[go: up one dir, main page]

WO2024076728A1 - Nucléotides cycliques et leurs utilisations - Google Patents

Nucléotides cycliques et leurs utilisations Download PDF

Info

Publication number
WO2024076728A1
WO2024076728A1 PCT/US2023/034632 US2023034632W WO2024076728A1 WO 2024076728 A1 WO2024076728 A1 WO 2024076728A1 US 2023034632 W US2023034632 W US 2023034632W WO 2024076728 A1 WO2024076728 A1 WO 2024076728A1
Authority
WO
WIPO (PCT)
Prior art keywords
groups
group
analog
composition
derivative
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.)
Ceased
Application number
PCT/US2023/034632
Other languages
English (en)
Inventor
Matthew Meyerson
Douglas Wheeler
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.)
Dana Farber Cancer Institute Inc
Broad Institute Inc
Original Assignee
Dana Farber Cancer Institute Inc
Broad Institute Inc
Priority date (The priority date 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 date listed.)
Filing date
Publication date
Application filed by Dana Farber Cancer Institute Inc, Broad Institute Inc filed Critical Dana Farber Cancer Institute Inc
Publication of WO2024076728A1 publication Critical patent/WO2024076728A1/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7115—Nucleic acids or oligonucleotides having modified bases, i.e. other than adenine, guanine, cytosine, uracil or thymine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/712—Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7125—Nucleic acids or oligonucleotides having modified internucleoside linkage, i.e. other than 3'-5' phosphodiesters
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators

Definitions

  • Second messenger molecules released by the cell in response to extracellular signaling molecules can trigger intracellular signal transduction cascades, and include cyclic adenosine monophosphate and cyclic guanosine monophosphate. Novel second messengers generated in human cells in response to challenges to the innate immune system.
  • compositions comprising a cyclic dinucleotide molecule, a cyclic trinucleotide molecule, an analog or derivative thereof, or any combination thereof.
  • a composition comprises a cyclic dinucleotide molecule comprising a cytidine moiety and an adenosine moiety (cCAMP molecule), a cyclic trinucleotide molecule comprising an adenosine moiety and two cytidine moieties (cACCMP molecule), an analog or derivative thereof, or any combination thereof.
  • a composition comprises an n’,n’ cyclic cytidine monophosphate-adenosine monophosphate analog (n’,n’ cCAMP analog), wherein each n’ is 2’ or 3’, an n’,n’,n’ cyclic adenosine monophosphate-cytidine monophosphate cytidine analog (n’,n’,n’ cACCMP analog), wherein each n’ is 2’ or 3’, an analog or derivative thereof, or any combination thereof.
  • a composition is according to:
  • a composition is according to:
  • a composition is an isonucleotide analog of any one of the previous embodiments.
  • an isonucleotide analog of any one of the previous embodiments comprises one or more sugar ring(s), each comprising the adenosine or the cytosine group at the 2’ carbon position versus the 1’ carbon position, and the R1 group at the 1 ’ carbon position versus the 2’ carbon position.
  • composition is a cCAMP isonucleotide analog according to:
  • R6 or R7 is an adenine moiety or an analog or derivative thereof, and, when not an adenine moiety or an analog or derivative thereof, R6 or R7 is selected from hydrogen, hydroxyl, and fluorine groups;
  • R8 or R9 is a cytidine moiety or an analog or derivative thereof, and, when not a cytidine moiety or an analog or a derivative thereof, R8 or R9 is selected from hydrogen, hydroxyl, and fluorine groups; each RIO is independently selected from oxygen and sulfur groups; and each R11 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R11 is optionally further substituted.
  • composition is a cACCMP isonucleotide analog wherein:
  • R6 or R7 is an adenine group or an analog or derivative thereof, and, when not an adenine group or an analog or derivative thereof, R6 or R7 is selected from hydrogen, hydroxyl, and fluorine groups; at each occurrence, R8 or R9 is a cytidine group or an analog or derivative thereof, and, at each occurrence, when not a cytidine group or an analog or a derivative thereof, R8 or R9 is selected from hydrogen, hydroxyl, and fluorine groups; each RIO is independently selected from oxygen and sulfur groups; and each R11 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R11 is optionally further substituted.
  • the adenine moiety of an isonucleotide analog of any one of the previous embodiments is according to: analog or derivative thereof; and/or the cytidine moiety of an isonucleotide analog of any one of the previous embodiments is according to: analog or derivative thereof; wherein each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and a detectable labels, and wherein each R4 can be optionally further substituted.
  • a composition is according to any one of the previous embodiments, wherein Rl, R6 or R7, and/or R8 or R9 is/are a fluorine group; R2 or R10 is a sulfur group; R3 or Rl 1 is selected from a methyl group, a hydroxyl group, and alkoxyl (-OR5) groups, wherein R5 is a C1-C10 alkyl group optionally substituted with a C1-C10 alkyl ester group, optionally wherein R5 is a group; and/or R4 is selected from a hydrogen group, a methyl group, and an alkyne group selected from cycloalkyne groups, optionally wherein the cycloalkyne group is a cyclooctyne group, or a detectable label, optionally selected from biotin, fluorophore, and a radiolabel.
  • a composition is according to any one of the previous embodiments, wherein the composition is a prodrug composition.
  • Illa, Illb, inc, Illd, or IV is according to:
  • R11 of a composition according to Formula III, Illa, Illb, inc, Hid, or IV is selected from a hydroxyl and alkoxyl (-OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group.
  • group, and/or the composition is a prodrug composition.
  • the present disclosure provides pharmaceutical compositions comprising one or more composition(s) of any one of the previous embodiments, or pharmaceutically acceptable salt(s) thereof.
  • the present disclosure provides methods of modulating immune signaling in a cell.
  • a method comprises administering one or more composition(s) of any one of the previous embodiments to the cell.
  • the present disclosure provides methods of modulating an immune signaling in a subject in need thereof.
  • a method of any one of the previous embodiments comprises administering an effective amount of one or more pharmaceutical composition(s) of any one of the previous embodiments to the subject.
  • a method of any one of the previous embodiments administers composition(s) or pharmaceutical composition(s) of any one of the previous embodiments via a delivery vehicle comprising liposomes, lipid particles, or nanoparticles.
  • the present disclosure provides methods of identifying one or more pathways modulated by one or more composition(s) of any one of the previous embodiments.
  • a method comprises delivering the composition(s) to a cell, and evaluating differential expression of one or more genes of the one or more pathways by RNAseq to thereby identify the one or more pathways.
  • FIG. 1 depiction of methodology approach for discovery of example molecules.
  • FIG. 2 - depiction of 2D metabolomics approach reveals a diverse array of dsRNA- induced second messengers.
  • FIG. 3A-3B - (A) schematic showing method of discovery using linkage and basespecific nuclease to enable the diagnosis of molecule structure of unknown molecules; (B) digestion with enzymes enables assignment of structure to example novel metabolites.
  • FIG. 4 depiction of analytical results and predicted structure identifying 3’,3’- cCAMP.
  • FIG. 5A-5B - (A) sensitivity and resistance to enzymes rule out a linear structure for putative cCAMP; (B) sensitivity and resistance to enzymes suggest cCAMP is 3’,3’-cCAMP.
  • FIG. 6 example alternative phosphodiester linkage isomers of cCAMP, circles indicate chemical modification relative to natural 3’,3’-cCAMP.
  • FIG. 7 example fluorinated analogs of cCAMP, circles indicate chemical modification relative to natural 3 ’,3 ’-cCAMP.
  • FIG. 8 example phosphorothioate analogs of cCAMP, circles indicate chemical modification relative to natural 3 ’,3 ’-cCAMP.
  • FIG. 9 example methylphosphonate analogs of cCAMP, circles indicate chemical modification relative to natural 3 ’,3 ’-cCAMP.
  • FIG. 10 example base modified analogs of cCAMP, circles indicate chemical modification relative to natural 3 ’,3 ’-cCAMP.
  • FIG. 11 depiction of analytical results and predicted structure identifying 3’,3’,3’- cACCMP
  • FIG. 12 example alternative phosphodiester linkage isomers of cACCMP, circles indicate chemical modification relative to natural 3’,3’,3’-cCAMP.
  • FIG. 13 example fluorinated analogs of cACCMP, circles indicate chemical modification relative to natural 3 ’,3 ’,3 ’-cACCMP.
  • FIG. 14 example phosphorothioate analogs of cACCMP, circles indicate chemical modification relative to natural 3’, 3’3’, -cACCMP.
  • FIG. 15 example methylphosphonate analogs of cACCMP, circles indicate chemical modification relative to natural 3 ’,3 ’,3’- cACCMP.
  • FIG. 16 example base modified analogs of cACCMP, circles indicate chemical modification relative to natural 3 ’,3 ’,3’- cACCMP.
  • FIG. 17 example cCAMP nucleotides and/or isonucleotides, where: if R1 is an adenine group, then R2 is either H, OH, or F; if R2 is an adenine group, then R1 is H or OH; if R3 is a cytosine group, then R4 is either H, OH or F; if R4 is a cytosine group, then R3 is H or OH; and/or where R5 is either an H or a handle, an acyl group with carbon tail, etc.
  • FIG. 18 example 3’,3’-cCAMP with an isonucleotidic AMP group.
  • FIG. 19 example 3’,3’-cCAMP with an isonucleotidic CMP group.
  • FIG. 20 example cACCMP nucleotides and/or isonucleotides, where: if R1 is an adenine group, then R2 is either H, OH, or F; if R2 is an adenine group, then R1 is H or OH; if R3 is a cytosine group, then R4 is either H, OH or F; if R4 is a cytosine group, then R3 is H or OH; and/or where R5 is either an H or a handle, an acyl group with carbon tail, etc.
  • a “biological sample” can contain whole cells and/or live cells and/or cell debris.
  • the biological sample can contain (or be derived from) a “bodily fluid”.
  • the present invention encompasses embodiments wherein the bodily fluid is selected from amniotic fluid, aqueous humour, vitreous humour, bile, blood serum, breast milk, cerebrospinal fluid, cerumen (earwax), chyle, chyme, endolymph, perilymph, exudates, feces, female ejaculate, gastric acid, gastric juice, lymph, mucus (including nasal drainage and phlegm), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheum, saliva, sebum (skin oil), semen, sputum, synovial fluid, sweat, tears, urine, vaginal secretion, vomit and mixtures of one or more thereof.
  • Biological samples include cell cultures, bodily fluids,
  • subject refers to a vertebrate, preferably a mammal, more preferably a human.
  • Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals, and pets. Tissues, cells and their progeny of a biological entity obtained in vivo or cultured in vitro are also encompassed.
  • group refers to a chemical entity that is monovalent (i.e., comprises one terminus that can be covalently bonded to other chemical species), divalent, or polyvalent (i.e., comprises two or more termini that can be covalently bonded to other chemical species).
  • group also includes radicals (e.g., monovalent and multivalent, such as, for example, divalent radicals, trivalent radicals, and the like).
  • radicals e.g., monovalent and multivalent, such as, for example, divalent radicals, trivalent radicals, and the like.
  • Illustrative, non-limiting examples of groups include:
  • aliphatic group refers to branched or unbranched hydrocarbon groups that, optionally, contain one or more degree(s) of unsaturation. Degrees of unsaturation include, but are not limited to, carbon-carbon double bonds and carbon-carbon triple bonds. Non-limiting examples, of aliphatic groups with one or more degree(s) of unsaturation include alkenyl groups, alkynyl groups, and aliphatic cyclic groups, and the like. An aliphatic group can be an alkyl group.
  • an aliphatic group is a Ci to C20 aliphatic group, including all integer numbers of carbons and ranges of numbers of carbons therebetween (e.g., Ci, C2, C3, C4, C5, C6, C7, C8, C9, C10, Cll, C12, C13, C14, C15, C16, C17, C18, C19, and C20, Cl to C10. C3 to C10, and C5 to C10).
  • An aliphatic group can be unsubstituted or substituted with one or more substituent(s).
  • substituent groups include, but are not limited to, various substituents such as, for example, halide groups (-F, -Cl, -Br, and -I), aliphatic groups (e.g., alkyl groups (e.g., a Cl to C30 alkyl groups (e.g., methyl, ethyl, propyl, and the like), monocycloalkyl groups (e.g., cyclohexyl, cyclopentyl, and the like), polycycloalkyl groups (e.g., bicyclic groups, and the like), alkenyl groups, alkynyl groups, and the like), halogenated aliphatic groups (e.g., trifluoromethyl group and the like), aryl groups (e.g., phenyl group and the like), polyaryl groups (e.g., pyrenyl group, and the like), halogenated aryl groups, hydroxyl groups, amine groups,
  • alkyl groups include, but are not limited to, methyl groups, ethyl groups, propyl groups, butyl groups, isopropyl groups, tert-butyl groups, cyclohexyl groups, and structural analogs thereof.
  • a substituent group of an aliphatic group can be further substituted with one or more substituent group(s) described herein.
  • alkyl group refers to branched or unbranched hydrocarbon groups that include only single bonds between carbon atoms (not including substituent(s), if any).
  • an alkyl group is a saturated group.
  • an alkyl group is a Ci to C20 alkyl group, including all integer numbers of carbons and ranges of numbers of carbons therebetween (e.g., Ci, C2, C3, C4, C5, C6, C7, C8, C9, C10, Cll, C12, C13, C14, C15, C16, C17, C18, C19, and C20, Cl to C10. C3 to C10, and C5 to C10).
  • an alkyl group is a cycloalkyl group, e.g., a monocycloalkyl group or a polycycloalkyl group (e.g. bicyclic and the like). In various examples, an alkyl group is unsubstituted or substituted with one or more substituent group(s).
  • substituent groups include, but are not limited to, various substituents such as, for example, halide groups (-F, -Cl, - Br, and -I), aliphatic groups (e.g., alkyl groups (e.g., a Cl to C20 alkyl groups (e.g., methyl, ethyl, propyl, and the like), monocycloalkyl groups (e.g., cyclohexyl, cyclopentyl, and the like), polycycloalkyl groups (e.g., bicyclic groups, and the like), alkenyl groups, alkynyl groups, and the like), halogenated aliphatic groups (e.g., trifluoromethyl group and the like), aryl groups (e.g., phenyl group and the like), polyaryl groups (e.g., pyrenyl group, and the like), halogenated aryl groups, hydroxyl groups, amine groups, nitro
  • alkyl groups include, but are not limited to, methyl groups, ethyl groups, propyl groups, butyl groups, isopropyl groups, tert-butyl groups, cyclohexyl groups, and structural analogs thereof.
  • a substituent group of an alkyl group can be further substituted with one or more substituent group(s) described herein.
  • alkenyl group refers to branched or unbranched hydrocarbon groups comprising one or more C-C double bond(s).
  • alkenyl groups include, but are not limited to, an ethenyl (vinyl) group, 1 -propenyl groups, 2- propenyl (allyl) groups, 1-, 2-, and 3-butenyl groups, isopropenyl groups, and the like.
  • an alkenyl group is a Ci to C20 alkenyl group, including all integer numbers of carbons and ranges of numbers of carbons therebetween (e.g., Ci, C2, C3, C4, C5, C6, C7, C8, C$>, C10, Cu, C12, C13, C14, C15, C16, C17, C18, C19, and C20, Cl to C10. C3 to C10, and C5 to C10).
  • An alkenyl group can be unsubstituted or substituted with one or more substituent(s).
  • substituent groups include, but are not limited to, various substituents such as, for example, halide groups (- F, -Cl, -Br, and -I), aliphatic groups (e.g., alkyl groups (e.g., a Cl to C30 alkyl groups (e.g., methyl, ethyl, propyl, and the like), monocycloalkyl groups (e.g., cyclohexyl, cyclopentyl, and the like), polycycloalkyl groups (e.g., bicyclic groups, and the like), alkenyl groups, alkynyl groups, and the like), halogenated aliphatic groups (e.g., trifluoromethyl group and the like), aryl groups (e.g., phenyl group and the like), polyaryl groups (e.g., pyrenyl group, and the like), halogenated aryl groups, hydroxyl groups, amine groups,
  • alkyl groups include, but are not limited to, methyl groups, ethyl groups, propyl groups, butyl groups, isopropyl groups, tert-butyl groups, cyclohexyl groups, and structural analogs thereof.
  • a substituent group of an alkenyl group can be further substituted with one or more substituent group(s) described herein.
  • alkynyl group refers to branched or unbranched hydrocarbon groups comprising one or more C-C triple bond(s).
  • alkynyl groups include, but are not limited to an ethyne group, 1- and 2-propyne groups, 1-, 2-, and 3-butyne groups, and the like.
  • an alkynyl group is a Ci to C20 alkynyl group, including all integer numbers of carbons and ranges of numbers of carbons therebetween (e.g., Cl, C2, C3, C4, C5, C6, C7, C8, C 9 , C10, Cll, C12, C13, C14, C15, C16, C17, C18, C19, and C20, Cl to C10, C3 to C10, and C5 to C10).
  • An alkynyl group can be unsubstituted or substituted with one or more substituent(s).
  • An alkynyl group can be unsubstituted or substituted with one or more substituent(s).
  • substituent groups include, but are not limited to, various substituents such as, for example, halide groups (-F, -Cl, -Br, and -I), aliphatic groups (e.g., alkyl groups (e.g., a Cl to C30 alkyl groups (e.g., methyl, ethyl, propyl, and the like), monocycloalkyl groups (e.g., cyclohexyl, cyclopentyl, and the like), poly cycloalkyl groups (e.g., bicyclic groups, and the like), alkenyl groups, alkynyl groups, and the like), halogenated aliphatic groups (e.g., trifluoromethyl group and the like), aryl groups (e.g., phenyl group and the like), polyaryl groups (e.g., pyrenyl group, and the like), halogenated aryl groups, hydroxyl groups, amine groups,
  • alkyl groups include, but are not limited to, methyl groups, ethyl groups, propyl groups, butyl groups, isopropyl groups, tert-butyl groups, cyclohexyl groups, and structural analogs thereof.
  • a substituent group of an alkynyl group can be further substituted with one or more substituent group(s) described herein.
  • aryl group refers to C5 to C30 aromatic or partially aromatic carbocyclic groups, including all integer numbers of carbons and ranges of numbers of carbons therebetween (e.g., C5, C6, C7, C8, C9, C10, Cll, C12, C13, C14, C15, C16, C17, C18, C19 C20, C21, C22, C23, C24, C25, C26, C27, C28, C29, and C30).
  • Aryl groups can comprise polyaryl groups such as, for example, fused ring groups, biaryl groups, and the like, and any combination thereof.
  • the aryl group is unsubstituted or substituted with one or more substituent group(s).
  • substituent groups include, but are not limited to, substituents such as, for example, halide groups (-F, -Cl, -Br, and -I), aliphatic groups (e.g., alkyl groups, alkenyl groups, alkynyl groups, and the like), halogenated aliphatic groups (e.g., trifluoromethyl group and the like), aryl groups, halogenated aryl groups, hydroxyl groups, amine groups, nitro groups, cyano groups, isocyano groups, silyl groups, alkoxide groups, alcohol groups, ether groups, ketone groups, carboxylate groups, carboxylic acid groups, ester groups, amide groups, thioether groups, structural analogs thereof, and the like, and any combination thereof.
  • Aryl groups can contain hetero atoms, such as, for example, oxygen, nitrogen (e.g., pyridinyl groups and the like), sulfur, and the like, and any combination thereof.
  • aryl groups include, but are not limited to, phenyl groups, biaryl groups (e.g., biphenyl groups and the like), fused ring groups (e.g., naphthyl groups and the like), hydroxybenzyl groups, tolyl groups, xylyl groups, furanyl groups, benzofuranyl groups, indolyl groups, imidazolyl groups, benzimidazolyl groups, pyridinyl groups, structural analogs thereof, and the like.
  • a substituent group of an aryl group can be further substituted with one or more substituent group(s) described herein.
  • analog refers to any compound or group that can be envisioned to arise from an original compound or group, respectively, if one atom or group of atoms, functional groups, or substructures is replaced with another atom or group of atoms, functional groups, substructures, or the like. Examples of analogs include, but are not limited to isomers, homologs, and the like. In various examples, an analog is not a functional analog (e.g., does not exhibit significantly different physical, chemical, biochemical, or pharmacological properties from the original compound or group).
  • the term “derivative” refers to any compound or group that is derived from an original compound or group, respectively, by a chemical reaction, where the compound or group is modified or partially substituted such that at least one structural feature of the original compound or group is retained.
  • “Diastereoisomers” are stereoisomers that have at least two asymmetric atoms, but which are not mirror-images of each other. The absolute stereochemistry is specified according to the Cahn-Ingold-Prelog R-S system When a compound is an enantiomer, the stereochemistry at each chiral carbon can be specified by either R or S.
  • Resolved compounds whose absolute configuration is unknown can be designated (+) or (-) depending on the direction (dextro- or levorotatory) which they rotate plane polarized light at the wavelength of the sodium D line.
  • Certain of the compounds described herein contain one or more asymmetric centers and can thus give rise to enantiomers, diastereomers, and other stereoisomeric forms that can be defined, in terms of absolute stereochemistry at each asymmetric atom, as (R)- or (S)-.
  • the present chemical entities, pharmaceutical compositions and methods are meant to include all such possible isomers, including racemic mixtures, optically substantially pure forms and intermediate mixtures.
  • stereocenters can be identified with "wavy" bonds indicating that the stereocenter can be in the R or S configuration, unless otherwise specified. However, stereocenters without a wavy bond (i.e., a "straight" bond) can also be in the (R) or (S) configuration, unless otherwise specified.
  • Compositions comprising compounds can comprise stereocenters which each can independently be in the (R) configuration, the (S) configuration, or racemic mixtures.
  • a bond substitution coming out of a ring means that the substitution can be at any of the available position on the ring.
  • Embodiments disclosed herein provide cyclic nucleotides generated in cells in response to innate immune stimulation with double stranded RNA (dsRNA).
  • the molecules disclosed herein can be useful as chemical tools or therapeutic agents, as cellular receptors for the molecules are likely modulated by the cyclic nucleotides.
  • Cyclic dinucleotide molecules and cyclic trinucleotide molecules are provided.
  • cyclic CMP -AMP molecules cyclic CMP -AMP molecules
  • cACCMP molecules cyclic AMP-CMP-CMP molecules
  • Compositions of the cyclic nucleotide molecules, including analogs or derivatives thereof are also provided.
  • Nonnatural analogs and derivatives of the molecules are also provided.
  • Example nonnatural analogs include isonucleotide analogs.
  • Example nonnatural analogs include isomers with phosphodiester linkages. Such isomers with nonnatural phosphodiester linkages can modulate target specificity or biological activity.
  • Cyclic analogs can comprise additional functional groups, for example, one or more fluorines, to enhance cell permeability.
  • Cyclic nucleotide derivatives and analogs detailed herein are provided with enhanced nuclease resistance relative to the naturally occurring cyclic nucleotides, for example, via phosphorothioation or methylphosphonation.
  • cyclic nucleotides modified via labels, e.g., biotin, or other modification, e.g., methylation are also provided and can be useful for applications including chemical probes.
  • Molecules and compositions can be utilized in methods, including methods of modulating immune signaling in a cell.
  • the molecule or composition is administered via a delivery vehicle.
  • methods of identifying one or more pathways modulated by the cyclic nucleotide molecules and compositions are provided.
  • Cyclic nucleotide compositions comprising a cyclic dinucleotide molecule comprising a cytidine moiety and an adenosine moiety, a cyclic trinucleotide molecule comprising an adenosine moiety and two cytidine moieties, an analog or derivative thereof, or any combination thereof are detailed herein.
  • cCAMP Molecules comprising a cyclic dinucleotide molecule comprising a cytidine moiety and an adenosine moiety, a cyclic trinucleotide molecule comprising an adenosine moiety and two cytidine moieties, an analog or derivative thereof, or any combination thereof are detailed herein.
  • compositions detailed herein comprise a cyclic dinucleotide molecule, an analog or derivative thereof, or any combination thereof.
  • the cyclic dinucleotide molecule comprises one adenosine monophosphate and one cytidine monophosphate (cCAMP molecule).
  • the cCAMP molecule comprises a phosphodiester linkage analog (e.g., a phosphodiester linkage isomer).
  • the cyclic dinucleotide molecule is an n’,n’ cCAMP analog, wherein each n’ is 2’ or 3’ (e.g., where n’,n’ indicates the carbon numbers of the AMP and CMP sugar rings, respectively, linked by a phosphodiester linkage to the 5’ sugar ring carbon of the CMP and AMP sugar rings, respectively).
  • a composition comprising a cCAMP molecule, analog or derivative thereof, or any combination thereof is a pharmaceutically active composition.
  • a composition comprising a cCAMP molecule, analog or derivative thereof, or any combination thereof is a prodrug composition.
  • the cCAMP molecule is a 3’3’ cCAMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R3 is optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups and detectable labels, wherein each R4 is optionally further substituted.
  • the cCAMP molecule is a 2’, 3’ cCAMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R3 is optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups and detectable labels, wherein each R4 is optionally further substituted.
  • the cCAMP molecule is a 3 ’,2’ cCAMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R3 is optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups and detectable labels, wherein each R4 is optionally further substituted.
  • the cCAMP molecule is a 2’, 2’ cCAMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from, oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R3 is optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups and detectable labels, wherein each R4 is optionally further substituted.
  • compositions according to any one of Formula la, lb, Ic, or Id can have various substituent groups.
  • R1 is a fluorine group.
  • R2 is a sulfur group.
  • R3 is a methyl group.
  • R3 is selected from a hydroxyl group and alkoxyl (-OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group.
  • R5 is a group.
  • the composition is a prodrug composition.
  • R5 is a group and the composition is a prodrug composition.
  • R4 is a hydrogen group.
  • R4 is a methyl group.
  • R4 is an alkyne group selected from cycloalkyne and groups, optionally wherein the cycloalkyne group is a cyclooctyne group.
  • R4 is a detectable label, optionally selected from biotin, fluorophore, and a radiolabel.
  • compositions detailed herein comprise a cyclic trinucleotide molecule, an analog or derivative thereof, or any combination thereof.
  • the cyclic trinucleotide molecule comprises one adenosine monophosphate and two cytidine monophosphates (cACCMP molecule).
  • the cyclic trinucleotide is an n’,n’,n’ cACCMP analog, wherein each n’ is 2’ or 3’ (e.g., where n’,n’,n’ indicates the carbon numbers of the AMP, first CMP, and second CMP sugar rings, respectively, linked by a phosphodiester linkage to the 5’ sugar ring carbon of the first CMP, the second CMP, and the AMP sugar rings, respectively).
  • a composition comprising a cACCMP molecule, analog or derivative thereof, or any combination thereof is a pharmaceutical composition.
  • a composition comprising a cACCMP molecule, analog or derivative thereof, or any combination thereof is a prodrug composition.
  • the cACCMP molecule is a 3 ’,3 ’,3 ’-cACCMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1-C10 alkyl group optionally substituted with a C1-C10 alkyl ester group, and wherein each R3 is optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and detectable labels, wherein each R4 is optionally further substituted.
  • the cACCMP molecule is a 2’, 3’, 3’-cACCMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from, oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R3 is optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and detectable labels, wherein each R4 is optionally further substituted.
  • the cACCMP molecule is a 2’,2’,3’-cACCMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R3 can be optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and detectable labels, wherein each R4 can be optionally further substituted.
  • the cACCMP molecule is a 2’,2’,2’-cACCMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R3 can be optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and detectable labels, wherein each R4 can be optionally further substituted.
  • the cACCMP molecule is a 2’,3’,2’-cACCMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R3 is optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and detectable labels, wherein each R4 is optionally further substituted.
  • the cACCMP molecule is a 3’, 2’, 2’-cACCMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R3 is optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and detectable labels, wherein each R4 is optionally further substituted.
  • the cACCMP molecule is a 3’, 2’, 3’- cACCMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R3 is optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and detectable labels, wherein each R4 is optionally further substituted.
  • the cACCMP molecule is a 3 ’,3 ’,2’ -cACCMP analog according to the formula:
  • each R1 is independently selected from hydrogen, oxygen, methoxy, amine, azide, and fluorine groups
  • each R2 is independently selected from oxygen and sulfur groups
  • each R3 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1-C10 alkyl group optionally substituted with a C1-C10 alkyl ester group, and wherein each R3 is optionally further substituted
  • each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and detectable labels, wherein each R4 is optionally further substituted.
  • compositions according to any one of Formula Ila, lib, lie, lid, lie, Ilf, Ilg, or Ilh can have various substituent groups.
  • R1 is a fluorine group.
  • R2 is a sulfur group.
  • R3 is a methyl group.
  • R3 is selected from a hydroxyl group and alkoxyl (-OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group.
  • R5 is a group.
  • the composition is a prodrug composition.
  • R5 is a group and the composition is a prodrug composition.
  • R4 is a hydrogen group.
  • R4 is a hydrogen group.
  • R4 is a methyl group.
  • R4 is an alkyne group selected from a cycloalkyne and groups, optionally wherein the cycloalkyne group is a cyclooctyne group.
  • R4 is a detectable label, optionally selected from biotin, fluorophore, and a radiolabel.
  • analogs and derivatives of the cyclic nucleotides include modifications or substitutions at one or more positions of the purine or pyrimidine moieties, one or more positions of the sugar ring, including sugar substitutions, and modifications and/or replacements of the phosphodiester moiety or linkage. Isomeric configurations are also contemplated for use. Each of the modifications described herein can be used in any combination independently with each of the other modifications described herein.
  • compositions detailed herein comprise a nucleotide analog of a cyclic dinucleotide molecule, a cyclic trinucleotide molecule, an analog or derivative thereof, or any combination thereof.
  • a composition comprises an isonucleotide analog of a cCAMP, a cACCMP, an analog or derivative thereof, or any combination thereof.
  • the composition comprises an isonucleotide analog of a cyclic nucleotide molecule according to any one of Formula la, lb, Ic, Id, Ila, lib, lie, lid, lie, Ilf, Ilg, or Ilh.
  • the isonucleotide analog comprises one or more sugar ring(s) each comprising the adenosine group or the cytosine group at the 2’ carbon position and the R1 group at the 1’ carbon position.
  • the R3 of the isonucleotide analog, an analog or derivative thereof, or any combination thereof is selected from a hydroxyl group and alkoxyl (-OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group.
  • R5 is a group, and/or the composition is a prodrug composition.
  • composition is a cCAMP isonucleotide analog according to:
  • R6 or R7 is an adenine moiety or an analog or derivative thereof, and, when not an adenine moiety or an analog or derivative thereof, R6 or R7 is selected from hydrogen, hydroxyl, and fluorine groups;
  • R8 or R9 is a cytidine moiety or an analog or derivative thereof, and, when not a cytidine moiety or an analog or a derivative thereof, R8 or R9 is selected from hydrogen, hydroxyl, and fluorine groups; each RIO is independently selected from oxygen and sulfur groups; and each R11 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group, and wherein each R11 is optionally further substituted.
  • a adenine moiety is according to: wherein each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and a detectable labels, wherein each R4 can be optionally further substituted.
  • R4 is a hydrogen group.
  • R4 is a methyl group.
  • R4 is an alkyne group selected from cycloalkyne and groups, optionally wherein the cycloalkyne group is a cyclooctyne group.
  • R4 is a detectable label, optionally selected from biotin, fluorophore, and a radiolabel.
  • R11 is selected from a hydroxyl group and alkoxyl (-OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group.
  • R5 is a group.
  • the composition is a prodrug composition.
  • R5 is a o group and the composition is a prodrug composition.
  • the composition is a cACCMP isonucleotide analog of
  • R6 or R7 is an adenine group or an analog or derivative thereof, and, when not an adenine group or an analog or derivative thereof, R6 or R7 is selected from hydrogen, hydroxyl, and fluorine groups; at each occurrence, R8 or R9 is a cytidine group or an analog or derivative thereof, and, at each occurrence, when not a cytidine group or an analog or a derivative thereof, R8 or R9 is selected from hydrogen, hydroxyl, and fluorine groups; each RIO is independently selected from oxygen and sulfur groups; and each R11 is independently selected from hydrogen, C1-C5 alkyl, hydroxyl, and alkoxyl (- OR5) groups, wherein R5 is a C1-C10 alkyl group optionally substituted with a C1-C10 alkyl ester group, and wherein each R11 can be optional
  • a adenine moiety is according to: wherein each R4 is independently selected from hydrogen, C1-C5 alkyl, alkyne, and azide groups, and a detectable labels, and wherein each R4 can be optionally further substituted.
  • R4 is a hydrogen group.
  • R4 is a methyl group.
  • R4 is an alkyne group selected from cycloalkyne and groups, optionally wherein the cycloalkyne group is a cyclooctyne group.
  • R4 is a detectable label, optionally selected from biotin, fluorophore, and a radiolabel.
  • R3 is selected from a hydroxyl and alkoxyl (-OR5) groups, wherein R5 is a C1 -C10 alkyl group optionally substituted with a C1 -C10 alkyl ester group. In one example embodiment, R5 is a group. In one example embodiment, the composition is a prodrug composition. In one example embodiment, R5 is a group and the composition is a prodrug composition.
  • the 3’,3’,3’-cACCMP isonucleotide analog comprises an isonucleotidic AMP, one or more isonucleotidic CMP(s), or any combination thereof.
  • the 3’,3’,3’-cACCMP isonucleotide analog is according to:
  • a cyclic nucleotide molecule analog or derivative comprises a cyclic n’,n’ CMP -AMP analog (e.g., isomer) or a cyclic n’,n’,n’ cyclic AMP-CMP- CMP (cACCMP) analog (e.g., isomer).
  • the cCAMP molecule is a n’,n’ cCAMP analog, where n’,n’ indicates the carbon numbers of the AMP and CMP sugar rings, respectively, linked by a phosphodiester linkage to the 5’ sugar ring carbon of the CMP and AMP sugar rings, respectively.
  • the cACCMP molecule is a n’,n’,n’ cACCMP analog, where n’,n’,n’ indicates the carbon numbers of AMP, first CMP, and second CMP sugar rings, respectively, linked by a phosphodiester linkage to the 5’ sugar ring carbon of the first CMP, second CMP, and AMP sugar rings, respectively.
  • the compositions comprise a 2’, 3’ cCAMP, a 2’, 2’ cCAMP, a 3’2’ cCAMP, a 2’, 3 ’,3 ’-cACCMP, a 2’, 2’, 3 ’-cACCMP, a 2’,2’,2’-cACCMP, a 2’,3’,2’-cACCMP, a 3’,2’,2’- cACCMP a 3’,2’,3’-cACCMP, a 3’,3’,2’-cACCMP, an analog (e.g., an isonucleotide analog, a phosphodiester linkage analog, a fluorinated analog, a phosphodiester analog, a modified nucleotide base analog, or the like) or derivative thereof, or any combination thereof Fluorinated Analogs
  • an analog e.g., an isonucleotide analog, a phosphodiester linkage analog, a flu
  • a cyclic nucleotide analog or derivative comprises one or more fluorine modifications.
  • the cyclic nucleotide analog or derivative can be a mono-fluorinated or di-fluorinated cCAMP molecule, a mono-fluorinated, di-fluorinated, or tri-fluorinated cACCMP molecule, analog (e.g., an isonucleotide analog, a phosphodiester linkage analog, a phosphodiester analog, a modified nucleotide base analog, or the like) or derivative thereof, or any combination thereof.
  • the fluorinated cyclic nucleotide molecule, analog or derivative thereof, or any combination thereof has increased cell permeability relative to a cyclic nucleotide that lacks fluorination. Additional modifications at the Ri can comprise amino, methoxy, and azido groups.
  • a cyclic nucleotide analog or derivative comprises one or more phosphorothioate modifications.
  • the cyclic nucleotide analog or derivative can be a mono-phosphorothioate or di- phosphorothioate cCAMP molecule, or a mono-phosphorothioate di-phosphorothioate, or tri-phosphorothioate cACCMP molecule, analog (e.g., an isonucleotide analog, a phosphodiester linkage analog, a fluorinated analog, a methylphosphonate modified analog, a modified nucleotide base analog, or the like) or derivative thereof, or any combination thereof.
  • analog e.g., an isonucleotide analog, a phosphodiester linkage analog, a fluorinated analog, a methylphosphonate modified analog, a modified nucleotide base analog, or the like
  • the phosphorothioate cyclic nucleotide molecule has increased resistance to cellular nucleases relative to a cyclic nucleotide molecule that lacks the phosphorothioate modification.
  • a cyclic nucleotide molecule comprises one or more methylphosphonate modifications.
  • the cyclic nucleotide can be a mono-methylphosphonate or di-methylphosphonate cCAMP molecule, a mono- methylphosphonate, di-methylphosphonate, or tri-methylphosphonate cACCMP, an analog (e.g., an isonucleotide analog, a phosphodiester linkage analog, a fluorinated analog, a phosphorothioate modified analog, a modified nucleotide base analog, or the like) or derivative thereof, or any combination thereof.
  • an analog e.g., an isonucleotide analog, a phosphodiester linkage analog, a fluorinated analog, a phosphorothioate modified analog, a modified nucleotide base analog, or the like
  • the methylphosphonate cyclic nucleotide molecule has increased resistance to cellular nucleases relative to a cyclic nucleotide molecule that lacks the methylphosphonate modifications.
  • a cyclic nucleotide molecule comprises one or more nucleotide base modifications.
  • the cyclic nucleotide can be a mono-, or di-, or tri -nucleotide base-substituted cCAMP molecule, a mono-, di-, tri-, tetra- or penta-nucleotide base-substituted cACCMP molecule, an analog (e.g., an isonucleotide analog, a phosphodiester linkage analog, a fluorinated analog, a phosphodiester analog, or the like) or derivative thereof, or any combination thereof.
  • an analog e.g., an isonucleotide analog, a phosphodiester linkage analog, a fluorinated analog, a phosphodiester analog, or the like
  • the cyclic nucleotide molecule is substituted with a chemical handle.
  • a cyclic nucleotide can comprise a handle via a click chemistry substitution at R4 of any one of Formula la, lb, Ic, Id, Ila, lib, lie, lid, lie, Ilf, Ilg, Ilh, III, IIIa-IIID, or IV, III, IIIa- IIID, or IV.
  • exemplary click chemistry molecules can comprise trans-cyclooctene, cyclooctyne, or terminal alkyne, [e.g.
  • BCN amine N-(lR,8S,9s)-Bicyclo[6.1.0]non-4-yn-9-ylmethyloxycarbonyl- l,8-diamino-3,6-di oxaoctane
  • BCN amine reagent N-(lR,8S,9s)-Bicyclo[6.1.0]non-4-yn-9-ylmethyloxycarbonyl- l,8-diamino-3,6-di oxaoctane
  • one or more of R4 is an alkyne selected from a cycloalkyne and .
  • the cycloalkyne is a cyclooctyne.
  • a detectable label can comprise radiolabels, biotin labels, fluorophores or other optical tags, including amine-reactive dyes.
  • the cyclic nucleotide molecules can comprise one or more non-naturally occurring nucleotide or nucleotide analog such as a nucleotide with phosphorothioate linkage, boranophosphate linkage, a locked nucleic acid (LNA) nucleotides comprising a methylene bridge between the 2’ and 4’ carbons of the ribose ring, an amino-LNA or thio-LNA, peptide nucleic acids (PNA), or bridged nucleic acids (BNA).
  • LNA locked nucleic acid
  • modified nucleotides include 2'- O-methyl analogs, 2'-deoxy analogs, 2-thiouridine analogs, N6-methyladenosine analogs, or 2'- fluoro analogs.
  • Further examples of modification to one or more nucleotides in the cyclic nucleotides disclosed herein include further linkage of chemical moieties at the 2' position, including but not limited to peptides, nuclear localization sequence (NLS), peptide nucleic acid (PNA), polyethylene glycol (PEG), triethylene glycol, or tetraethyleneglycol (TEG).
  • Synthetic nucleic acid analogies comprising a different sugar backbone, e.g.
  • xeno nucleic acid are also included as analogs that can be incorporated in the compositions detailed herein., and can include 1,5-anhydrohexitol nucleic acid (HNA), Cyclohexene nucleic acid (CeNA), Threose nucleic acid (TNA), and glycol nucleoic acid (GNA)., and 2'-Fluoro-arabinonucleic Acid (FANA).
  • HNA 1,5-anhydrohexitol nucleic acid
  • CeNA Cyclohexene nucleic acid
  • TPA Threose nucleic acid
  • GNA glycol nucleoic acid
  • FANA 2'-Fluoro-arabinonucleic Acid
  • XNAs can be chosen for particular applications, including, e.g., probing biomolecular interactions.
  • Methods of use of the compositions include use of the cyclic nucleotides in modulating immune signaling in the cell, which can comprise administering any of the compositions as disclosed herein to a cell. Methods of modulating immune signaling in a subject in need thereof can comprise administration of an effective amount a pharmaceutical composition as detailed herein. Further methods of identifying novel cyclic nucleotide molecules, pathways modulated by the molecules, and cell receptors of the molecules are also provided.
  • the cyclic nucleotides, their analogs and derivatives can be utilized to module immune signaling in a cell.
  • modulate broadly denotes a qualitative and/or quantitative alteration, change or variation in that which is being modulated. Where modulation can be assessed quantitatively - for example, where modulation comprises or consists of a change in a quantifiable variable such as a quantifiable property of a cell or where a quantifiable variable provides a suitable surrogate for the modulation - modulation specifically encompasses both increase (e g., activation) or decrease (e.g., inhibition) in the measured variable.
  • modulation can encompass an increase in the value of the measured variable by at least about 10%, e.g., by at least about 20%, preferably by at least about 30%, e.g., by at least about 40%, more preferably by at least about 50%, e.g., by at least about 75%, even more preferably by at least about 100%, e.g., by at least about 150%, 200%, 250%, 300%, 400% or by at least about 500%, compared to a reference situation without said modulation; or modulation can encompass a decrease or reduction in the value of the measured variable by at least about 10%, e.g., by at least about 20%, by at least about 30%, e.g., by at least about 40%, by at least about 50%, e.g., by at least about 60%, by at least about 70%, e.
  • modulating or “to modulate” generally means either reducing or inhibiting the expression or activity of, or alternatively increasing the expression or activity of a target or antigen.
  • modulating or “to modulate” can mean either reducing or inhibiting the activity of, or alternatively increasing a (relevant or intended) biological activity of, a target or antigen as measured using a suitable in vitro, cellular or in vivo assay (which will usually depend on the target involved), by at least 5%, at least 10%, at least 25%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or more, compared to activity of the target in the same assay under the same conditions but without the presence of an agent.
  • an “increase” or “decrease” refers to a statistically significant increase or decrease respectively.
  • an increase or decrease will be at least 10% relative to a reference, such as at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, a t least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97%, at least 98%, or more, up to and including at least 100% or more, in the case of an increase, for example, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 50-fold, at least 100-fold, or more.
  • Modulating can also involve effecting a change (which can either be an increase or a decrease) in affinity, avidity, specificity and/or selectivity of a target or antigen. “Modulating” can also mean effecting a change with respect to one or more biological or physiological mechanisms, effects, responses, functions, pathways or activities in which the target or antigen (or in which its substrate(s), ligand(s) or pathway(s) are involved, such as its signaling pathway or metabolic pathway and their associated biological or physiological effects) is involved.
  • such an action as an agonist or an antagonist can be determined in any suitable manner and/or using any suitable assay known or described herein (e.g., in vitro or cellular assay), depending on the target or antigen involved.
  • Modulating can, for example, also involve allosteric modulation of the target and/or reducing or inhibiting the binding of the target to one of its substrates or ligands and/or competing with a natural ligand, substrate for binding to the target. Modulating can also involve activating the target or the mechanism or pathway in which it is involved. Modulating can for example also involve effecting a change in respect of the folding or confirmation of the target, or in respect of the ability of the target to fold, to change its conformation (for example, upon binding of a ligand), to associate with other (sub)units, or to disassociate. Modulating can for example also involve effecting a change in the ability of the target to signal, phosphorylate, dephosphorylate, and the like.
  • agent broadly encompasses any condition, substance or agent capable of modulating one or more phenotypic aspects of a cell or cell population as disclosed herein. Such conditions, substances or agents can be of physical, chemical, biochemical and/or biological nature.
  • the agent is a cyclic nucleotide, derivative, analog, or any combination thereof, as described herein.
  • candidate agent refers to any condition, substance or agent that is being examined for the ability to modulate one or more phenotypic aspects of a cell or cell population as disclosed herein in a method comprising applying the candidate agent to the cell or cell population (e.g., exposing the cell or cell population to the candidate agent or contacting the cell or cell population with the candidate agent) and observing whether the desired modulation takes place.
  • Agents can include any potential class of biologically active conditions, substances or agents, such as for instance antibodies, proteins, peptides, nucleic acids, oligonucleotides, small molecules, or combinations thereof, as described herein.
  • the methods of phenotypic analysis can be utilized for evaluating environmental stress and/or state, for screening of chemical libraries, and to screen or identify structural, syntenic, genomic, and/or organism and species variations.
  • a culture of cells can be exposed to an environmental stress, such as but not limited to heat shock, osmolarity, hypoxia, cold, oxidative stress, radiation, starvation, a chemical (for example a therapeutic agent or potential therapeutic agent) and the like.
  • a representative sample can be subjected to analysis, for example at various time points, and compared to a control, such as a sample from an organism or cell, for example a cell from an organism, or a standard value.
  • a further aspect of the invention relates to a method for identifying the modulating of one or more phenotypic aspects of a cell or cell population as disclosed herein, comprising: a) applying a candidate agent to the cell or cell population; b) detecting modulation of one or more phenotypic aspects of the cell or cell population by the candidate agent, thereby identifying the agent.
  • the phenotypic aspects of the cell or cell population that is modulated can be a gene signature or biological program specific to a cell type or cell phenotype or phenotype specific to a population of cells (e.g., an inflammatory phenotype or suppressive immune phenotype).
  • steps can include administering candidate modulating agents to cells, detecting identified cell (sub)populations for changes in signatures, or identifying relative changes in cell (sub) populations which can comprise detecting relative abundance of particular gene signatures.
  • aspects of the present disclosure relate to the correlation of an agent with the spatial proximity and/or epigenetic profile of the nucleic acids in a sample of cells.
  • the disclosed methods can be used to screen the compositions for modulation of chromatin architecture epigenetic profiles, and/or relationships thereof.
  • screening of test agents involves testing a combinatorial library containing a large number of potential modulator compounds.
  • a combinatorial chemical library can be a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis, by combining a number of chemical "building blocks" such as reagents.
  • a linear combinatorial chemical library such as a polypeptide library, is formed by combining a set of chemical building blocks (amino acids) in every possible way for a given compound length (for example the number of amino acids in a polypeptide compound). Millions of chemical compounds can be synthesized through such combinatorial mixing of chemical building blocks.
  • the present invention provides for gene signature screening.
  • signature screening was introduced by Stegmaier et al. (Gene express! on -based high-throughput screening (GE-HTS) and application to leukemia differentiation. Nature Genet. 36, 257-263 (2004)), who realized that if a gene-expression signature was the proxy for a phenotype of interest, it could be used to find small molecules that effect that phenotype without knowledge of a validated drug target.
  • the signatures or biological programs of the present invention can be used to screen for drugs that reduce the signature or biological program in cells as described herein.
  • the signature or biological program can be used for GE-HTS.
  • pharmacological screens can be used to identify drugs that are selectively toxic to cells having a signature.
  • the Connectivity Map is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes (see, Lamb et al., The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease. Science 29 Sep 2006: Vol. 313, Issue 5795, pp. 1929-1935, DOI: 10.1126/science.1132939; and Lamb, J., The Connectivity Map: a new tool for biomedical research. Nature Reviews Cancer January 2007: Vol. 7, pp. 54-60).
  • Cmap can be used to screen for small molecules capable of modulating a signature or biological program of the present invention in silica.
  • Detection of differential expression of one or more genes for identification of one or more pathways modulated by the compositions is provided. It is to be understood that also when referring to proteins (e.g. differentially expressed proteins), such can fall within the definition of “gene” signature. Levels of expression or activity or prevalence can be compared between different cells in order to characterize or identify for instance signatures specific for cell (sub)populations. Increased or decreased expression or activity of signature genes can be compared between different cells in order to characterize or identify for instance specific cell (sub)populations. The detection of a signature in single cells can be used to identify and quantitate for instance specific cell (sub)populations.
  • proteins e.g. differentially expressed proteins
  • a signature can include a gene or genes, protein or proteins, or epigenetic element(s) whose expression or occurrence is specific to a cell (sub)population, such that expression or occurrence is exclusive to the cell (sub)population.
  • a gene signature as used herein can thus refer to any set of up- and down-regulated genes that are representative of a cell type or subtype.
  • a gene signature as used herein can also refer to any set of up- and down-regulated genes between different cells or cell (sub)populations derived from a gene-expression profile.
  • a gene signature can comprise a list of genes differentially expressed in a distinction of interest.
  • the signature as defined herein can be used to indicate the presence of a cell type, a subtype of the cell type, the state of the microenvironment of a population of cells, a particular cell type population or subpopulation, and/or the overall status of the entire cell (sub)population. Furthermore, the signature can be indicative of cells within a population of cells in vivo.
  • the signature according to certain embodiments of the present invention can comprise or consist of one or more genes, proteins and/or epigenetic elements, such as for instance 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more.
  • the signature can comprise or consist of two or more genes, proteins and/or epigenetic elements, such as for instance 2, 3, 4, 5, 6, 7, 8, 9, 10 or more.
  • the signature can comprise or consist of three or more genes, proteins and/or epigenetic elements, such as for instance 3, 4, 5, 6, 7, 8, 9, 10 or more.
  • the signature can comprise or consist of four or more genes, proteins and/or epigenetic elements, such as for instance 4, 5, 6, 7, 8, 9, 10 or more.
  • the signature can comprise or consist of five or more genes, proteins and/or epigenetic elements, such as for instance 5, 6, 7, 8, 9, 10 or more. In certain embodiments, the signature can comprise or consist of six or more genes, proteins and/or epigenetic elements, such as for instance 6, 7, 8, 9, 10 or more. In certain embodiments, the signature can comprise or consist of seven or more genes, proteins and/or epigenetic elements, such as for instance 7, 8, 9, 10 or more. In certain embodiments, the signature can comprise or consist of eight or more genes, proteins and/or epigenetic elements, such as for instance 8, 9, 10 or more. In certain embodiments, the signature can comprise or consist of nine or more genes, proteins and/or epigenetic elements, such as for instance 9, 10 or more.
  • the signature can comprise or consist of ten or more genes, proteins and/or epigenetic elements, such as for instance 10, 11, 12, 13, 14, 15, or more. It is to be understood that a signature according to the invention can for instance also include genes or proteins as well as epigenetic elements combined.
  • a signature is characterized as being specific for a particular target cell or target cell (sub)population if it is upregulated or only present, detected or detectable in that particular target cell or target cell (sub)population, or alternatively is downregulated or only absent, or undetectable in that particular target cell or target cell (sub)population.
  • a signature consists of one or more differentially expressed genes/proteins or differential epigenetic elements when comparing different cells or cell (sub)populations, including comparing different target cell or target cell (sub)populations, as well as comparing target cell or target cell (sub)populations with non-target cell or non-target cell (sub)populations.
  • genes/proteins include genes/proteins which are up- or down-regulated as well as genes/proteins which are turned on or off.
  • up- or down-regulation in certain embodiments, such up- or down-regulation is preferably at least two-fold, such as two-fold, three-fold, four-fold, five-fold, or more, such as for instance at least ten-fold, at least 20-fold, at least 30-fold, at least 40-fold, at least 50-fold, or more.
  • differential expression can be determined based on common statistical tests, as is known in the art.
  • differentially expressed genes/proteins, or differential epigenetic elements can be differentially expressed on a single cell level, or can be differentially expressed on a cell population level.
  • the differentially expressed genes/ proteins or epigenetic elements as discussed herein, such as constituting the gene signatures as discussed herein, when as to the cell population or subpopulation level refer to genes that are differentially expressed in all or substantially all cells of the population or subpopulation (such as at least 80%, preferably at least 90%, such as at least 95% of the individual cells). This allows one to define a particular subpopulation of target cells.
  • a “subpopulation” of cells preferably refers to a particular subset of cells of a particular cell type which can be distinguished or are uniquely identifiable and set apart from other cells of this cell type.
  • the cell subpopulation can be phenotypically characterized and is preferably characterized by the signature as discussed herein.
  • a cell (sub)population as referred to herein can constitute of a (sub)population of cells of a particular cell type characterized by a specific cell state.
  • induction or alternatively suppression of a particular signature preferable is meant induction or alternatively suppression (or upregulation or downregulation) of at least one gene/protein and/or epigenetic element of the signature, such as for instance at least two, at least three, at least four, at least five, at least six, or all genes/proteins and/or epigenetic elements of the signature.
  • Detection of differential expression can comprise single cell RNA sequencing.
  • the invention involves single cell RNA sequencing (see, e.g., Kalisky, T., Blainey, P. & Quake, S. R. Genomic Analysis at the Single-Cell Level. Annual review of genetics 45, 431-445, (2011); Kalisky, T. & Quake, S. R. Single-cell genomics. Nature Methods 8, 311- 314 (2011); Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Research, (2011); Tang, F. et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell.
  • the invention involves plate based single cell RNA sequencing (see, e.g., Picelli, S. et al., 2014, “Full-length RNA-seq from single cells using Smart-seq2” Nature protocols 9, 171-181, doi:10.1038/nprot.2014.006).
  • the invention involves high-throughput single-cell RNA-seq.
  • Macosko et al. 2015, “Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets” Cell 161, 1202-1214; International patent application number PCT/US2015/049178, published as WQ2016/040476 on March 17, 2016; Klein et al., 2015, “Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells” Cell 161, 1187-1201; International patent application number PCT/US2016/027734, published as WO2016168584A1 on October 20, 2016; Zheng, et al., 2016, “Haplotyping germline and cancer genomes with high-throughput linked-read sequencing” Nature Biotechnology 34, 303-311; Zheng, et al., 2017, “Massively parallel digital transcriptional profiling of single cells” Nat.
  • the invention involves single nucleus RNA sequencing.
  • Swiech et al., 2014 “In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9” Nature Biotechnology Vol. 33, pp. 102-106; Habib et al., 2016, “Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons” Science, Vol. 353, Issue 6302, pp. 925-928; Habib et al., 2017, “Massively parallel single-nucleus RNA-seq with DroNc-seq” Nat Methods.
  • the invention involves the Assay for Transposase Accessible Chromatin using sequencing (ATAC-seq) as described, (see, e.g., Buenrostro, et al., Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature methods 2013; 10 (12): 1213-1218; Buenrostro et al., Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486-490 (2015); Cusanovich, D. A., Daza, R., Adey, A., Pliner, H., Christiansen, L., Gunderson, K.
  • TPP thermal proteome profiling
  • Exemplary methods of detection and identification of novel cyclic nucleotides can comprise stimulating innate immune signaling of a population of cells, extracting polar metabolites from the cells, fractionating extract via reversed-phase high pressure liquid chromatography, and analyzing the fractions by liquid chromatography-tandem mass spectrometry (LC-MS/MS) thereby detecting novel second messenger small molecules, e.g., cyclic nucleotides.
  • Stimulating the cells typically comprises exposing the cells to double stranded RNA or double stranded DNA.
  • Elucidating the chemical structures of the small molecules identified comprises digestion with one or more enzymes to assign structure to novel metabolites, which can comprise one or more of rsAP, RNAseA, RNaseTl, RNAse T2, Nuclease SI and/or PDEII, as described in more detail in the examples.
  • formulations include, for example, powders, pastes, ointments, jellies, waxes, oils, lipids, lipid (cationic or anionic) containing vesicles (such as LipofectinTM), DNA conjugates, anhydrous absorption pastes, oil-in- water and water-in-oil emulsions, emulsions carbowax (polyethylene glycols of various molecular weights), semi-solid gels, and semi-solid mixtures containing carbowax.
  • vesicles such as LipofectinTM
  • DNA conjugates such as LipofectinTM
  • anhydrous absorption pastes oil-in- water and water-in-oil emulsions
  • emulsions carbowax polyethylene glycols of various molecular weights
  • semi-solid gels and semi-solid mixtures containing carbowax.
  • the medicaments of the invention are prepared in a manner known to those skilled in the art, for example, by means of conventional dissolving, lyophilizing, mixing, granulating or confectioning processes. Methods well known in the art for making formulations are found, for example, in Remington: The Science and Practice of Pharmacy, 20th ed., ed. A. R. Gennaro, 2000, Lippincott Williams & Wilkins, Philadelphia, and Encyclopedia of Pharmaceutical Technology, eds. J. Swarbrick and J. C. Boylan, 1988-1999, Marcel Dekker, New York.
  • Administration of medicaments of the invention can be by any suitable means that results in a compound concentration that is effective for treating or inhibiting (e.g., by delaying) the development of a disease.
  • the compound is admixed with a suitable carrier substance, e.g., a pharmaceutically acceptable excipient that preserves the therapeutic properties of the compound with which it is administered.
  • a suitable carrier substance e.g., a pharmaceutically acceptable excipient that preserves the therapeutic properties of the compound with which it is administered.
  • One exemplary pharmaceutically acceptable excipient is physiological saline.
  • the suitable carrier substance is generally present in an amount of 1-95% by weight of the total weight of the medicament.
  • the medicament can be provided in a dosage form that is suitable for administration.
  • the medicament can be in form of, e.g., tablets, capsules, pills, powders, granulates, suspensions, emulsions, solutions, gels including hydrogels, pastes, ointments, creams, plasters, drenches, delivery devices, injectables, implants, sprays, or aerosols.
  • Pharmaceutical Compositions including hydrogels, pastes, ointments, creams, plasters, drenches, delivery devices, injectables, implants, sprays, or aerosols.
  • compositions of the present disclosure include pharmaceutical composition comprising one or more molecules or compositions as detailed herein, or pharmaceutically acceptable salts thereof.
  • the agents disclosed herein e.g., cyclic nucleotides
  • Such compositions comprise a therapeutically effective amount of the agent and a pharmaceutically acceptable carrier.
  • Such a composition can also further comprise (in addition to an agent and a carrier) diluents, fdlers, salts, buffers, stabilizers, solubilizers, and other materials well known in the art.
  • Compositions comprising the agent can be administered in the form of salts provided the salts are pharmaceutically acceptable. Salts can be prepared using standard procedures known to those skilled in the art of synthetic organic chemistry.
  • salts refers to salts prepared from pharmaceutically acceptable non-toxic bases or acids including inorganic or organic bases and inorganic or organic acids.
  • Salts derived from inorganic bases include aluminum, ammonium, calcium, copper, ferric, ferrous, lithium, magnesium, manganic salts, manganous, potassium, sodium, zinc, and the like. Particularly preferred are the ammonium, calcium, magnesium, potassium, and sodium salts.
  • Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines, and basic ion exchange resins, such as arginine, betaine, caffeine, choline, N,N'-dibenzylethylenediamine, diethylamine, 2- diethylaminoethanol, 2-dimethylaminoethanol, ethanolamine, ethylenediamine, N-ethyl- morpholine, N-ethylpiperidine, glucamine, glucosamine, histidine, hydrabamine, isopropylamine, lysine, methylglucamine, morpholine, piperazine, piperidine, polyamine resins, procaine, purines, theobromine, triethylamine, trimethylamine, tripropylamine, tromethamine, and the like.
  • basic ion exchange resins such
  • pharmaceutically acceptable salt further includes all acceptable salts such as acetate, lactobionate, benzenesulfonate, laurate, benzoate, malate, bicarbonate, maleate, bisulfate, mandelate, bitartrate, mesylate, borate, methylbromide, bromide, methylnitrate, calcium edetate, methylsulfate, camsylate, mucate, carbonate, napsylate, chloride, nitrate, clavulanate, N- methylglucamine, citrate, ammonium salt, dihydrochloride, oleate, edetate, oxalate, edisylate, pamoate (embonate), estolate, palmitate, esylate, pantothenate, fumarate, phosphate/di phosphate, gluceptate, polygalacturonate, gluconate, salicylate, glutamate, stearate, glycosulfonate
  • composition of the invention can also advantageously be formulated in order to release 2’ -ATP mimetics or derivatives, and/or agonist in the subject in a timely controlled fashion.
  • composition of the invention is formulated for controlled release.
  • the agents of the present invention can be modified, such that they acquire advantageous properties for therapeutic use (e.g., stability and specificity), but maintain their biological activity.
  • the agents include a protecting group covalently joined to the N-terminal amino group.
  • a protecting group covalently joined to the N-terminal amino group of the agonists reduces the reactivity of the amino terminus under in vivo conditions.
  • Amino protecting groups include — Cl-10 alkyl, — Cl- 10 substituted alkyl, — C2-10 alkenyl, — C2-10 substituted alkenyl, aryl, — Cl-6 alkyl aryl, — C(O)— (CH2)l-6— COOH, — C(O)— Cl-6 alkyl, — C(O)-aryl, — C(O)— O— Cl-6 alkyl, or — C(O) — O-aryl.
  • the amino terminus protecting group is selected from the group consisting of acetyl, propyl, succinyl, benzyl, benzyloxycarbonyl, and t- butyloxy carbonyl.
  • deamination of the N-terminal amino acid is another modification that can be used for reducing the reactivity of the amino terminus under in vivo conditions.
  • compositions of the agents are also included within the scope of the present invention.
  • the polymer selected is usually modified to have a single reactive group, such as an active ester for acylation or an aldehyde for alkylation, so that the degree of polymerization can be controlled.
  • Included within the scope of polymers is a mixture of polymers.
  • the polymer will be pharmaceutically acceptable.
  • the polymer or mixture thereof can include but is not limited to polyethylene glycol (PEG), monomethoxy-polyethylene glycol, dextran, cellulose, or other carbohydrate based polymers, poly-(N-vinyl pyrrolidone) polyethylene glycol, propylene glycol homopolymers, a polypropylene oxide/ethylene oxide co-polymer, polyoxyethylated polyols (for example, glycerol), and polyvinyl alcohol.
  • PEG polyethylene glycol
  • monomethoxy-polyethylene glycol dextran, cellulose, or other carbohydrate based polymers
  • poly-(N-vinyl pyrrolidone) polyethylene glycol propylene glycol homopolymers
  • a polypropylene oxide/ethylene oxide co-polymer for example, glycerol
  • polyoxyethylated polyols for example, glycerol
  • the present invention provides for one or more therapeutic agents.
  • the one or more agents comprises a small molecule inhibitor, small molecule degrader (e.g., PROTAC), genetic modifying agent, antibody, antibody fragment, antibody-like protein scaffold, aptamer, protein, or any combination thereof.
  • small molecule inhibitor e.g., PROTAC
  • PROTAC small molecule degrader
  • genetic modifying agent e.g., antibody, antibody fragment, antibody-like protein scaffold, aptamer, protein, or any combination thereof.
  • therapeutic agent refers to a molecule or compound that confers some beneficial effect upon administration to a subject.
  • the beneficial effect includes enablement of diagnostic determinations; amelioration of a disease, symptom, disorder, or pathological condition; reducing or preventing the onset of a disease, symptom, disorder or condition; and generally counteracting a disease, symptom, disorder or pathological condition.
  • treatment or “treating,” or “palliating” or “ameliorating” are used interchangeably. These terms refer to an approach for obtaining beneficial or desired results including but not limited to a therapeutic benefit and/or a prophylactic benefit.
  • therapeutic benefit is meant any therapeutically relevant improvement in or effect on one or more diseases, conditions, or symptoms under treatment.
  • the compositions can be administered to a subject at risk of developing a particular disease, condition, or symptom, or to a subject reporting one or more of the physiological symptoms of a disease, even though the disease, condition, or symptom can not have yet been manifested.
  • treating includes ameliorating, curing, preventing it from becoming worse, slowing the rate of progression, or preventing the disorder from re-occurring (i.e., to prevent a relapse).
  • the present invention provides for one or more therapeutic agents against combinations of targets identified. Targeting the identified combinations can provide for enhanced or otherwise previously unknown activity in the treatment of disease.
  • PROTAC Proteolysis Targeting Chimera
  • combinations of targets are modulated (e.g., one or more targets related to cyclic nucleotide generation or modulation).
  • an agent against one of the targets in a combination can already be known or used clinically.
  • targeting the combination can require less of the agent as compared to the current standard of care and provide for less toxicity and improved treatment.
  • Methods of administrating the pharmacological compositions, including agonists, antagonists, antibodies or fragments thereof, to an individual include, but are not limited to, intradermal, intrathecal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, by inhalation, and oral routes.
  • the compositions can be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (for example, oral mucosa, rectal and intestinal mucosa, and the like), ocular, and the like and can be administered together with other biologically-active agents. Administration can be systemic or local.
  • compositions into the central nervous system can be advantageous to administer by any suitable route, including intraventricular and intrathecal injection.
  • Pulmonary administration can also be employed by use of an inhaler or nebulizer, and formulation with an aerosolizing agent.
  • the agent can be delivered in a vesicle, in particular a liposome.
  • a liposome the agent is combined, in addition to other pharmaceutically acceptable carriers, with amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers in aqueous solution.
  • Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithin, phospholipids, saponin, bile acids, and the like. Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, for example, in U.S. Pat. No. 4,837,028 and U.S. Pat. No. 4,737,323.
  • the pharmacological compositions can be delivered in a controlled release system including, but not limited to: a delivery pump (See, for example, Saudek, et al., New Engl. J. Med.
  • the controlled release system can be placed in proximity of the therapeutic target (e g., a tumor), thus requiring only a fraction of the systemic dose. See, for example, Goodson, In: Medical Applications of Controlled Release, 1984. (CRC Press, Boca Raton, Fla.).
  • Anderson et al. provides a modified dendrimer nanoparticle for the delivery of therapeutic, prophylactic and/or diagnostic agents to a subject, comprising: one or more zero to seven generation alkylated dendrimers; one or more amphiphilic polymers; and one or more therapeutic, prophylactic and/or diagnostic agents encapsulated therein.
  • One alkylated dendrimer can be selected from the group consisting of poly(ethyleneimine), poly(polyproylenimine), diaminobutane amine polypropylenimine tetramine and poly(amido amine).
  • Anderson et al. (US20050123596) provides examples of microparticles that are designed to release their payload when exposed to acidic conditions, wherein the microparticles comprise at least one agent to be delivered, a pH triggering agent, and a polymer, wherein the polymer is selected from the group of polymethacrylates and polyacrylates.
  • Anderson et al (US 20020150626) providing lipid-protein-sugar particles for delivery of nucleic acids, wherein the polynucleotide is encapsulated in a lipid-protein-sugar matrix by contacting the polynucleotide with a lipid, a protein, and a sugar; and spray drying mixture of the polynucleotide, the lipid, the protein, and the sugar to make microparticles.
  • Nanoparticles with one half hydrophilic and the other half hydrophobic are termed Janus particles and are particularly effective for stabilizing emulsions. They can self-assemble at water/oil interfaces and act as solid surfactants.
  • a nanolipid delivery system in particular a nano-particle concentrate, comprising: a composition comprising a lipid, oil or solvent, the composition having a viscosity of less than 100 cP at 25°C and a Kauri Butanol solvency of greater than 25 Kb; and at least one amphipathic compound selected from the group consisting of an alkoxylated lipid, an alkoxylated fatty acid, an alkoxylated alcohol, a heteroatomic hydrophilic lipid, a heteroatomic hydrophilic fatty acid, a heteroatomic hydrophilic alcohol, a diluent, and combinations thereof, wherein the compound is derived from a starting compound having a viscosity of less than 1000 cP at 50° C, wherein the concentrate is configured to provide a stable nano emulsion having a D50 and a mean average particle size distribution of less than 100 nm when diluted.
  • Liu et al. provides a protocell nanostructure comprising: a porous particle core comprising a plurality of pores; and at least one lipid bilayer surrounding the porous particle core to form a protocell, wherein the protocell is capable of loading one or more cargo components to the plurality of pores of the porous particle core and releasing the one or more cargo components from the porous particle core across the surrounding lipid bilayer.
  • Bader et al. provides a method for producing a lipid particle comprising the following: i) providing a first solution comprising denatured apolipoprotein, ii) adding the first solution to a second solution comprising at least two lipids and a detergent but no apolipoprotein, and iii) removing the detergent from the solution obtained in ii) and thereby producing a lipid particle.
  • the delivery system can be an administration device.
  • an administration device can be any pharmaceutically acceptable device adapted to deliver a composition of the invention (e.g., to a subject's nose).
  • a nasal administration device can be a metered administration device (metered volume, metered dose, or metered-weight) or a continuous (or substantially continuous) aerosol -producing device. Suitable nasal administration devices also include devices that can be adapted or modified for nasal administration. In some embodiments, the nasally administered dose can be absorbed into the bloodstream of a subject.
  • a metered nasal administration device delivers a fixed (metered) volume or amount (dose) of a nasal composition upon each actuation.
  • Exemplary metered dose devices for nasal administration include, by way of example and without limitation, an atomizer, sprayer, dropper, squeeze tube, squeeze-type spray bottle, pipette, ampule, nasal cannula, metered dose device, nasal spray inhaler, breath actuated bi-directional delivery device, pump spray, pre-compression metered dose spray pump, monospray pump, bispray pump, and pressurized metered dose device.
  • the administration device can be a single-dose disposable device, single-dose reusable device, multidose disposable device or multi-dose reusable device.
  • the compositions of the invention can be used with any known metered administration device.
  • a continuous aerosol-producing device delivers a mist or aerosol comprising droplet of a nasal composition dispersed in a continuous gas phase (such as air).
  • a nebulizer, pulsating aerosol nebulizer, and a nasal continuous positive air pressure device are exemplary of such a device.
  • Suitable nebulizers include, by way of example and without limitation, an air driven jet nebulizer, ultrasonic nebulizer, capillary nebulizer, electromagnetic nebulizer, pulsating membrane nebulizer, pulsating plate (disc) nebulizer, pulsating/vibrating mesh nebulizer, vibrating plate nebulizer, a nebulizer comprising a vibration generator and an aqueous chamber, a nebulizer comprising a nozzle array, and nebulizers that extrude a liquid formulation through a self- contained nozzle array.
  • the device can be any commercially available administration devices that are used or can be adapted for nasal administration of a composition of the invention (see, e.g., US patent publication US20090312724A1).
  • the amount of the agents (e.g., cyclic nucleotides, analogs and derivatives) which will be effective in the treatment of a particular disorder or condition will depend on the nature of the disorder or condition, and can be determined by standard clinical techniques by those of skill within the art. In addition, in vitro assays can optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the overall seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. Ultimately, the attending physician will decide the amount of the agent with which to treat each individual patient. In certain embodiments, the attending physician will administer low doses of the agent and observe the patient's response.
  • the agents e.g., cyclic nucleotides, analogs and derivatives
  • suitable dosage ranges for intravenous administration of the agent are generally about 5-500 micrograms (pg) of active compound per kilogram (Kg) body weight.
  • suitable dosage ranges for intranasal administration are generally about 0.01 pg/kg body weight to 1 mg/kg body weight.
  • a composition containing an agent of the present invention is subcutaneously injected in adult patients with dose ranges of approximately 5 to 5000 pg/human and preferably approximately 5 to 500 pg/human as a single dose. It is desirable to administer this dosage 1 to 3 times daily. Effective doses can be extrapolated from dose-response curves derived from in vitro or animal model test systems. Suppositories generally contain active ingredient in the range of 0.5% to 10% by weight; oral formulations preferably contain 10% to 95% active ingredient. Ultimately the attending physician will decide on the appropriate duration of therapy using compositions of the present invention. Dosage will also vary according to the age, weight and response of the individual patient.
  • small particle aerosols of antibodies or fragments thereof can be administered (see e.g., Piazza et al., J. Infect. Dis., Vol. 166, pp. 1422-1424, 1992; and Brown, Aerosol Science and Technology, Vol. 24, pp. 45-56, 1996).
  • antibodies are used as agonists to depress inflammatory diseases.
  • antibodies can be administered in liposomes, i.e., immunoliposomes (see, e.g., Maruyama et al., Biochim. Biophys. Acta, Vol. 1234, pp. 74-80, 1995).
  • immunoconjugates, immunoliposomes or immunomicrospheres containing an agent of the present invention is administered by inhalation.
  • antibodies can be topically administered to mucosa, such as the oropharynx, nasal cavity, respiratory tract, gastrointestinal tract, eye such as the conjunctival mucosa, vagina, urogenital mucosa, or for dermal application.
  • mucosa such as the oropharynx
  • nasal cavity such as the oropharynx
  • respiratory tract such as the conjunctival mucosa, vagina, urogenital mucosa, or for dermal application.
  • antibodies are administered to the nasal, bronchial or pulmonary mucosa.
  • a surfactant such as a phosphoglyceride, e.g. phosphatidylcholine, and/or a hydrophilic or hydrophobic complex of a positively or negatively charged excipient and a charged antibody of the opposite charge.
  • excipients suitable for pharmaceutical compositions intended for delivery of antibodies to the respiratory tract mucosa can be a) carbohydrates, e.g., monosaccharides such as fructose, galactose, glucose. D-mannose, sorbiose, and the like; disaccharides, such as lactose, trehalose, cellobiose, and the like; cyclodextrins, such as 2-hydroxypropyl-P-cyclodextrin; and polysaccharides, such as raffinose, maltodextrins, dextrans, and the like; b) amino acids, such as glycine, arginine, aspartic acid, glutamic acid, cysteine, lysine and the like; c) organic salts prepared from organic acids and bases, such as sodium citrate, sodium ascorbate, magnesium gluconate, sodium gluconate, tromethamine hydrochloride, and the like: d)
  • the antibodies of the present invention can suitably be formulated with one or more of the following excipients: solvents, buffering agents, preservatives, humectants, chelating agents, antioxidants, stabilizers, emulsifying agents, suspending agents, gelforming agents, ointment bases, penetration enhancers, and skin protective agents.
  • solvents are e.g. water, alcohols, vegetable or marine oils (e.g. edible oils like almond oil, castor oil, cacao butter, coconut oil, com oil, cottonseed oil, linseed oil, olive oil, palm oil, peanut oil, poppy seed oil, rapeseed oil, sesame oil, soybean oil, sunflower oil, and tea seed oil), mineral oils, fatty oils, liquid paraffin, polyethylene glycols, propylene glycols, glycerol, liquid polyalkylsiloxanes, and mixtures thereof.
  • vegetable or marine oils e.g. edible oils like almond oil, castor oil, cacao butter, coconut oil, com oil, cottonseed oil, linseed oil, olive oil, palm oil, peanut oil, poppy seed oil, rapeseed oil, sesame oil, soybean oil, sunflower oil, and tea seed oil
  • mineral oils e.g. water, alcohols, vegetable or marine oils (e.g. edible oils like almond oil, castor oil, cacao butter, coconut oil
  • buffering agents are e.g. citric acid, acetic acid, tartaric acid, lactic acid, hydrogenphosphoric acid, diethyl amine etc.
  • preservatives for use in compositions are parabenes, such as methyl, ethyl, propyl p-hydroxybenzoate, butylparaben, isobutylparaben, isopropylparaben, potassium sorbate, sorbic acid, benzoic acid, methyl benzoate, phenoxyethanol, bronopol, bronidox, MDM hydantoin, iodopropynyl butylcarbamate, EDTA, benzalconium chloride, and benzylalcohol, or mixtures of preservatives.
  • humectants are glycerin, propylene glycol, sorbitol, lactic acid, urea, and mixtures thereof.
  • antioxidants are butylated hydroxy anisole (BHA), ascorbic acid and derivatives thereof, tocopherol and derivatives thereof, cysteine, and mixtures thereof.
  • emulsifying agents are naturally occurring gums, e.g. gum acacia or gum tragacanth; naturally occurring phosphatides, e.g. soybean lecithin, sorbitan monooleate derivatives: wool fats; wool alcohols; sorbitan esters; monoglycerides; fatty alcohols; fatty acid esters (e.g. triglycerides of fatty acids); and mixtures thereof.
  • naturally occurring gums e.g. gum acacia or gum tragacanth
  • naturally occurring phosphatides e.g. soybean lecithin
  • sorbitan monooleate derivatives wool fats; wool alcohols; sorbitan esters; monoglycerides; fatty alcohols; fatty acid esters (e.g. triglycerides of fatty acids); and mixtures thereof.
  • suspending agents are e.g., celluloses and cellulose derivatives such as, e.g., carboxymethyl cellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropylmethylcellulose, carraghenan, acacia gum, arabic gum, tragacanth, and mixtures thereof.
  • gel bases examples include: liquid paraffin, polyethylene, fatty oils, colloidal silica or aluminum, zinc soaps, glycerol, propylene glycol, tragacanth, carboxyvinyl polymers, magnesium-aluminum silicates, Carbopol®, hydrophilic polymers such as, e.g. starch or cellulose derivatives such as, e.g., carboxymethylcellulose, hydroxyethylcellulose and other cellulose derivatives, water-swellable hydrocolloids, carragenans, hyaluronates (e.g. hyaluronate gel optionally containing sodium chloride), and alginates including propylene glycol alginate.
  • liquid paraffin such as, e.g. starch or cellulose derivatives such as, e.g., carboxymethylcellulose, hydroxyethylcellulose and other cellulose derivatives, water-swellable hydrocolloids, carragenans, hyaluronates (e.g. hyal
  • ointment bases are e.g., beeswax, paraffin, cetanol, cetyl palmitate, vegetable oils, sorbitan esters of fatty acids (Span), polyethylene glycols, and condensation products between sorbitan esters of fatty acids and ethylene oxide, e g., polyoxyethylene sorbitan monooleate (Tween).
  • hydrophobic or water-emulsifying ointment bases are paraffins, vegetable oils, animal fats, synthetic glycerides, waxes, lanolin, and liquid polyalkylsiloxanes.
  • hydrophilic ointment bases are solid macrogols (polyethylene glycols).
  • Other examples of ointment bases are triethanolamine soaps, sulphated fatty alcohol and polysorbates.
  • excipients examples include polymers such as carmelose, sodium carmelose, hydroxypropylmethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, pectin, xanthan gum, locust bean gum, acacia gum, gelatin, carbomer, emulsifiers like vitamin E, glyceryl stearates, cetanyl glucoside, collagen, carrageenan, hyaluronates and alginates and chitosans.
  • the dose of antibody required in humans to be effective in the treatment or prevention of allergic inflammation differs with the type and severity of the allergic condition to be treated, the type of allergen, the age and condition of the patient, etc.
  • Typical doses of antibody to be administered are in the range of 1 pg to 1 g, preferably 1-1000 pg, more preferably 2-500, even more preferably 5-50, most preferably 10-20 pg per unit dosage form.
  • infusion of antibodies of the present invention can range from 10-500 mg/m 2 .
  • nucleic acids there are a variety of techniques available for introducing nucleic acids into viable cells.
  • the techniques vary depending upon whether the nucleic acid is transferred into cultured cells in vitro, or in vivo in the cells of the intended host.
  • Techniques suitable for the transfer of nucleic acid into mammalian cells in vitro include the use of liposomes, electroporation, microinjection, cell fusion, DEAE-dextran, the calcium phosphate precipitation method, etc.
  • the currently preferred in vivo gene transfer techniques include transfection with viral (typically retroviral) vectors and viral coat protein-liposome mediated transfection.
  • an administration device comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions, sch as a cyclic nucleotide analog or derivative of the disclosure, and/or additional therapeutic agents.
  • treating as referred to herein encompasses enhancing treatment, or improving treatment efficacy.
  • Treatment can include modulation of immune signaling, which can include inhibition of an inflammatory response, tumor regression as well as inhibition of tumor growth, metastasis or tumor cell proliferation, or inhibition or reduction of otherwise deleterious effects associated with the tumor.
  • Efficaciousness of treatment is determined in association with any known method for diagnosing or treating the particular disease.
  • the invention comprehends a treatment method comprising any one of the methods or uses herein discussed.
  • therapeutically effective amount refers to a sufficient amount of a drug, agent, or compound to provide a desired therapeutic effect.
  • Therapy or treatment according to the invention can be performed alone or in conjunction with another therapy, and can be provided at home, the doctor’s office, a clinic, a hospital’s outpatient department, or a hospital. Treatment generally begins at a hospital so that the doctor can observe the therapy’s effects closely and make any adjustments that are needed. The duration of the therapy depends on the age and condition of the patient, the stage of the cancer, and how the patient responds to the treatment.
  • a person having a greater risk of developing an inflammatory response e.g., a person who is genetically predisposed or predisposed to allergies or a person having a disease characterized by episodes of inflammation
  • LC-MS/MS liquid chromatographytandem mass spectrometry
  • Applicants coupled it with a reversed-phase high pressure liquid chromatography (RP-HPLC) step prior to LC-MS/MS.
  • RP-HPLC reversed-phase high pressure liquid chromatography
  • This enabled us to scale up the amount of biological material (cultured cells) used as source material from which Applicants extracted polar metabolites.
  • Applicants were able to positively identify many second messengers downstream of dsDNA or dsRNA that are not identifiable in whole cell extracts with traditional approaches. Because it is analogous to other approaches with two separation steps, Applicants term this approach “2 dimensional LC-MS/MS.”
  • RNA molecules whose synthesis appears to be stimulated by double stranded RNA (dsRNA). Cyclic CMP-AMP (cCAMP) and cyclic AMP- CMP-CMP (cACCMP).
  • cCAMP Cyclic CMP-AMP
  • cACCMP cyclic AMP- CMP-CMP
  • Applicants first utilized 2D LC-MSMS to enrich and deconvolute observable metabolites.
  • Cells treated with dsRNA or dsDNA were grown and subsequently lysed in MeOH/CHCL, with polar phase metabolites fractionated by RP-HPLC (45 fractions).
  • HPLC fractions (2’ each) were resuspended in water, with 1 uL of each fraction assayed by LC-MS/MS to achieve more identifiable novel metabolites.
  • FIG. 1 As depicted in FIG. 2, the 2D metabolomics approach revealed a diverse array of dsRNA-induced second messengers, identified in FIG. 2 by retention time.
  • Applicants used linkage and base specific nucleases to enable the diagnosis of molecule structure of unknown molecules.
  • dsRNA double stranded RNA
  • the individual fractions that had been characterized by LC-MS/MS were treated with the enzymes rsAP, RNAseA, RNAseTl, RNAse T2, Nuclease SI and PDEII (FIG. 3B).
  • the sensitivity or resistance of the dsRNA-induced small molecules to each enzyme gave insight into the potential structures for each individual molecule.
  • Example analogs of cCAMP molecules e.g., 3’,3’-cCAMP
  • alternative phosphodiester linkages e.g., AMP 3’ to CMP 5’ and/or CMP 3’ to AMP 5’
  • FIG. 6 Example analogs of cCAMP molecules (e.g., 3’,3’-cCAMP) having alternative fluorinated substituents (e.g., mono- or di- fluorinated versions) are depicted in FIG. 7 which could have different (e.g., increased) cell permeability.
  • Example analogs of the cCAMP molecules (e g., 3’,3’-cCAMP) having alternative phosphodiester substituents are depicted in FIG. 8 (e.g., mono- or bis-phosphorothioate versions) and in FIG. 9 (e.g., mono- or bis-methylphosphonate versions) which could have different (e.g., increased) resistance to cellular nucleases.
  • Example analogs of cCAMP molecules (e.g., 3 ’,3’- cCAMP) having alternative nucleotide bases (e.g., mono- or poly-substituted nucleotide bases) are depicted in FIG. 10 which could have various purpose (e.g., labeling and the like).
  • Example analogs of cACCMP molecules e.g., 3’,3’,3;-cACCMP
  • alternative fluorinated substituents e.g., mono- or poly -fluorinated versions
  • FIG. 13 which could have different (e.g., increased) cell permeability
  • Example analogs of the cACCMP molecules (e.g., 3’,3’,3’- cACCMP) having alternative phosphodiester substituents are depicted in FIG. 14 (e.g., mono- or poly-phosphorothioate versions) and in FIG. 15 (e.g., mono- orpoly-methylphosphonate versions) which could have different (e.g., increased) resistance to cellular nucleases.
  • Example analogs of cACCMP molecules e.g., 3’,3’,3’-cACCMP
  • nucleotide bases e.g., mono- or poly-substituted nucleotide bases
  • FIG. 16 which could have various purpose (e.g., labeling and the like).
  • FIG. 17 Examples of combinations of cCAMP nucleotides and/or isonucleotides are shown in FIG. 17.
  • FIG. 18 shows examples of 3’,3’-cCAMP with an isonucleotidic AMP group
  • FIG. 19 shows examples of 3’,3’-cCAMP with an isonucleotidic CMP group.
  • Examples of combinations of cACCMP nucleotides and/or isonucleotides are shown in FIG. 20.
  • FIG. 21 shows examples of 3’,3’-cACCMP with an isonucleotidic AMP group.
  • Applicants can perform any modification or combination of modifications (e.g., various fluorinated, phosphorothioate, methyl phosphonate, and/or modified nucleotide base versions) on any cCAMP of any analog configuration (e.g., 2’, 3’; 3’, 3’; and the like)(nucleotides and/or isonucleotides) or any cACCMP of any analog configuration (e g., 3’, 3’; 2’, 3’, 3’; and the like)(nucleotides and/or isonucleotides).
  • modifications e.g., various fluorinated, phosphorothioate, methyl phosphonate, and/or modified nucleotide base versions

Landscapes

  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Epidemiology (AREA)
  • Medicinal Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Animal Behavior & Ethology (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Genetics & Genomics (AREA)
  • Biotechnology (AREA)
  • Engineering & Computer Science (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Abstract

La présente invention concerne de nouveaux dérivés et analogues de nucléotides cycliques basés sur la découverte de nouveaux seconds messagers générés dans des cellules humaines en réponse à des défis du système immunitaire inné. Les compositions trouvent une utilisation dans la modulation de la signalisation immunitaire innée.
PCT/US2023/034632 2022-10-06 2023-10-06 Nucléotides cycliques et leurs utilisations Ceased WO2024076728A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202263413769P 2022-10-06 2022-10-06
US63/413,769 2022-10-06

Publications (1)

Publication Number Publication Date
WO2024076728A1 true WO2024076728A1 (fr) 2024-04-11

Family

ID=88793175

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2023/034632 Ceased WO2024076728A1 (fr) 2022-10-06 2023-10-06 Nucléotides cycliques et leurs utilisations

Country Status (1)

Country Link
WO (1) WO2024076728A1 (fr)

Citations (23)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4737323A (en) 1986-02-13 1988-04-12 Liposome Technology, Inc. Liposome extrusion method
US4837028A (en) 1986-12-24 1989-06-06 Liposome Technology, Inc. Liposomes with enhanced circulation time
US20020150626A1 (en) 2000-10-16 2002-10-17 Kohane Daniel S. Lipid-protein-sugar particles for delivery of nucleic acids
US20050123596A1 (en) 2003-09-23 2005-06-09 Kohane Daniel S. pH-triggered microparticles
US20090312724A1 (en) 2007-06-28 2009-12-17 Cydex Pharmaceuticals, Inc. Nasal and Ophthalmic Delivery of Aqueous Corticosteroid Solutions
US20140301951A1 (en) 2009-01-05 2014-10-09 Juewen Liu Porous nanoparticle supported lipid nanostructures
WO2014210353A2 (fr) 2013-06-27 2014-12-31 10X Technologies, Inc. Compositions et procédés de traitement d'échantillon
US20150250725A1 (en) 2010-08-30 2015-09-10 Hoffmann-La Roche Inc. Method for producing a lipid particle, the lipid particle itself and its use
US20160060691A1 (en) 2013-05-23 2016-03-03 The Board Of Trustees Of The Leland Stanford Junior University Transposition of Native Chromatin for Personal Epigenomics
WO2016040476A1 (fr) 2014-09-09 2016-03-17 The Broad Institute, Inc. Procédé à base de gouttelettes et appareil pour l'analyse composite d'acide nucléique de cellules uniques
US20160174546A1 (en) 2014-12-22 2016-06-23 Oro Agri Inc Nano particulate delivery system
US20160208323A1 (en) 2013-06-21 2016-07-21 The Broad Institute, Inc. Methods for Shearing and Tagging DNA for Chromatin Immunoprecipitation and Sequencing
WO2016168584A1 (fr) 2015-04-17 2016-10-20 President And Fellows Of Harvard College Systèmes de codes barres et procédés de séquençage de gènes et autres applications
US20170079916A1 (en) 2015-09-23 2017-03-23 Massachusetts Institute Of Technology Compositions and methods for modified dendrimer nanoparticle delivery
WO2017106740A1 (fr) * 2015-12-16 2017-06-22 Aduro Biotech, Inc. Procédés servant à identifier des inhibiteurs de la production d'interféron dépendant du stimulateur du gène d'interféron
WO2017156336A1 (fr) 2016-03-10 2017-09-14 The Board Of Trustees Of The Leland Stanford Junior University Imagerie médiée par une transposase du génome accessible
WO2017164936A1 (fr) 2016-03-21 2017-09-28 The Broad Institute, Inc. Procédés de détermination de la dynamique d'expression génique spatiale et temporelle dans des cellules uniques
WO2018009652A1 (fr) * 2016-07-06 2018-01-11 Sperovie Biosciences, Inc. Composés, compositions et méthodes de traitement de maladie
WO2018009648A1 (fr) * 2016-07-06 2018-01-11 Sperovie Biosciences, Inc. Composés, compositions et méthodes de traitement de maladie
WO2019094984A1 (fr) 2017-11-13 2019-05-16 The Broad Institute, Inc. Procédés de détermination de la dynamique d'expression génique spatiale et temporelle pendant la neurogenèse adulte dans des cellules uniques
WO2019161171A1 (fr) * 2018-02-16 2019-08-22 Sperovie Biosciences, Inc. Formulations de nanoparticules d'agonistes de sting
WO2020014127A1 (fr) * 2018-07-10 2020-01-16 Sperovie Biosciences, Inc. Composés, compositions et procédés pour le traitement d'une maladie
WO2020077236A1 (fr) 2018-10-12 2020-04-16 The Broad Institute, Inc. Procédés d'extraction de noyaux et de cellules à partir de tissus fixés au formol et inclus en paraffine

Patent Citations (23)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4737323A (en) 1986-02-13 1988-04-12 Liposome Technology, Inc. Liposome extrusion method
US4837028A (en) 1986-12-24 1989-06-06 Liposome Technology, Inc. Liposomes with enhanced circulation time
US20020150626A1 (en) 2000-10-16 2002-10-17 Kohane Daniel S. Lipid-protein-sugar particles for delivery of nucleic acids
US20050123596A1 (en) 2003-09-23 2005-06-09 Kohane Daniel S. pH-triggered microparticles
US20090312724A1 (en) 2007-06-28 2009-12-17 Cydex Pharmaceuticals, Inc. Nasal and Ophthalmic Delivery of Aqueous Corticosteroid Solutions
US20140301951A1 (en) 2009-01-05 2014-10-09 Juewen Liu Porous nanoparticle supported lipid nanostructures
US20150250725A1 (en) 2010-08-30 2015-09-10 Hoffmann-La Roche Inc. Method for producing a lipid particle, the lipid particle itself and its use
US20160060691A1 (en) 2013-05-23 2016-03-03 The Board Of Trustees Of The Leland Stanford Junior University Transposition of Native Chromatin for Personal Epigenomics
US20160208323A1 (en) 2013-06-21 2016-07-21 The Broad Institute, Inc. Methods for Shearing and Tagging DNA for Chromatin Immunoprecipitation and Sequencing
WO2014210353A2 (fr) 2013-06-27 2014-12-31 10X Technologies, Inc. Compositions et procédés de traitement d'échantillon
WO2016040476A1 (fr) 2014-09-09 2016-03-17 The Broad Institute, Inc. Procédé à base de gouttelettes et appareil pour l'analyse composite d'acide nucléique de cellules uniques
US20160174546A1 (en) 2014-12-22 2016-06-23 Oro Agri Inc Nano particulate delivery system
WO2016168584A1 (fr) 2015-04-17 2016-10-20 President And Fellows Of Harvard College Systèmes de codes barres et procédés de séquençage de gènes et autres applications
US20170079916A1 (en) 2015-09-23 2017-03-23 Massachusetts Institute Of Technology Compositions and methods for modified dendrimer nanoparticle delivery
WO2017106740A1 (fr) * 2015-12-16 2017-06-22 Aduro Biotech, Inc. Procédés servant à identifier des inhibiteurs de la production d'interféron dépendant du stimulateur du gène d'interféron
WO2017156336A1 (fr) 2016-03-10 2017-09-14 The Board Of Trustees Of The Leland Stanford Junior University Imagerie médiée par une transposase du génome accessible
WO2017164936A1 (fr) 2016-03-21 2017-09-28 The Broad Institute, Inc. Procédés de détermination de la dynamique d'expression génique spatiale et temporelle dans des cellules uniques
WO2018009652A1 (fr) * 2016-07-06 2018-01-11 Sperovie Biosciences, Inc. Composés, compositions et méthodes de traitement de maladie
WO2018009648A1 (fr) * 2016-07-06 2018-01-11 Sperovie Biosciences, Inc. Composés, compositions et méthodes de traitement de maladie
WO2019094984A1 (fr) 2017-11-13 2019-05-16 The Broad Institute, Inc. Procédés de détermination de la dynamique d'expression génique spatiale et temporelle pendant la neurogenèse adulte dans des cellules uniques
WO2019161171A1 (fr) * 2018-02-16 2019-08-22 Sperovie Biosciences, Inc. Formulations de nanoparticules d'agonistes de sting
WO2020014127A1 (fr) * 2018-07-10 2020-01-16 Sperovie Biosciences, Inc. Composés, compositions et procédés pour le traitement d'une maladie
WO2020077236A1 (fr) 2018-10-12 2020-04-16 The Broad Institute, Inc. Procédés d'extraction de noyaux et de cellules à partir de tissus fixés au formol et inclus en paraffine

Non-Patent Citations (56)

* Cited by examiner, † Cited by third party
Title
"Current Protocols in Molecular Biology", 1987
"Encyclopedia of Pharmaceutical Technology", 1988, MARCEL DEKKER
"Molecular Biology and Biotechnology", 1995, VCH PUBLISHERS, INC., article "a Comprehensive Desk Reference"
"The Encyclopedia of Molecular Biology", 1994, BLACKWELL SCIENCE
BALDRICK P: "Pharmaceutical excipient development: the need for preclinical guidance.", REGUL. TOXICOL PHARMACOL., vol. 32, no. 2, 2000, pages 210 - 8
BENJAMIN LEWIN: "Genes IX", 2008, JONES AND BARTLET
BLAUG, SEYMOUR: "Remington's Pharmaceutical Sciences", vol. 87, 1975, MACK PUBLISHING COMPANY
BONDESONCREWS: "Targeted Protein Degradation by Small Molecules", ANNU REV PHARMACOL TOXICOL., vol. 57, 6 January 2017 (2017-01-06), pages 107 - 123
BROWN, AEROSOL SCIENCE AND TECHNOLOGY, vol. 24, 1996, pages 45 - 56
BUENROSTRO ET AL.: "Single-cell chromatin accessibility reveals principles of regulatory variation.", NATURE, vol. 523, 2015, pages 486 - 490, XP055782270, DOI: 10.1038/nature14590
BUENROSTRO ET AL.: "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.", NATURE METHODS, vol. 10, no. 12, 2013, pages 1213 - 1218, XP055554120, DOI: 10.1038/nmeth.2688
CAO ET AL.: "Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing", BIORXIV, 2 February 2017 (2017-02-02)
CAO ET AL.: "Comprehensive single-cell transcriptional profiling of a multicellular organism.", SCIENCE, vol. 357, no. 6352, 2017, pages 661 - 667, XP055624798, DOI: 10.1126/science.aam8940
CAPOBIANCO MASSIMO L. ET AL: "One pot solution synthesis of cyclic oligodeoxyribonucleotides", NUCLEIC ACIDS RESEARCH, vol. 18, no. 9, 1 January 1990 (1990-01-01), GB, pages 2661 - 2669, XP093117672, ISSN: 0305-1048, Retrieved from the Internet <URL:https://dx.doi.org/10.1093/nar/18.9.2661> DOI: 10.1093/nar/18.9.2661 *
CHARMAN WN: "Lipids, lipophilic drugs, and oral drug delivery-some emerging concepts.", J PHARM SCI., vol. 89, no. 8, 2000, pages 967 - 78, XP008099512
CUSANOVICH, D. A.DAZA, R.ADEY, A.PLINER, HCHRISTIANSEN, L.GUNDERSON, K. L.STEEMERS, F. J.TRAPNELL, C.SHENDURE, J.: "Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing.", SCIENCE, vol. 348, no. 6237, 2015, pages 910 - 4, XP055416774, DOI: 10.1126/science.aab1601
DROKHLYANSKY ET AL.: "The enteric nervous system of the human and mouse colon at a single-cell resolution", BIORXIV 746743
FANTONI ET AL.: "A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids", CHEM. REV., vol. 121, no. 12, 2021, pages 7122 - 7154, XP055944634, DOI: 10.1021/acs.chemrev.0c00928
GIERAHN ET AL.: "Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput", NATURE METHODS, vol. 14, 2017, pages 395 - 398
GOODSON: "Medical Applications of Controlled Release", 1984, CRC PRESS
HABIB ET AL.: "Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons", SCIENCE, vol. 353, 2016, pages 925 - 928, XP055608529, DOI: 10.1126/science.aad7038
HABIB ET AL.: "Massively parallel single-nucleus RNA-seq with DroNc-seq", NAT METHODS., vol. 14, no. 10, 2017, pages 955 - 958, XP055651390, DOI: 10.1038/nmeth.4407
HASHIMSHONY, T.WAGNER, F.SHER, N.YANAI, I.: "CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification. Cell Reports", CELL REPORTS, vol. 2, 2012, pages 666 - 673, XP055111758, DOI: 10.1016/j.celrep.2012.08.003
HOU ET AL., CELL CHEM. BIOL., vol. 29, no. 1, 2022, pages 133 - 144
HOU ET AL.: "Protocol for identification and validation of 2'3'-cGAMP-binding proteins by photoaffinity probes", STAR PROTOCOLS, vol. 3, 18 March 2022 (2022-03-18), pages 101076
HOWARD ET AL., J. NEUROSURG., vol. 71, 1989, pages 105
HUGHES ET AL.: "Highly Efficient, Massively-Parallel Single-Cell RNA-Seq Reveals Cellular States and Molecular Features of Human Skin Pathology", BIORXIV 689273
ISLAM, S. ET AL.: "Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.", GENOME RESEARCH, 2011
KALISKY, T.BLAINEY, P.QUAKE, S. R.: "Genomic Analysis at the Single-Cell Level.", ANNUAL REVIEW OF GENETICS, vol. 45, 2011, pages 431 - 445
KALISKY, T.QUAKE, S. R.: "Single-cell genomics.", NATURE METHODS, vol. 8, 2011, pages 311 - 314
KLEIN ET AL.: "Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells", CELL, vol. 161, 2015, pages 1187 - 1201, XP055731640, DOI: 10.1016/j.cell.2015.04.044
LAI ET AL.: "Modular PROTAC Design for the Degradation of Oncogenic BCR-ABL", ANGEW CHEM INT ED ENGL., vol. 55, no. 2, 11 January 2016 (2016-01-11), pages 807 - 810, XP055734239, DOI: 10.1002/anie.201507634
LAMB ET AL.: "The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease.", SCIENCE, vol. 3, no. 13, 29 September 2006 (2006-09-29), pages 1929 - 1935
LAMB, J.: "The Connectivity Map: a new tool for biomedical research.", NATURE REVIEWS CANCER, vol. 7, January 2007 (2007-01-01), pages 54 - 60, XP002543990, DOI: 10.1038/nrc2044
MACOSKO ET AL.: "Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets", CELL, vol. 161, 2015, pages 1202 - 1214, XP055586617, DOI: 10.1016/j.cell.2015.05.002
MARUYAMA ET AL., BIOCHIM. BIOPHYS. ACTA, vol. 1234, 1995, pages 74 - 80
MATEUS ET AL., MOL SYST BIOL, vol. 16, no. 3, March 2020 (2020-03-01), pages 9232
PCR 2: A PRACTICAL APPROACH, 1995
PIAZZA ET AL., J. INFECT. DIS., vol. 166, 1992, pages 1422 - 1424
PICELLI, S. ET AL.: "Full-length RNA-seq from single cells using Smart-seq2", NATURE PROTOCOLS, vol. 9, 2014, pages 171 - 181, XP002742134, DOI: 10.1038/nprot.2014.006
POWELL ET AL.: "Compendium of excipients for parenteral formulations", PDA J PHARM SCI TECHNOL., vol. 52, 1998, pages 238 - 311, XP009119027
RAMSKOLD, D. ET AL.: "Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.", NATURE BIOTECHNOLOGY, vol. 30, 2012, pages 777 - 782, XP037004921, DOI: 10.1038/nbt.2282
ROSENBERG ET AL.: "Scaling single cell transcriptomics through split pool barcoding", BIORXIV PREPRINT FIRST POSTED ONLINE, 2 February 2017 (2017-02-02)
ROSENBERG ET AL.: "Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding", SCIENCE, 15 March 2018 (2018-03-15)
SAUDEK ET AL., NEW ENGL. J. MED., vol. 321, no. 574, 1989
STEGMAIER ET AL.: "Gene expression-based high-throughput screening (GE-HTS) and application to leukemia differentiation.", NATURE GENET., vol. 36, 2004, pages 257 - 263, XP008039240, DOI: 10.1038/ng1305
SWIECH ET AL.: "In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9", NATURE BIOTECHNOLOGY, vol. 33, 2014, pages 102 - 106, XP055176807, DOI: 10.1038/nbt.3055
TANG, F. ET AL.: "mRNA-Seq whole-transcriptome analysis of a single cell.", NATURE METHODS, vol. 6, 2009, pages 377 - 382, XP055037482, DOI: 10.1038/nmeth.1315
TANG, F. ET AL.: "RNA-Seq analysis to capture the transcriptome landscape of a single cell.", NATURE PROTOCOLS, vol. 5, 2010, pages 516 - 535, XP009162232, DOI: 10.1038/nprot.2009.236
VITAK ET AL.: "Sequencing thousands of single-cell genomes with combinatorial indexing", NATURE METHODS, vol. 14, no. 3, 2017, pages 302 - 308
WANG W: "Lyophilization and development of solid protein pharmaceuticals.", INT. J. PHARM., vol. 203, no. 1-2, 2000, pages 1 - 60, XP002428586, DOI: 10.1016/S0378-5173(00)00423-3
ZENG FAN ET AL: "SYNTHESIS OF CYCLIC DINUCLEOTIDES BY AN H-PHOSPHONATE METHOD IN SOLUTION", NUCLEOSIDES AND NUCLEOTIDES, vol. 15, no. 11-12, 22 November 1996 (1996-11-22), US, pages 1679 - 1686, XP093117675, ISSN: 0732-8311, Retrieved from the Internet <URL:https://dx.doi.org/10.1080/07328319608002723> DOI: 10.1080/07328319608002723 *
ZHENG ET AL.: "Haplotyping germline and cancer genomes with high-throughput linked-read sequencing", NATURE BIOTECHNOLOGY, vol. 34, 2016, pages 303 - 311, XP055486933, DOI: 10.1038/nbt.3432
ZHENG ET AL.: "Massively parallel digital transcriptional profiling of single cells", NAT. COMMUN., vol. 8, 2017, pages 14049
ZHOU ET AL.: "Discovery of a Small-Molecule Degrader of Bromodomain and Extra- Terminal (BET) Proteins with Picomolar Cellular Potencies and Capable of Achieving Tumor Regression.", J. MED. CHEM., vol. 61, 2018, pages 462 - 481
ZILIONIS ET AL.: "Single-cell barcoding and sequencing using droplet microfluidics", NAT PROTOC., vol. 12, no. 1, 2017, pages 44 - 73, XP055532179, DOI: 10.1038/nprot.2016.154

Similar Documents

Publication Publication Date Title
JP2022519557A (ja) 脂質ナノ粒子の調製方法
JP2022501367A (ja) 脂質ナノ粒子の調製及びその投与方法
CN104922676B (zh) 聚胺衍生物
KR102262260B1 (ko) 엔도좀 탈출능을 갖는 펩티드 핵산 복합체 및 이의 용도
US10538757B2 (en) Nanozymes, methods of making nanozymes, and methods of using nanozymes
US20150064233A1 (en) Lipid-coated nucleic acid nanostructures of defined shape
JP2020532528A (ja) 脂質ナノ粒子の生成方法
US9061042B2 (en) Composition for suppressing expression of target gene
KR20190020299A (ko) 면역 조정 폴리펩타이드를 암호화하는 mRNA의 조합물 및 이의 용도
JP6124078B2 (ja) 巨大環状脂肪族化合物及びその応用
JP2017531451A (ja) 抗ｔｎｆ化合物
JP2024535004A (ja) イオン化可能な脂質その調製および遺伝子送達における使用
CN113121381B (zh) 一种神经酰胺类化合物及其阳离子脂质体、制备方法和应用
Ji et al. Lipid microparticles show similar efficacy with lipid nanoparticles in delivering mRNA and preventing cancer
JP2017509648A (ja) 局所送達用アプタマー
Kwon et al. Ligand-induced GPR110 activation facilitates axon growth after injury
TW201821125A (zh) 皮膚纖維化症治療劑
Ceccarelli et al. Human microglia extracellular vesicles derived from different microglia cell lines: similarities and differences
WO2024076728A1 (fr) Nucléotides cycliques et leurs utilisations
JP2023541886A (ja) 超長鎖多価不飽和脂肪酸、エロバノイドヒドロキシル化誘導体、及び使用方法
Yin et al. Nano-adjuvant based on lipo-imiquimod self-assembly for enhanced foot-and-mouth disease virus vaccine immune responses via intradermal immunization
US20180016582A1 (en) Dna aptamer binding to non-small cell lung cancer cells (h1975)
EP4609867A1 (fr) Conjugué de molécule chargée de lipides, nanoparticule lipidique inhalable, procédé de préparation s&#39;y rapportant et utilisation associée
CN105085292B (zh) 3‑((2‑(二甲氨基)乙烷基)(甲基)氨基)丙酸的两亲性衍生物及其用途
CN117257965A (zh) 一种核酸递送载体组合物及其应用

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 23805717

Country of ref document: EP

Kind code of ref document: A1

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 23805717

Country of ref document: EP

Kind code of ref document: A1