IL309001A - Antisense compounds and methods for targeting cug repeats - Google Patents

Antisense compounds and methods for targeting cug repeats

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Publication number
IL309001A
IL309001A IL309001A IL30900123A IL309001A IL 309001 A IL309001 A IL 309001A IL 309001 A IL309001 A IL 309001A IL 30900123 A IL30900123 A IL 30900123A IL 309001 A IL309001 A IL 309001A
Authority
IL
Israel
Prior art keywords
compound
cag cag
peptide
side chain
amino acid
Prior art date
Application number
IL309001A
Other languages
Hebrew (he)
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Entrada Therapeutics Inc
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Publication date
Application filed by Entrada Therapeutics Inc filed Critical Entrada Therapeutics Inc
Publication of IL309001A publication Critical patent/IL309001A/en

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/70Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088Compounds having three or more nucleosides or nucleotides
    • A61K31/712Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/62Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being a protein, peptide or polyamino acid
    • A61K47/64Drug-peptide, drug-protein or drug-polyamino acid conjugates, i.e. the modifying agent being a peptide, protein or polyamino acid which is covalently bonded or complexed to a therapeutically active agent
    • A61K47/645Polycationic or polyanionic oligopeptides, polypeptides or polyamino acids, e.g. polylysine, polyarginine, polyglutamic acid or peptide TAT
    • A61K47/6455Polycationic oligopeptides, polypeptides or polyamino acids, e.g. for complexing nucleic acids
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P21/00Drugs for disorders of the muscular or neuromuscular system
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00Drugs for disorders of the nervous system
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K19/00Hybrid peptides, i.e. peptides covalently bound to nucleic acids, or non-covalently bound protein-protein complexes
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K7/00Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/64Cyclic peptides containing only normal peptide links
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01KANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00Genetically modified animals
    • A01K2217/07Animals genetically altered by homologous recombination
    • A01K2217/072Animals genetically altered by homologous recombination maintaining or altering function, i.e. knock in
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01KANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2227/00Animals characterised by species
    • A01K2227/10Mammal
    • A01K2227/105Murine
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01KANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2267/00Animals characterised by purpose
    • A01K2267/03Animal model, e.g. for test or diseases
    • A01K2267/0306Animal model for genetic diseases
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2300/00Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00Medicinal preparations containing peptides
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/10Type of nucleic acid
    • C12N2310/11Antisense
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/30Chemical structure
    • C12N2310/32Chemical structure of the sugar
    • C12N2310/323Chemical structure of the sugar modified ring structure
    • C12N2310/3233Morpholino-type ring
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/30Chemical structure
    • C12N2310/35Nature of the modification
    • C12N2310/351Conjugate
    • C12N2310/3513Protein; Peptide

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Animal Behavior & Ethology (AREA)
  • Biomedical Technology (AREA)
  • Biophysics (AREA)
  • Epidemiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Biotechnology (AREA)
  • Neurology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Microbiology (AREA)
  • Plant Pathology (AREA)
  • Physical Education & Sports Medicine (AREA)
  • Orthopedic Medicine & Surgery (AREA)
  • Physics & Mathematics (AREA)
  • Neurosurgery (AREA)
  • Immunology (AREA)
  • Peptides Or Proteins (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Acyclic And Carbocyclic Compounds In Medicinal Compositions (AREA)
  • Medicinal Preparation (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Claims (39)

252 CLAIMS
1. A compound comprising: (a) an antisense compound that is complementary to at least a portion of an expanded CUG repeat in a target mRNA sequence; (b) a cyclic peptide of the formula: or a protonated form thereof, wherein: R1, R2, and R3 are each independently H or an aromatic or heteroaromatic side chain of an amino acid; at least one of R1, R2, and R3 is an aromatic or heteroaromatic side chain of an amino acid; R4, R5, R6, R7 are independently H or an amino acid side chain; AASC is an amino acid side chain; and q is 1, 2, 3 or 4, wherein at least two amino acids of the cyclic peptide are charged amino acids, at least two amino acids of the cyclic peptide are aromatic hydrophobic amino acids, and at least two amino acids of the cyclic peptide are uncharged, non-aromatic amino acids.
2. The compound of claim 1, wherein at least two of R1, R2, and R3 are side chains of aromatic hydrophobic amino acids.
3. The compound of claim 1, wherein at least two of R1, R2, and R3 are independently phenylalanine or naphthylalanine. 253
4. The compound of claim 1 or claim 2, wherein at least two of R5, R6, and R7 are side chains of charged amino acids.
5. The compound of claim 1 or 2, wherein at least two of R5, R6, and R7 are independently arginine, homoarginine, N-methylarginine, and N,N-dimethylarginine.
6. The compound of any one of claims 1 to 5, wherein q is 1.
7. The compound of any one of claims 1 to 6, wherein R4 is H.
8. A compound comprising: (a) an antisense compound that is complementary to at least a portion of an expanded CUG repeat in a target mRNA sequence; (b) a cyclic peptide of the formula: , , or a protonated form thereof, wherein: R1, R2, and R3 are each independently H or an amino acid residue having a side chain comprising an aromatic group; at least two of R1, R2, and R3 are the side chain of phenylalanine; R4 is H or an amino acid side chain; AASC is an amino acid side chain; and each m is independently an integer of 0, 1, 2, or 3. 254
9. The compound of claim 8, wherein one of R1, R2, and R3 is naphthylalanine.
10. The compound of claim 8, wherein one of R1, R2, and R3 is H.
11. The compound of any one of claims 8 to 10, wherein R4 is H.
12. The compound of any one of claims 1 to 11, wherein the cyclic cell penetrating peptide is selected from , , 255 , , or a protonated form thereof.
13. The compound of any one of claims 1 to 12, wherein the compound further comprises an exocyclic peptide.
14. The compound of claim 13, wherein the exocyclic peptide comprises from 2 to 10 amino acids. 256
15. The compound of claim 13 or 14, wherein the exocyclic peptide comprises 2, 3, or 4 lysine residues.
16. The compound of any one of claims 13 to 15, wherein the exocyclic peptide comprises at least 2 amino acid residues with a hydrophobic side chain.
17. The compound of any one of claims 13 to 15, wherein the exocyclic peptide comprises PGKKRKV.
18. The compound of any one of claims 13 to 15, wherein the exocyclic peptide comprises PKKKRKV.
19. The compound of any one of claims 13 to 15, wherein the exocyclic peptide comprises PKKKGKV.
20. The compound of any one of claims 13 to 15, wherein the exocyclic peptide comprises PKKKRKG.
21. The compound of any one of claims 13 to 20, further comprising a linker, wherein the linker conjugates the antisense compound and the exocyclic peptide to the cyclic peptide.
22. The compound of claim 21, wherein the linker has the following structure: , wherein A1, B1, and C1, each independently comprise a hydrocarbon linker, a polyethylene glycol (PEG) linker, or one or more amino acid residue.
23. The compound of claim 21, wherein the linker has the following formula: 257 wherein: x’ is an integer from 1-23; y is an integer from 1-5; z’ is an integer from 1-23; * is the point of attachment to the AASC of the cyclic peptide; and M is a bonding group.
24. The compound of claim 23, wherein z’ is 11.
25. The compound of claim 23 or 24, wherein x’ is 1.
26. The compound of any one of claims 23 to 25, wherein the exocyclic peptide is conjugated to the linker at the amino end of the linker and the antisense compound is conjugated to M.
27. The compound of any one of claims 23 to 26, wherein M is -C(O)-.
28. The compound of claim 23, wherein the compound is selected from 258 259 or a protonated form or salt thereof, wherein EP is the exocyclic peptide, and 260 oligonucleotide is the antisense compound.
29. The compound of any one of claims 1 to 28, wherein the antisense compound comprises AG(CAG)n, G(CAG)n, (CAG)nAG, or (CAG)nA, wherein n is an integer from 1 to 50.
30. The compound of any one of claims 1 to 28, wherein the antisense compound comprises 5 to 10 CAG repeats.
31. The compound of any one of claims 1 to 28, wherein the antisense compound comprises 5’-CAG CAG CAG CAG CAG CAG CAG CAG-3’.
32. The compound of any one of claims 1 to 28, wherein the antisense compound comprises 5’-CAG CAG CAG CAG CAG CAG CAG CAG CAG-3’.
33. The compound of any one of claims 1 to 28, wherein the antisense compound comprises 5’-CAG CAG CAG CAG CAG CAG CAG-3’.
34. The compound of any one of claims 29 or claim 33, wherein the antisense compound further comprises any one of GGGCCTTTTATTCGCGAGGGTCGGG; GAGGGCCTTTTATTCGCGAGGGTCG; TGGAGGGCCTTTTATTCGCGAGGGT; GATGGAGGGCCTTTTATTCGCGAGG; CAGATGGAGGGCCTTTTATTCGCGA; GGCAGATGGAGGGCCTTTTATTCGC; TGGGCAGATGGAGGGCCTTTTATTC; TTTGGGCAGATGGAGGGCCTTTTAT; GCTTTGGGCAGATGGAGGGCCTTTT; GAGCTTTGGGCAGATGGAGGGCCTT; CAGAGCTTTGGGCAGATGGAGGGCC; 261 TCCAGAGCTTTGGGCAGATGGAGGG; AGTCCAGAGCTTTGGGCAGATGGAG; GGAGTCCAGAGCTTTGGGCAGATGG; GTGGAGTCCAGAGCTTTGGGCAGAT; CTGTGGAGTCCAGAGCTTTGGGCAG; CACTGTGGAGTCCAGAGCTTTGGGC; GACACTGTGGAGTCCAGAGCTTTGG; CGGACACTGTGGAGTCCAGAGCTTT; CGCGGACACTGTGGAGTCCAGAGCT; ACCGCGGACACTGTGGAGTCCAGAG; AAACCGCGGACACTGTGGAGTCCAG; GCAAACCGCGGACACTGTGGAGTCC; ACGCAAACCGCGGACACTGTGGAGT; or CAACGCAAACCGCGGACACTGTGGA.
35. A pharmaceutical composition comprising the compound of any one of claims 1 to 34.
36. A method of treating myotonic dystrophy (DM) in a subject in need thereof, comprising administering the compound of any one of claims 1 to 34 or the composition of claim 35 to the subject.
37. The method of claim 36, wherein the administering results in an increase in the expression of a wild-type protein in muscle tissue, wherein the wild-type protein is expressed from a gene that does not have an expanded CUG repeat.
38. The method of 37, wherein the muscle tissue is diaphragm tissue, quadricep tissues, heat tissue, or any combination thereof.
39. The method of any one of claims 36 to 38, wherein the administration prevents or reduces foci formation.
IL309001A 2021-06-23 2022-06-22 Antisense compounds and methods for targeting cug repeats IL309001A (en)

Applications Claiming Priority (16)

Application Number Priority Date Filing Date Title
US202163213900P 2021-06-23 2021-06-23
US202163239847P 2021-09-01 2021-09-01
US202163239671P 2021-09-01 2021-09-01
US202163290892P 2021-12-17 2021-12-17
US202163290960P 2021-12-17 2021-12-17
US202263298565P 2022-01-11 2022-01-11
US202263305071P 2022-01-31 2022-01-31
US202263268577P 2022-02-25 2022-02-25
US202263314369P 2022-02-26 2022-02-26
US202263316634P 2022-03-04 2022-03-04
US202263317856P 2022-03-08 2022-03-08
US202263326201P 2022-03-31 2022-03-31
US202263362295P 2022-03-31 2022-03-31
US202263327179P 2022-04-04 2022-04-04
US202263339250P 2022-05-06 2022-05-06
PCT/US2022/034517 WO2022271818A1 (en) 2021-06-23 2022-06-22 Antisense compounds and methods for targeting cug repeats

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IL309001A true IL309001A (en) 2024-02-01

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EP (1) EP4359006A1 (en)
JP (1) JP2024524291A (en)
KR (1) KR20240038967A (en)
AU (1) AU2022298774A1 (en)
CA (1) CA3222824A1 (en)
CL (1) CL2023003840A1 (en)
CO (1) CO2023018002A2 (en)
DO (1) DOP2023000279A (en)
EC (1) ECSP23096162A (en)
IL (1) IL309001A (en)
MX (1) MX2023015509A (en)
WO (1) WO2022271818A1 (en)

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WO2023219933A1 (en) * 2022-05-09 2023-11-16 Entrada Therapeutics, Inc. Compositions and methods for delivery of nucleic acid therapeutics
GB2628421A (en) * 2023-03-24 2024-09-25 Syntherix Ltd Peptides and uses thereof

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