H, t, J = 6.4 Hz), 6.73 (2H, d, J = 8.4 Hz), 7.05 (1H, d, J = 2.0 Hz), 7.22-7.29 (1H, m).
Example 26. Synthesis of tert- butyl N-[8-[[3-methoxy-4-(prop-2-ynylamino)phenyl]sulfonyl- methyl-amino] octyl] carbamate.
[0415] Step 1 : The synthesis of tert-butyl A-[8-(methylamino)octyl]carbamate. A solution of tert-butyl A-(8-bromooctyl)carbamate (3.0 g, 9.73 mmol) and methanamine (2 M, 29.20 mL) in THF (5 mL) was stirred at 60 °C for 12 hours in a 30 mL sealed tube. TLC (silica gel plate, petroleum etherethyl acetate = 1:1, Rf = 0.28) showed that compound 1 was consumed and a new spot formed. The mixture was concentrated in vacuo to give tert-butyl TV- [8- (methylamino)octyl]carbamate (2.4 g) as a white solid, which was used into the next step without further purification.
[0416] Step 2 : The synthesis of N-[8-[(3-methoxy-4-nitro-phenyl)sulfonyl-methyl- amino]octyl]carbamate. To a solution of tert-butyl N-[8-(methylamino)octyl]carbamate (2 g, 7.74 mmol) in pyridine (20 mL) 3- methoxy-4-nitro-benzenesulfonyl chloride (2.34 g, 9.29 mmol) was added. The mixture was stirred at 25 °C for 12 hours. 26 % of desired mass was detected by LC- MS. The mixture was concentrated in vacuo to give an oil residue. The residue was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column; eluent: 0 to 30% ethylacetate/petroleum ether gradient at 70 mL/min) to give the desired product tert-butyl N-[8- [(3-methoxy-4-nitro-phenyl)sulfonyl-methyl-amino]octyl]carbamate (1.0 g, 27% yield) as a yellow oil.
[0417] Step 3 : The synthesis of tert-butyl N-[8-[(4-amino-3-methoxy-phenyl)sulfonyl- methyl-amino]octyl]carbamate. To a suspension of Pd/C (100 mg, 2.11 mmol, 10% purity) in MeOH (10 mL) under nitrogen atmosphere tert-butyl N-[8-[(3-methoxy-4- nitro-phenyl)sulfonyl- methyl-amino]octyl]carbamate (1 g, 2.11 mmol) was added. The mixture was degassed and purged with H2 3 times and then stirred at 25 °C for 12 hrs under H2(15 Psi) atmosphere. LCMS showed that compound 3 was consumed completely and 91 % of desired mass was detected. The precipitate was filtered off, washed by THF (30mLx3), and collected filtrate was concentrated in vacuo to give tert-butyl N-[8-[(4-amino-3-methoxy-phenyl)sulfonyl-methyl- amino]octyl]carbamate (930 mg, 2.10 mmol, 99% yield) as a colorless oil.
[0418] Step 4 : The synthesis of tert-butyl A-[8-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonyl-methyl-amino]octyl]carbamate. To a solution of tert-butyl 7V-[8-[(4- amino-3-methoxy-phenyl)sulfonyl-methyl-amino]octyl]carbamate (930 mg, 2.10 mmol) in DMF (5 mL) K2CO3 (580 mg, 4.19 mmol), KI (35 mg, 210 pmol) and 3 -bromoprop- l-yne (468 mg, 3.14 mmol) were added. The mixture was stirred at 80 °C for 12 hrs. LCMS showed that compound 4 was consumed completely and 67 % of desired mass was detected. Ethyl acetate (100 mL) and water (30 mL) were added to the mixture and then layers were separated. The aqueous phase was extracted with ethyl acetate (30 mLx3). The combined organic layers were washed with brine (50 mL), dried over ISfeSCL, filtered and concentrated in vacuo to give a residue. The residue was purified by prep-HPLC (Column: Phenomenex luna Cl 8 150x40mm;
15 pm; mobile phase: [water(FA)-MeCN]; gradient: 59%-79% MeCN over 15 min) to give tertbutyl JV-[8-[[3-methoxy-4-(prop-2-ynylamino)phenyl]sulfonyl-methyl-amino]octyl]carbamate (442.19 mg, 44% yield, 99% purity) as an brown gum. 'H NMR (400 MHz, DMSO-d6) δ 1.23 (8H, br s), 1.37 (11H, s), 1.40-1.46 (2H, m), 2.59 (3H, s), 2.83-2.92 (4H, m), 3.08 (1H, t, J = 2.4 Hz), 3.85 (3H, s), 3.94-4.03 (2H, m), 6.23 (1H, t, J = 6.4 Hz), 6.73 (2H, d, J = 8.4 Hz), 7.03 (1H, d, J = 2.0 Hz), 7.21-7.28 (1H, m).
Example 27. Synthesis of tert- butyl N-[2-[2- [2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl] sulfonylamino] ethoxy] ethoxy] ethoxy] ethyl] carbamate.
[0419] Step 1: The synthesis of A-[2-[2-[2-[2-[(3-methoxy-4- nitrophenyl)sulfonylamino]ethoxy] ethoxy]ethoxy]ethyl]carbamate. A mixture of 3 -methoxy-4- nitro-benzenesulfonyl chloride (2.07 g, 8.21 mmol) and ZerLbutyl A-[2-[2-[2-(2- aminoethoxy)ethoxy]ethoxy]ethyl]carbamate (2.0 g, 6.84 mmol) in pyridine (10 mL) was degassed, purged with N2 3 times, and then stirred at 25 °C for 1 h under N2 atmosphere. LCMS showed complete consumption of starting and formation of desired product. The mixture was concentrated in vacuo to give an oil residue. The residue was purified by flash silica gel chromatography (ISCO®; 10 g SepaFlash® Silica Flash Column, Eluent 0-50% ethyl acetate/petroleum ether gradient at 70 mL/min) to give product tert-butyl 7V-[2-[2-[2-[2-[(3- methoxy-4-nitrophenyl)sulfonylamino]ethoxy]ethoxy]ethoxy]ethyl]carbamate (2.2 g, 63% yield) as a yellow oil.
[0420] Step 2: The synthesis of tert-butyl A-[2-[2-[2-[2-(tert- butoxycarbonylamino)ethoxy] ethoxy] ethoxy ] ethyl] -N-(3 -methoxy-4-ni trophenyl)sulfonyl- carbamate. To a solution of tert-butyl A-[2-[2-[2-[2-[(3-methoxy-4- nitrophenyl)sulfonylamino] ethoxy] ethoxy] ethoxy] ethyl] carbamate (1.8 g, 3.55 mmol) in DCM (20 mL) DMAP (44 mg, 355 pmol) and EtsN (1.08 g, 10.64 mmol) were added followed by (BOC)2O (1.08 g, 4.96 mmol). The mixture was stirred at 25 °C for 12 hrs. LCMS showed complete consumption of starting material and formation of the desired product. The mixture was concentrated in vacuo to give an oil residue. The residue was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column; eluent: 0-10% ethyl acetate/petroleum ether gradient at 70 mL/min) to give the desired product /cr/-butyl A-[2-[2-[2- [2-(tert-butoxycarbonylamino)ethoxy] ethoxy ] ethoxy] ethyl] -N-(3 -methoxy-4- nitrophenyl)sulfonyl-carbamate (1.6 g, 74% yield) as a colorless oil.
[0421] Step 3 : The synthesis of tert A-b-(u4ty-almino-3-methoxy-phenyl)sulfonyl-A-[2-[2- [2-[2-(tertbutoxycarbonylamino)ethoxy]ethoxy]ethoxy]ethyl]carbamate. To a suspension of Pd/C (200 mg, 10% purity) in MeOH (10 mL) under nitrogen atmosphere A-[2-[2-t[e2rt-[-2b-utyl (tertbutoxycarbonylamino)ethoxy]ethoxy]ethoxy]ethyl]-A-(3-methoxy-4-nitro-phenyl)sulfonyl- carbamate (1.6 g, 2.63 mmol) was added. The mixture was degassed, purged with H23 times, and stirred under H2 (15 Psi) atmosphere at 25°C for 12 hrs. LCMS showed complete consumption of starting material and formation of the desired product. The reaction was filtered, solid residue was washed by THF (30mLx3), and collected filtrate was concentrated in vacuo to give tert-butyl A-(4-amino-3 -methoxy -phenyl )sulfonyl -A- [2- [2- [2- [2- (tertbutoxycarbonylamino)ethoxy]ethoxy]ethoxy]ethyl]carbamate (1.3 g, 85% yield) as a colorless oil.
[0422] Step 4: The synthesis of tert- Ab-u[t2y-l[2-[2-[2-(tert- butoxycarbonylamino)ethoxy] ethoxy] ethoxy ] ethyl] -N- [3 -methoxy-4-(prop2- ynylamino)phenyl]sulfonyl-carbamate. A mixture of A-(4t-eartm-binuoty-3l -methoxy - phenyl (sulfonyl -A- [2- [2- [2- [2-(tertbutoxycarbonylamino)ethoxy]ethoxy] ethoxy ] ethyl] carbamate (1.3 g, 2.25 mmol), 3 -bromoprop- 1-yne (435 mg, 2.93 mmol), K2CO3 (622 mg, 4.50 mmol), and KI (75 mg, 450 pmol) in DMF (5 mL) was degassed, purged with N2 3 times, and stirred under nitrogen atmosphere at 80 °C for 12 hrs. LCMS showed complete consumption of starting materials and formation of the desired product. Ethyl acetate (25 mL) and water (15 mL) were added and then layers were separated. The aqueous phase was extracted with ethyl acetate (15 mL*3). The combined organic layers were washed with brine (50 mL), dried overNa2SO4, filtered and concentrated in vacuo to give an oil residue. The residue was purified by pre p-HPLC (column: Phenomenex luna Cl 8 150x40mm 15pm; mobile phase: [water(FA)-MeCN]; gradient: 57%-87% MeCN over 15 min) to give tert-butyl A-[2-[2-[2-[2-(tert- butoxycarbonylamino)ethoxy] ethoxy] ethoxy ] ethyl] -N- [3 -methoxy-4-(prop2- ynylamino)phenyl]sulfonyl-carbamate (410 mg, 665.87 pmol) as a yellow oil.
[0423] Step 5: The synthesis of tert- Ab-u [t2y-l [2- [2-[2-[[3-methoxy-4-(prop-2- ynylamino)phenyl]sulfonylamino]ethoxy]ethoxy]ethoxy]ethyl]carbamate. To a solution of tertbutyl A-[2-[2-[2-[2-(tert-butoxycarbonylamino)ethoxy]ethoxy]ethoxy]ethyl]-A-[3-methoxy-4- (prop-2-ynylamino)phenyl]sulfonyl-carbamate (410 mg, 665.87 pmol) in MeOH (20 mL) K2CO3 (184 mg, 1.33 mmol) was added. The mixture was stirred at 50 °C for 12 hrs. LCMS showed complete consumption of starting material and formation of the desired product. The reaction mixture was concentrated in vacuo to give an oil residue. The residue was purified by flash silica gel chromatography (ISCO®; 10 g SepaFlash® Silica Flash Column; eluent 0-50% ethylacetate/petroleum ether gradient at 70 mL/min) to give the desired product tert-butyl 7V-[2- [2- [2-[2-[[3-methoxy-4-(prop-2-ynylamino)phenyl]sulfonylamino]ethoxy]ethoxy]ethoxy] ethyl] carbamate (418.24 mg, 90.64% purity) as yellow oil. 1H NMR (400 MHz, DMSO-d6) δ 1.36 (9H, s), 2.82 (2H, br d, J = 5.6 Hz), 2.98-3.11 (3H, m), 3.34-3.39 (4H, m), 3.41-3.49 (8H, m), 3.83 (3H, s), 3.91-4.04 (2H, m), 6.13 (1H, t, J = 6.0 Hz), 6.64-6.78 (2H, m), 7.16 (1H, d, J = 1.6 Hz), 7.23-7.31 (2H, m).
Example 28. Cell viability assays showing bifunctional molecule induced cell death
[0424] OmniTAC compounds are created that include targeting ligands for p53 and recruiting ligands for proteins capable of modulating p53 activity. Linkers connect the targeting and recruiting ligands. A screening of the compounds determines the best binders to certain modifier proteins and p53 using a cell viability assay. Cell viability in p53 WT, p53 mutant and/or p53 null cell lines is compared. The compounds are then tested in vitro. Cells are cultured at 37 °C at proper humidity levels. A control group is created that only contains cells and vehicle treatment. A treatment group with OmniTAC is tested, and compared to the control group.
[0425] Selected OmniTAC compounds are added to the treated cells at various concentrations, for example, 250 nM, 500 nM, and 1,000 nM. The compounds are incubated with the cells for various time intervals such as 24, 48, and 72 hours. Following incubation, cell viability is measured by monitoring luminescence.
[0426] For instance, NUGC3 (500 cells per well) or NUGC3 Y220C KO cells (375 cells per well) were treated with DMSO, control compounds or BFMs for 120 h in 384 well plate (50 pL media per well). Cell viability was measured through measuring the amount of available ATP via luciferase activity as detailed in the Promega’s CellTiter Gio™ protocol: 25 pL of 20% solution of Promega’s Cell Titer Gio 2.0 (CTG) reagent in PBS was added to each well. Plates with cells and CTG reagent were placed on orbital shaker for 15-30 min and luminescence was recorded for each well (0.3s integration time). Signal was normalized by DMSO and results graphed as “fold change over DMSO” on y-axis and concentration of tested compounds on x-axis using GraphPad PRISM 10 software. IC50 values were obtained after automatic fitting of data using “[inhibitor] vs response - variable slope (four parameters)” method. Results are shown in FIG. 3 and Table 6.
Table 6: Summary of the Effects of OmniTAC treatment on the Viability of NUGC3 and NUGC3 p53 Y220C KO Cells. IC50 indicates the concentration of compound at which 50% of maximum of cell viability is observed. a 3 -day viability instead of 5 -day b H1299 Y220C cells were used instead of NUGC-3 c Hl 299 cells were used instead of NUGC-3 KO d NUGC-4 cells were used instead of NUGC-3 KO
“+” IC50 > 5000 nM; “++” 5000 nM > IC50 > 1000 nM; “+++” 1000 nM > IC50 > 200 nM; “++++” IC5o < 200 nM
Example 29. Live cell ternary complex formation assay
[0427] OmniTAC compounds are created that include targeting ligands for p53 and recruiting ligands for proteins capable of modulating p53 activity. Linkers connect the targeting and recruiting ligands. A screening of the compounds determines the best binders to certain modifier proteins and p53 using ternary complex formation assay. Cells are cultured at 37 °C and proper humidity levels. A control group is created using a reference compound, here compound 1.
[0428] For instance, H1299 cells stably expressing SmBiT-p53 Y220C and LgBiT-BRD4 (5000 cells/wells) were plated in each well of 384 well plate using phenol red-free OPTI-MEM media (30 pL per well). Tested compounds, reference compound 1 and DMSO control were added to cells using Tecan D300e compound printer (12 concentration in triplicates, two-fold dilution from 20 or 10 pM highest concentration). Cells were incubated with compounds for 3 h, then plates were cooled to room temperature over 15 min. Furimazine was added (50 pM final concentration) and luminescence was read immediately in kinetics mode until signal reached its maximum value. Signal was normalized by DMSO and maximum luminescence observed in this experiment with reference compound. TC50 and TCmax values were obtained after removal of points at higher doses and automatic fitting of remaining data using “[inhibitor] vs response - variable slope (four parameters)” method using GraphPad PRISM 10 software. Results are shown in FIG. 4 and Table 7.
Table 7: Summary of the ternary complex formation results in cell lysate. TC50 indicates the concentration of compound at which 50% of maximum luminescence is observed; TCmax indicates the percentage of maximum luminescence compared to reference compound 1.
TCF from transient transfection in HEK293T cells
“+” TCso > 100 nM; “++” 10 nM < TC50 < 100 nM; “+++” 10 nM < TC50; “+” TCmax < 100%; “++” 100 % < TCmaX < 200%; “+++” 200% > TCmax
Example 30. Ternary Complex formation assay in cell lysate
[0429] OmniTAC compounds are created that include targeting ligands for p53 and recruiting ligands for proteins capable of modulating p53 activity. Linkers connect the targeting and recruiting ligands. A screening of the compounds determines the best binders to certain modifier proteins and p53 using ternary complex formation assay. Cells are cultured at 37 °C and proper humidity levels. A control group is created using a reference compound, here reference compound 1.
[0430] For instance, H1299 cells stably expressing SmBiT-p53 Y220C and LgBiT-BRD4 were harvested from confluent T175 flask and lysed by sonication in 50 mM HEPES buffer supplemented with 200 mM KC1 and protease/phosphatase inhibitor cocktail. Lysate was separated from cell debris using centrifugation at 15 000 rpm for 15 min (4 °C). Cell lysate concentration was measured using Pierce™ BCA Protein Assay Kits and concentration of proteins adjusted to 0.5 pg/pL. 20 pL of cell lysate was added to each well of 384 well plates. Tested compounds, reference compound 1 and DMSO control were added to lysate using Tecan D300e compound printer (12 concentration in triplicates, two-fold dilution from 20 or 10 pM highest concentration). Cell lysate was incubated with compounds for 15 min at room temperature, furimazine was added (50 pM final concentration) and luminescence was read immediately in kinetics mode until signal reached its maximum value. Signal was normalized by DMSO and maximum luminescence observed in this experiment with reference compound. TCso and TCmax values were obtained after removal of points at higher doses and automatic fitting of remaining data using “[inhibitor] vs response - variable slope (four parameters)” method using GraphPad PRISM 10 software. Results are shown in FIG. 5 and Table 8.
Table 8: Summary of the ternary complex formation results in cells. TCso indicates the concentration of compound at which 50% of maximum luminescence is observed; TCmax indicates the percentage of maximum luminescence compared to reference compound 1.
“+” TCso > 1000 nM; “++” 200 nM < TCso < 1000 nM; “+++” 200 nM < TC5o;TCmaX < 150%;
“++” 150 % < TC max < 200%; “+++” 200% > TCmax
[0431] While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

Claims

CLAIMS What is claimed is:
1. A modifier protein targeting chimeric (OmniTAC) compound which targets a transcription factor p53, comprising a targeting ligand, a recruiting ligand, and a linker, wherein the targeting ligand is attached to the recruiting ligand via the linker; wherein the targeting ligand is configured to bind to a target protein, wherein the target protein is a wild-type (WT) p53 or a mutant p53, and the recruiting ligand is configured to bind to a modifier protein such that the modifier protein induces a change to the WT p53 or mutant p53; and wherein the modifier protein comprises a non-degradative protein that activates, stabilizes, and/or corrects misfolding of the target protein.
2. The compound of claim 1, wherein the target protein comprises a mutant or a truncation of p53.
3. The compound of claim 2, wherein the target protein comprises at least one mutation, wherein the at least one mutation results in an inactive or a dominant form of p53.
4. The compound of claim 2, wherein the target protein comprises a loss-of function mutation of p53.
5. The compound of claim 2, wherein the target protein comprises p53 Y220C mutant.
6. The compound of any one of claims 1 to 5, wherein the targeting ligand comprises a small molecule moiety.
7. The compound of any one of claims 1 to 6, wherein the recruiting ligand is derived from any small molecule, or analogues of any small molecule in FIG. 1 and FIG. 2.
8. The compound of any one of claims 1 to 7, wherein the modifier protein comprises an epigenetic modifier, epigenetic reader, chaperone, or nuclear targeting protein.
9. The compound of any one of claims 1 to 8, wherein the modifier protein comprises a acylase, deacylase, organelle specific protein, kinase, phosphatase, palmitoyltransferase, methyltransferase, demethylase, acetyltransferase, deacetylase, glycosyltransferase, E3 ligase, SUMO ligase, ubiquitin ligase, deubiquitinase, tyrosine sulfotransferase, heat shock protein, bromodomain, Tudor domain, PWWP domain, chromodomain, ankyrin repeat, 14-3-3 protein, BRCT domain, DNA recognition protein, DNA modifying protein, or nucleus localization protein.
10. The compound of any one of claims 1 to 9, wherein the modifier protein comprises 14-3- 3o, 14-3-3y, 14-3 -3s, ABL, AEP1, AhR, ALK, AMPK, AR, ATAD2, ATAD2B, BAZ1A, BAZ1B, BAZ2A, BAZ2B, BCR-ABL, BRAF, BRD2, BRD3, BRD4, BRD7, BRD9, BRDT, BRFA, BRPF1A, BRPF1B, BTK, BRWD3, CBP, CREBBP, CDK2, CDK4, CDK6, CDK7, CDK9, CDK12, CECR2, cIAP, CK1, CRBN, CSF1R, CSN, DCAF11, DCAF15, DCAF16, DOTI, EGFR, ER, EZH2, FAK, FALZ, FEM1B, FKBP12, FLT3, FUT8, G9a, GCN5, GKC, GLP, HDAC1, HDAC2, HDAC3, HDAC6, HDAC8, HDAC10, HDAC11, HER2, HER4, HSC70, HSP70, HSP90, IGF2R, JAK1, JAK2, JAK3, KAT6A, KAT6B, KAT7, KDM1, KDM2, KDM4, KDM5, KDM6, KEAP1, KIT, KRAS, L3MBTL3, LRRK2, LSD1, LYN, MAPK, MAX, MEK, MET, MDM2, MLL, MOZ, mTOR, MYC, NBR1, NMT1, NSD2, NSD3, NTRK1, NTRK2, NTRK3, OTUB1, pl 10, p300, PAX3-FOXO1, PBRM1, PB1, PCAF, PDK1, PDK2, PDGFR, PHID, PHF1, PHF19, PIGK, PI3K, PKC, PKG, PKM2, PKR, PP2A, PP2B, PPP1R15A, PRMT1, PRMT3, PRMT4, PRMT5, PRMT6, PTP1B, Raf-1, RET, RNF4, RNF114, ROCK, ROS1, RPN11, SETD2, SFN, SHP1, SHP2, SIRT1, SIRT3, SIRT6, SMARCA2, SMARCA4, SMYD2, SMYD3, S0S1, SRC, ST6GAL1, SYK, TAF1, TDRD, Tie2, TOPI, TPST1, TRAF6, TRIM22, TRIM24, TRIM33, TRIM33B, TRIM66, TrkB, TYK2, UAF1, UCHL1, ULK1, USP1, USP7, USP8, USP9X, USP14, USP30, VEGFR1, VEGFR2, VEGFR3, VE-PTP, VHL, WRD9/BRWD 1 , XIAP, YWHAE, YWHAG, ZDHHC11, ZDHHC21, ZDHHC3, ZUP1, ZMYND8, or ZMYND11.
11. The compound of any one of claims 1 to 10, wherein the modifier protein comprises BRD2, BRD3, BRD4, BRD7, BRD9, BRDT, CREBBP, PCAF, GCN5, p300, or PB1.
12. The compound of any one of claims 1 to 10, wherein the modifier protein comprises BRD2, BRD3, BRD4, or BRDT.
13. The compound of any one of claims 1 to 10, wherein the modifier protein comprises CREBBP or p300.
14. The compound of any one of claims 1 to 10, wherein the modifier protein comprises PCAF.
15. The compound of any one of claims 1 to 14, wherein the linker comprises: (a) polyethylene glycol, an aromatic group, an alkyl, an alkenyl, an alkyl phosphate, an alkyl siloxane, an epoxy, an amide, a sulfonamide, a sulfone, a sulfoxide, a sulfonate, a glycidyl, cycloalkane, spirocyclic cores, heterocycloalkane, a carboxylate, an anhydride, a piperazine, a piperidyl, a triazole, or a combination thereof; or (b) a polypeptide having a chain length of between 2 to 24 amino acids.
16. The compound of any one of claims 1 to 15, wherein the compound induces proximity between the target protein and modifier protein, thereby increasing the activity of the target protein.
17. The compound of any one of claims 1 to 16, wherein the compound induces proximity between the target protein and modifier protein, thereby activating/re-activating the target protein directly or activating/re-activating its downstream pathways.
18. The compound of any one of claims 1 to 17, wherein the compound has a structure of Formula (I):
R1 - L - R2 (i) wherein:
R1 is the targeting ligand with a structure of Formula (II):
R2 is a recruiting ligand;
L is a linker with the following structure: -(AP)m-L1A-L1B-(AP)m-;
AP is PEG, ether, amide, sulfonamide, sulfone, sulfoxide, sulfonate, phosphonate, ester, urea, carbamate, substituted phosphine oxide, optionally substituted C1-6 alkyl, optionally substituted C3-12 cycloalkyl, optionally substituted 3- to 12- membered heterocycloalkyl, optionally substituted 3- to 12- membered heteroaryl, or optionally substituted Ce-12 aryl;
L1A and L1B are each independently polyethylene glycol (PEG), C1-50 alkylene-PEG, C2-50 alkenylene-PEG, C2-50 alkynylene-PEG, C1-50 alkylene, C2-50 alkenylene, C2-50 alkynylene, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, 3- to 12- membered heteroaryl, 3- to 12- membered heterocycloalkyl-Ci-io alkylene, 3- to 12- membered heterocycloalkyl-PEG, or PEG-3- to 12- membered heterocycloalkyl-PEG, spirocyclic cores, or a combination thereof, each of which may be substituted with one or more halogen, deuterium, methyl, deuterated methyl, trifluoromethyl, amide, sulfonamide, sulfone, ester, urea, carbamate, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-naryl, or 3- to 12- membered heteroaryl;
RA is C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl or 3- to 12- membered heteroaryl;
Y1, Y2, Y3, Y4, Y5, and Y6 are each independently CH, C, NH, N, NO, S, SO, or absent, wherein at least two of Y1, Y2, Y3 and Y4 is CH, C, NH, N, NO, S, or SO, and wherein at least one of Y5 and Y6 is CH, C, NH, N, NO, S, or SO;
Y7 and Y8 are each independently C or N; R1A is a cysteine reactive group, C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, -SOR1A1, or -COR1A1, wherein the C1-6 alkyl and C3 -12 cycloalkyl is optionally substituted with -CN, halogen, or C1-6 alkylamines;
R1B is deuterium, halogen, -CN, -OH, -OC1-6 alkyl, -OC1-6 haloalkyl, -NH2, NHC1-6 alkyl, -N(C1-6 alkyl)2, -NHCOMe, -OCOMe, -OCONR1BAR1BB, C1-6 alkyl, -COOR1BB, -CONR1BAR1BB, - NR1BACOR1BB, _N02, _NRIBSO25 -SO2(C1-6alkyl), -SO2NR1BAR1BB, -SO2NH-heteroaryl, or two R1G taken together form an aryl or heteroaryl ring;
R1BA is hydrogen or C1-6 alkyl;
R1BB is hydrogen, -COC1-6 alkyl, Ci-ealkyl, Ce-12 aryl, 3- to 12- membered heteroaryl;
R1C is deuterium, halogen, -OH, -OC1-6 alkyl, -OC1-6 haloalkyl, -NH2, NHC1-6 alkyl, - N(C1-6 alkyl)2, -NO2, -NHCOMe, or -OCOMe;
R1D is hydrogen or C1-6 alkyl;
R1E is C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, or 3- to 12- membered heteroaryl, wherein the C1-6 alkyl, C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, and 3- to 12- membered heteroaryl are optionally substituted with halogen, C1-6 alkyl, C1-6 alkoxy, C1-6 carboxylic acid, -NH2, or -N(Ci-ealkyl)2; or R1D and R1E combine with the carbon to which is attached to form a cyclic structure, wherein the cyclic structure is C3-12 cycloalkyl, 3- to 12- membered heterocycloalkyl, Ce-12 aryl, and 3- to 12- membered heteroaryl, wherein the cyclic structure is optionally substituted with one or more R1DE;
R1DE is deuterium, halogen, -CN, -OH, -NH2, -NH(C1-6 alkyl), -NH(C1-6 haloalkyl), - N(C1-6 alkyl)2, -OC1-6 alkyl, -OC1-6 haloalkyl, C1-6 alkyl, C1-6 alkoxy, C1-6 haloalkyl, C1-6 haloalkoxy, -NHCO(C 1-6 haloalkyl), -CO2(C 1-6 alkyl), -CONH(C 1-6 alkyl), -SO2NH(C1-6 alkyl), - SO2N(C1-6 alkyl)2, -SO2(C1-6 alkyl), or -SO2NMe(C1-6 alkyl);
R1F is hydrogen or C1-6 alkyl; m is 0 or 1; n is 0 to 5; o is 0 or 1; and wherein an atom on one of R1B, R1DE, or R1E or the cyclic structure of R1D and R1E is covalently linked to L.
19. The compound of claim 18, wherein R1D and R1E combine to form a cyclic structure, wherein the cyclic structure is 3- to 7- membered heterocycloalkyl.
20. The compound of claim 19, wherein the cyclic structure is pyridinyl.
21. The compound of claim 18, wherein R1 has a structure of Formula (II-A): wherein:
RB is 3- to 12- membered heterocycloalkyl;
R1DE is deuterium, halogen, -OH, -OMe, -OCF3, -NH2, -NH(C1-6alkyl), or -N(C1-6alkyl)2; and p is 0 to 5.
22. The compound of claim 21, wherein R1 has a structure of Formula (II -B): wherein:
X1, X2, X3, and X4 are each independently C, CH, NH, N, NO, S, SO or absent, wherein at least two of X1, X2, X3, and X4 are C, CH, NH, N, NO, S, or SO; and p is 1 to 3.
23. The compound of claim 21, wherein the compound has a structure of Formula
(III- A) or Formula (III-B):
24. The compound of claim 23, wherein the compound has a structure of Formula (III-A1) or Formula (III-B1): wherein:
B is a absent, -NH-, -0-, CO, amide, C1-6 alkylene, C2-6 alkenylene, or C2-6 alkynylene, wherein the C1-6 alkylene, C2-6 alkenylene, and C2-6 alkynylene is optionally substituted with deuterium, halogen, or C1-3 alkoxy;
W1 and W2 are each independently NH, N, O, or S;
Rc and RD are each independently optionally substituted C3-12 cycloalkyl, optionally substituted 3- to 12- membered heterocycloalkyl, optionally substituted C6-12 aryl or optionally substituted 3- to 12- membered heteroaryl; and
R1H and R11 are each independently hydrogen or C1-6 alkyl, wherein the C1-6 alkyl is optionally substituted with deuterium or halogen.
25. The compound of claim 24, wherein B is C1-3 alkylene.
26. The compound of claim 25, wherein B is methylene.
27. The compound of any one of claims 24 to 26, wherein Rc and RD are each independently 3- to 7- membered heterocycloalkyl, Ce-io aryl, or 3- to 7- membered heteroaryl.
28. The compound of any one of claims 24 to 27, wherein the compound has a structure of Formula (III-A2) or Formula (III-B2):
(III-B2) wherein:
X1, X2, X3, and X4 are each independently C, CH, NH, N, NO, S, SO or absent, and wherein at least two of X1, X2, X3, and X4 is C, CH, NH, N, NO, S, SO.
29. The compound of claim 23, wherein R2 is: wherein:
X5, X6, X7, X8, and X14 are each independently C, CH, CD, CF, NH, N, NO, S, SO or absent, and wherein at least one of X5 and X6 is C, CH, CD, CF, NH, N, NO, S, or SO;
X9, X10, X11, X12, and X13 are each independently C, CH, CD, CF, NH, N, NO, S, SO or absent, and wherein at least two of X9, X10, X11, X12, and X13 are C, CH, CD, CF, CCH3, CCD3, CCF3, N, NH, NO, S, or SO;
R1Jis NH2, NH(C1-6 alkyl), N(C1-6 alkyl)2 or absent; and
Z is C=O, C=S, C-NH2, C-C1-6 alkyl, C-NH(C1-6 alkyl), NH, N(C1-6 alkyl), N, O, S, SO, SO2, or CH.
30. The compound of claim 29, wherein the compound has a structure of Formula
(IV-A), Formula (IV-B), Formula (IV-C), or Formula (IV-D):
31. The compound of claim 30, wherein the compound has a structure of Formula
(IV-A1), Formula (IV-B1), Formula (IV-C1), or Formula (IV-D1): wherein:
X1, X2, X3, and X4 are each independently CH, N, NO, S, SO or absent, and wherein at least two of X1, X2, X3, and X4 is CH, N, NO, S, SO;
R1B, R1C, and R1L are each independently halogen, -OH, -NH2, -NH(C1-6 alkyl), -NH(CI-6 alkyl)2, -OC1-6 alkyl, -OCH3, -OCF3, -NO2, -NHAc, or -OAc;
R1DE is halogen, deuterium, hydroxyl, trifluoromethoxy, or amine; or wherein when R1DE is in (R1DE)p-i, then R1DE is deuterium, halogen, -CN, -OH, -NH2, - NH(C 1-6 alkyl), -NH(C1-6haloalkyl), -OC1-6 alkyl, -OC1-6 haloalkyl, C1-6 alkyl, C1-6 haloalkyl, - NHCO(C1-6 haloalkyl), -CO2(C1-6 alkyl), -CONH(C1-6 alkyl), -SO2NH(C1-6 alkyl), -SO2N(C1-6 alkyl)2, -SO2(C 1-6 alkyl), or -SO2NMe(C1-6 alkyl); and q is 0 to 5.
32. The compound of claim 23, wherein R2 is: wherein:
X15, X16, X17, X18, and X19 are each independently C, CH, CMe, CCD3, N, NH, NMe, NCD3, CF, CD;
X20 is absent, -NH-, -CH2-, -CH(OH)-, -CH(C1-6alkyl)-, -NHCH2-, or -NHCH(Me)-;
X21 is C, CH, or N;
X22, and X23 are each independently C, CH, CO, N, NH, CNH2, or CO(C1-6 alkyl); and
X22 and X23 can optionally be linked to form a second 5- or 6- membered heterocycle, resulting in a fused bicycle.
33. The compound of claim 32, wherein the compound has a structure of Formula (IV-A2) or Formula (IV-C2):
(IV-C2).
34. The compound of any one of claims 18 to 33, wherein R1A is a cysteine reactive group or C1-6 alkyl, wherein the C1-6 alkyl is optionally substituted with halogen.
35. The compound of any one of claims 18 to 34, wherein R1B is -OC1-6 alkyl, -OC1-6 haloalkyl, -OCON(C1-6 alkyl)2, -SO2(C1-6 alkyl), or -SO2N(C1-6 alkyl)2.
36. The compound of any one of claims 18 to 35, wherein R1DEis deuterium, halogen, -OH, -OMe, or -OCF3.
37. The compound of any one of claims 18 to 36, wherein R1F is hydrogen or methyl.
38. The compound of any one of claims 18 to 37, wherein R1 is:
39. The compound of any one of claims 18 to 38, wherein R2 is: -QLZ- -I LZ,-
-LLZ-
40. The compound of any one of claims 18 to 39, wherein AP is:
41. The compound of any one of claims 18 to 40, wherein L1 is:
42. A compound represented by Formula V:
R1 - L - Y1
(V) or a pharmaceutically acceptable salt thereof; wherein:
R1 is one of the following:
• -(phenyl substituted with 0 or 1 C1-4 alkoxyl, 0 or 1 C1-4 deuteroalkoxyl, and 0, 1, or 2 occurrences of halo, hydroxyl, -S(O)2(C1-6 alkyl), or C1-4 alkyl)-N(R2)-(C2-4 alkynylene)-(indolyl substituted with C1-4haloalkyl and 0 or 1 -N(R3)-(3-6 membered saturated heterocyclyl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclyl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); or
• -(3-6 membered saturated heterocyclylene containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R2)-(indolyl substituted with C1-4haloalkyl and 0 or 1 -N(R3)-(C2-4alkynylene)-N(R2)-(phenyl substituted with 0 or 1 C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl or -S(O)2-(C1-4 alkyl));
R2, R3, R4 and independently hydrogen or C1-4 alkyl);
Y1 is one of the following: • -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5- membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(imidazo[4,5-b]pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))- (5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)- (pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); • -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl, and 5-membered heteroaryl)- (C1-6 alkylene substituted by 1 or 2 hydroxyl)-(phenyl or pyridinyl substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl), wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(pyridin-2- onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)- (5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); or
• -(phenylene or pyridinylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)-(pyridin-2-onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(O)-(pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, or 5- membered heteroaryl, wherein the 5 -membered heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R4)-(C1-6 alkylene)-(phenyl or pyridinyl substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl);
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl)-(5-10 membered heteroaryl substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and 5 -membered heteroaryl, wherein the 5- membered heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene, wherein the C1-6 alkylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of C1-4 alkyl and 6-membered heteroaryl); and
L is a bivalent, saturated or unsaturated, straight or branched C1-60 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -S-, - N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O)2-, -N(H)S(O)2-, -N(C1-6 alkyl)S(O)2-, -S(O)2N(H)-, -S(O)2N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, - C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6 alkyl)-, -N(H)C(O)O-, -N(C1-6 alkyl)C(O)O-, - N(C3-6 cycloalkyl)-, -C(H)(C3-6 cycloalkyl)-, optionally substituted 3-10 membered carbocyclyl, or optionally substituted 3-11 membered heterocyclyl containing 1, 2, 3, or 4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
43. The compound of claim 42, wherein R1 is -(phenyl substituted with 0 or 1 C1-4 alkoxyl, 0 or 1 C1-4 deuteroalkoxyl, and 0, 1, or 2 occurrences of halo, hydroxyl, -S(O)2(C1-6 alkyl), or C1-4 alkyl)-N(R2)-(C2-4 alkynylene)-(indolyl substituted with C1-4 haloalkyl and 0 or 1 - N(R3)-(3-6 membered saturated heterocyclyl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclyl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
44. The compound of claim 42, wherein R1 is -(3-6 membered saturated heterocyclylene containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclylene is substituted by 0, 1, or 2 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-N(R2)-(indolyl substituted with C1-4 haloalkyl and 0 or 1 -N(R3)-(C2-4alkynylene)-N(R2)-(phenyl substituted with 0 or 1 C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl or -S(O)2-(C1-4 alkyl)).
45. The compound of claim 42, wherein R1 is
46. The compound of any one of claims 42 to 45, wherein Y1 is -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)- (benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, - N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
47. The compound of any one of claims 42 to 45, wherein Y1 is -
(benzo [d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, - N(R2)2, or -(C1-4 alkylene)-(3-7 membered heterocyclyl))-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
48. The compound of any one of claims 42 to 45, wherein Y1 is -(imidazo[4,5- b]pyridinylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, C1-4 alkyl, -N(R2)2, or - (C1-4 alkylene)-(3-7 membered heterocyclyl))-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
49. The compound of any one of claims 42 to 45, wherein Y1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)-(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
50. The compound of any one of claims 42 to 45, wherein Y1 is -(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5- membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
51. The compound of any one of claims 42 to 45, wherein Y1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, C1-4 alkyl, and 5-membered heteroaryl)-(C1-6 alkylene substituted by 1 or 2 hydroxyl)- (phenyl or pyridinyl substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl), wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
52. The compound of any one of claims 42 to 45, wherein Y1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(pyridin-2-onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
53. The compound of any one of claims 42 to 45, wherein Y1 is -(phenylene or pyridinylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)-(pyridin-2-onylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
54. The compound of any one of claims 42 to 45, wherein Y1 is one of the following:
55. The compound of any one of claims 42 to 54, wherein L is a bivalent, saturated or unsaturated, straight or branched C5-30 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, - C(O)-, -S(O)-, -S(O)2-, -N(H)S(O)2-, -N(C1-6 alkyl)S(O)2-, -S(O)2N(H)-, -S(O)2N(C1-6 alkyl)-, - N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, -C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6 alkyl)-, optionally substituted 3-10 membered carbocyclyl, or optionally substituted 3-11 membered heterocyclyl containing 1, 2, 3, or 4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
56. The compound of any one of claims 42 to 54, wherein L is a bivalent, saturated or unsaturated, straight or branched C5-30 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, - C(O)-, -S(O)-, -S(O)2-, -N(H)S(O)2-, -N(C1-6 alkyl)S(O)2-, -S(O)2N(H)-, or -S(O)2N(C1-6 alkyl)-.
57. A compound represented by Formula VI:
R1 - L - Y1
(VI) or a pharmaceutically acceptable salt thereof; wherein:
R1 is -(phenyl substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-N(R2)-(C2-4alkynylene)-(indolyl substituted with C1-4haloalkyl and -N(R3)-(3-6 membered saturated heterocyclyl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heterocyclyl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl);
R2, R3, R4 and independently hydrogen or C1-4 alkyl);
Y1 is one of the following:
• -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-(benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); or
• -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)- (pyridinylene substituted with C 1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5-membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl); and L is a bivalent, saturated or unsaturated, straight or branched C1-60 hydrocarbon chain, wherein 0-20 methylene units of the hydrocarbon are independently replaced with -O-, -S-, - N(H)-, -N(C1-6 alkyl)-, -OC(O)-, -C(O)O-, -C(O)-, -S(O)-, -S(O)2-, -N(H)S(O)2-, -N(C1-6 alkyl)S(O)2-, -S(O)2N(H)-, -S(O)2N(C1-6 alkyl)-, -N(H)C(O)-, -N(C1-6 alkyl)C(O)-, -C(O)N(H)-, - C(O)N(C1-6 alkyl)-, -OC(O)N(H)-, -OC(O)N(C1-6 alkyl)-, -N(H)C(O)O-, -N(C1-6 alkyl)C(O)O-, - N(C3-6 cycloalkyl)-, -C(H)(C3-6 cycloalkyl)-, optionally substituted 3-10 membered carbocyclyl, or optionally substituted 3-11 membered heterocyclyl containing 1, 2, 3, or 4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
58. The compound of claim 57, wherein R1 is -(phenyl substituted with methoxy and 0 or 1 occurrences of halo, hydroxyl, or C1-4 alkyl)-N(R2)-(C3 alkynylene)-(indolyl substituted with -CH2CF3 and -N(R3)-(piperidinyl substituted by 1 or 2 substituents independently selected from the group consisting of fluoro and methyl).
59. The compound of claim 57, wherein R1 is
60. The compound of claim 57, wherein R1 is
61. The compound of any one of claims 57 to 60, wherein Y1 is -(phenylene or pyridinylene, each of which is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)- (benzo[d]imidazolylene substituted with 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)- (5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
62. The compound of any one of claims 57 to 60, wherein Y1 is -(phenylene substituted by 0 or 1 substituent independently selected from the group consisting of halo and C1-4 alkyl)-(C1-4 alkylene)-(benzo[d]imidazolylene substituted with 0 or 1 occurrences of halo or C1-4 alkyl)-(5-isoxazolyl substituted by 1, 2, or 3 C1-4 alkyl).
63. The compound of any one of claims 57 to 60, wherein Y1 is -(phenylene substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl)-(C1-6 alkylene)-N(R4)-(pyridinylene substituted with C1-4 alkoxyl and 0, 1, or 2 occurrences of halo, hydroxyl, or C1-4 alkyl)-(5 -membered heteroaryl containing 1 or 2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein the heteroaryl is substituted by 0, 1, 2, or 3 substituents independently selected from the group consisting of halo, hydroxyl, and C1-4 alkyl).
64. The compound of any one of claims 57 to 60, wherein Y1 is -(phenylene substituted by 0 or 1 substituent independently selected from the group consisting of halo and C1-4 alkyl)-(C1-4 alkylene)-N(R4)-(pyridinylene substituted with C1-4 alkoxyl and 0 or 1 occurrences of halo or C1-4 alkyl)-(isoxazolyl substituted by 1, 2, or 3 C1-4 alkyl).
65. The compound of any one of claims 57 to 60, wherein Y1 is one of the following:
66. The compound of any one of claims 57 to 65, wherein L is -S(O)2N(C1-6 alkyl)-, - S(0)2N(C1-6 alkyl)-(Co-6-alkylene)-(3-6 membered heterocyclyl containing 1 nitrogen atom)- C(O)-, -S(O)2N(C1-6 alkyl)-(C3-6-cycloalkylene)-N(H)C(O)-, or -S(O)2N(C1-6 alkyl)-(C3-6- cycloalkylene)-(C1-6-alkylene)-N(H)C(O)-.
67. A compound in any one of Tables 1-5 or a pharmaceutically acceptable salt thereof.
68. A pharmaceutical composition comprising a compound of any one of claims 1 to 67 and a pharmaceutically acceptable carrier.
69. A method of treating cancer, comprising administering to a patient in need thereof a therapeutically effective amount of a compound of any one of claims 1 to 67 to treat the cancer.
70. The method of claim 69, wherein the cancer is a solid tumor.
71. The method of claim 69, wherein the cancer is ovarian cancer, uterine cancer, endometrial cancer, cervical cancer, prostate cancer, testicular cancer, breast cancer, brain cancer, lung cancer, oral cancer, esophageal cancer, head and neck cancer, stomach cancer, colon cancer, rectal cancer, skin cancer, sebaceous gland carcinoma, bile duct cancer, gallbladder cancer, liver cancer, pancreatic cancer, bladder cancer, urinary tract cancer, kidney cancer, eye cancer, thyroid cancer, lymphoma, or leukemia.
72. The method of claim 69, wherein the cancer is ovarian cancer, endometrial cancer, cervical cancer, or breast cancer.
73. The method of any one of claims 69 to 72, wherein the cancer has p53 mutation.
74. A method of causing death of a cancer cell, comprising contacting a cancer cell with an effective amount of a compound of any one of claims 1 to 67 to cause death of the cancer cell.
75. The method of claim 74, wherein the cancer cell is selected from an ovarian cancer, uterine cancer, endometrial cancer, cervical cancer, prostate cancer, testicular cancer, breast cancer, brain cancer, lung cancer, oral cancer, esophageal cancer, head and neck cancer, stomach cancer, colon cancer, rectal cancer, skin cancer, sebaceous gland carcinoma, bile duct cancer, gallbladder cancer, liver cancer, pancreatic cancer, bladder cancer, urinary tract cancer, kidney cancer, eye cancer, thyroid cancer, lymphoma, or leukemia cell.
76. The method of claim 74, wherein the cancer cell is an ovarian cancer, endometrial cancer, cervical cancer, or breast cancer.
77. The method of any one of claims 74 to 76, wherein the cancer cell has a p53 mutation.
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Citations (2)

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WO2022225728A2 (en) * 2021-04-09 2022-10-27 The Broad Institute, Inc. Bifunctional molecules for selective modification of target substrates
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WO2022225728A2 (en) * 2021-04-09 2022-10-27 The Broad Institute, Inc. Bifunctional molecules for selective modification of target substrates
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