Capsid variants and methods of using the same

{
  "publication_number": "US2026102516A1",
  "country": "US",
  "kind": "A1",
  "title": "Capsid variants and methods of using the same",
  "abstract": "The disclosure is directed in part to variant capsid polypeptides that can be used to deliver pay loads.",
  "claims": [
    "1. A variant capsid polypeptide comprising a polypeptide that has at least 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99%, or 100% identity to a VP1, VP2, or VP3 sequence of SEQ ID NO: 17, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, or SEQ ID NO: 46. 2. The variant capsid polypeptide of claim 1, wherein the polypeptide comprises: a mutation selected from a mutation associated with any of VAR-1 to VAR-13. 3. The variant capsid polypeptide of claim 2, wherein: the mutation associated with any of VAR-1 to VAR-13 comprises mutations at positions corresponding to residues 551-597 as compared to SEQ ID NO: 1. 4. The variant capsid polypeptide of any one of the preceding claims, wherein the polypeptide comprises a sequence having at least 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% identity to SEQ ID NO: 1 and comprises a mutation selected from a mutation associated with any of VAR-1 to VAR-13. 5. The variant capsid polypeptide of any one of the preceding claims, wherein the polypeptide comprises a sequence having at least 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% identity to SEQ ID NO: 1 and wherein the variant capsid polypeptide comprises a mutation that corresponds to a mutation at position 551, 575, 584, 586, 587, 589, 591, or 597, or any combination thereof, an insertion between positions 584 and 585, 586 and 587, or 587 and 588, or any combination thereof according to SEQ ID NO: 1, optionally wherein the mutation comprises an insertion, a deletion or a substitution. 6. The variant capsid polypeptide of any one of the preceding claims, wherein the polypeptide comprises: an insertion between positions 584 and 585, 586 and 587, or 587 and 588 or any combination thereof, according to SEQ ID NO: 1; a mutation that corresponds to a mutation at position 551, 586 (e.g., an insertion of one or more amino acids after position 586), 587, 589, and 597 as compared to SEQ ID NO: 1; a mutation that corresponds to a mutation at position 584 (e.g., an insertion of one or more amino acids after position 584), 586, and 587 as compared to SEQ ID NO: 1; a mutation that corresponds to a mutation at position 586 (e.g., an insertion of one or more amino acids after position 586) and 587 as compared to SEQ ID NO: 1; a mutation that corresponds to a mutation at position 586 (e.g., an insertion of one or more amino acids after position 586), 587, and 597 as compared to SEQ ID NO: 1; a mutation that corresponds to a mutation at position 575, 586 (e.g., an insertion of one or more amino acids after position 586), and 587 as compared to SEQ ID NO: 1; a mutation that corresponds to a mutation at position 584 (e.g., an insertion of one or more amino acids after position 584) and 587 as compared to SEQ ID NO: 1; a mutation that corresponds to a mutation at position 587 (e.g., an insertion of one or more amino acids after position 587) as compared to SEQ ID NO: 1; a mutation that corresponds to a mutation at position 587 (e.g., an insertion of one or more amino acids after position 587) and 591 as compared to SEQ ID NO: 1; an insertion, e.g., an insertion of 1 or more amino acids, e.g., 1 amino acid, e.g., 1-2 amino acids, that corresponds to an insertion between positions 584 and 585, 586 and 587, or 587 and 588, as compared to SEQ ID NO: 1; a mutation comprising a T597 substitution as compared to SEQ ID NO: 1, and optionally further comprising an insertion after glycine (G) at position 586 as compared to SEQ ID NO: 1; a mutation comprising a T597 as compared to SEQ ID NO: 1 and the threonine-arginine-proline-alanine (“TRPA”) sequence, and optionally wherein the TRPA sequence is at a location N-terminal to a position corresponding to 588, as compared to SEQ ID NO: 1; a mutation comprising a T597 substitution as compared to SEQ ID NO: 1 and the methionine-arginine-proline-alanine (“MRPA”) sequence, and optionally wherein the MRPA sequence is at a location N-terminal to a position corresponding to 588, as compared to SEQ ID NO: 1; an insertion comprising a sequence ANALAIEQTRP (SEQ ID NO: 39) inserted between positions G586 and N587 compared to SEQ ID NO: 1, and optionally further comprising a mutation at position N587 to an alanine as compared to SEQ ID NO: 1; an insertion comprising a sequence RARLDETA (SEQ ID NO: 37) inserted between positions Q584 and R585 compared to SEQ ID NO: 1, and optionally further comprising a mutation at position G586 to a proline and a mutation at position N587 to an alanine as compared to SEQ ID NO: 1; or a combination of any of the foregoing. 7. The variant capsid polypeptide of any one of the preceding claims, wherein the capsid polypeptide comprises: a mutation of N551H, N587A, Q589A, and T597N, and an insertion between positions 586 and 587 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of LAKGETMRP (SEQ ID NO: 36), or a fragment of at least 4, at least 5, at least 6, at least 7, or at least 8 amino acids thereof; a mutation of G586P and N587A, and an insertion between positions 584 and 585 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of RARLDETA (SEQ ID NO: 37) or a fragment of at least 4, at least 5, at least 6, or at least 7 amino acids thereof; a mutation of N587A and an insertion between positions 586 and 587 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of LAKGETMRP (SEQ ID NO: 36), or a fragment of at least 4, at least 5, at least 6, at least 7, or at least 8 amino acids thereof; a mutation of N587A and T597W, and an insertion between positions 586 and 587 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of GVRAETTRP (SEQ ID NO: 38) or a fragment of at least 4, at least 5, at least 6, at least 7, or at least 8 amino acids thereof; a mutation of N587A and T597N, and an insertion between positions 586 and 587 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of GVRAETTRP (SEQ ID NO: 38) or a fragment of at least 4, at least 5, at least 6, at least 7, or at least 8 amino acids thereof; a mutation of N587A, and an insertion between positions 586 and 587 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of ANLAIEQTRP (SEQ ID NO: 39) or a fragment of at least 5, at least 6, at least 7, at least 8, or at least 9 amino acids thereof; a mutation of N587A, and an insertion between positions 586 and 587 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of PNLALGATARP (SEQ ID NO: 40) or a fragment of at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 amino acids thereof; a mutation of Q575S and N587A, and an insertion between positions 586 and 587 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of QNLALGNTTRQ (SEQ ID NO: 41) or a fragment of at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 amino acids thereof; a mutation of N587A, and an insertion between positions 584 and 585 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of RASNDT (SEQ ID NO: 42) or a fragment of at least 3, at least 4, or at least 5 amino acids thereof; a mutation of N587A and T597L, and an insertion between positions 586 and 587 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of INMAKGETARP (SEQ ID NO: 43) or a fragment of at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 amino acids thereof; an insertion between positions 587 and 588 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of LNISPQTKPA (SEQ ID NO: 44) or a fragment of at least 5, at least 6, at least 7, at least 8, or at least 9, amino acids thereof; a mutation of A591I, and an insertion between positions 587 and 588 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of RQAGETARPA (SEQ ID NO: 45) or a fragment of at least 5, at least 6, at least 7, at least 8, or at least 9 amino acids thereof; or a mutation of N587A, and an insertion between positions 586 and 587 as compared to SEQ ID NO: 1, wherein the insertion comprises a polypeptide of GVRAETTRP (SEQ ID NO: 38) or a fragment of at least 4, at least 5, at least 6, at least 7, or at least 8 amino acids thereof. 8. A variant capsid polypeptide, comprising (a) a polypeptide of any one of SEQ ID NO: 17, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, (b) the VP2 or VP3 sequence of any one of SEQ ID NO: 17, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, and SEQ ID NO: 46 (c) a polypeptide comprising a sequence having at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity thereto, wherein said sequence comprises at least one (e.g., one, two, three or more, e.g., all) of the mutation differences associated with any of SEQ ID NO: 12 through SEQ ID NO: 23 and SEQ ID NO: 46, relative to SEQ ID NO: 1; or (d) a polypeptide having at least 1, but no more than 20, no more than 19, no more than 18, no more than 17, no more than 16, no more than 15, no more than 14, no more than 13, no more than 12, no more than 10, no more than 9, no more than 8, no more than 7, no more than 6, no more than 5, no more than 3, or no more than 2 amino acid mutations relative to the polypeptide of (a) or (b), wherein said polypeptide comprises at least one (e.g., one, two, three or more, e.g., all) of the mutation differences associated with any of SEQ ID NO: 12 through SEQ ID NO: 23 and SEQ ID NO: 46, relative to SEQ ID NO: 1. 9. A variant capsid polypeptide comprising: an amino acid sequence that has 95% or more amino acid sequence identity to an amino acid sequence of one of SEQ ID NO: 17, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 and SEQ ID NO: 46, and has at least 80% of the mutations in the amino acid sequence of one of SEQ ID NO: 17, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 and SEQ ID NO: 46 as compared to SEQ ID NO: 1. 10. A variant capsid polypeptide comprising: an amino acid sequence that has less than 95% amino acid sequence identity to an amino acid sequence of one of SEQ ID NO: 17, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 and SEQ ID NO: 46, and has at least 80% of the mutations in the amino acid sequence of one of SEQ ID NO: 17, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 and SEQ ID NO: 46 as compared to SEQ ID NO: 1. 11. A variant capsid polypeptide comprising: an amino acid sequence that has 95% or more amino acid sequence identity to an amino acid sequence of one of SEQ ID NO: 17, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 and SEQ ID NO: 46, and has less than 80% of the mutations in the amino acid sequence of one of SEQ ID NO: 17, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 and SEQ ID NO: 46 as compared to SEQ ID NO: 1. 12. A nucleic acid molecule comprising a sequence encoding a variant capsid polypeptide of any one of claims 1-11. 13. The nucleic acid molecule of claim 12, comprising one or more regulatory elements operably linked to the sequence encoding the variant capsid polypeptide. 14. The nucleic acid molecule of any one of claims 12-13, comprising SEQ ID NO: 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 47, or a fragment thereof, or a variant thereof having at least 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% sequence identity thereto. 15. A virus particle (e.g., adeno-associated virus (“AAV”) particle) comprising the variant capsid polypeptide of any one of claims 1-11 or comprising a variant capsid polypeptide encoded by the nucleic acid molecule of any one of claims 12-14. 16. The virus particle of claim 15, comprising a nucleic acid comprising a heterologous transgene and one or more regulatory elements. 17. A virus particle of any of claims 15-16 comprising the variant capsid polypeptide of any one of claims 1 - 72, wherein said virus particle, or a virus particle comprising said variant capsid polypeptide or a virus particle comprising a variant capsid polypeptide encoded by a nucleic acid molecule of any one of claims 73 - 76 exhibits increased ocular transduction, e.g., as measured in a mouse or in NHP, e.g., as described herein, relative to wild-type AAV2 (e.g., a virus particle comprising capsid polypeptides of SEQ ID NO: 1 or encoded by SEQ ID NO: 2). 18. A method of producing a virus particle comprising a variant AAV2 capsid polypeptide, said method comprising introducing a nucleic acid molecule of any one of claims 12-14 into a cell (e.g., a HEK293 cell), and harvesting said virus particle therefrom. 19. A method of delivering a payload (e.g., a nucleic acid) to a cell comprising contacting the cell with a dependoparvovirus particle comprising a variant capsid polypeptide of any one of claims 1-11 or the virus particle of any of claims 15-17 and a payload. 20. The method of claim 19, wherein the cell is an ocular cell. 21. The method of claim 20, wherein the ocular cell is in the retina, the macula, or the trabecular meshwork. 22. A method of delivering a payload (e.g., a nucleic acid) to a subject comprising administering to the subject a dependoparvovirus particle comprising a variant capsid polypeptide of any one of claims 1-11 and the payload, or administering to the subject the virus particle of any one of claims 15-17. 23. The method of claim 22, wherein the particle delivers the payload to the eye. 24. The method of claim 22, wherein the particle delivers the payload to the retina, the macular, or the trabecular meshwork. 25. The method of any one of claims 22-24, wherein the particle delivers the payload to the eye with increased transduction in one or more regions of the eye as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1, wherein the one or more regions of the eye is selected from the retina, the macula, the trabecular meshwork, or any combination thereof. 26. The method of claim 25, wherein the retina comprises non-macular retina. 27. The variant capsid polypeptide of any of claims 1-11, the virus particle of any of claims 15-17 or the method of any one of claims 18-26, wherein the particle (e.g., particle comprising the variant capsid polypeptide) delivers the payload to the eye with increased transduction in one or more regions of the eye as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1, and wherein the increase in transduction is at least 1.5-times, 2-times, 4-times, 5-times, 6-times, 7-times, 8-times, 9-times, 10-times, 11-times, 13-times, 15-times, 16-times, 19-times, 20-times, 30-times, 40-times, 50-times, 60-times, 80-times, 240-times, or 440-times as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1. 28. The variant capsid polypeptide of any of claims 1-11, the virus particle of any of claims 15-17 or the method of any one of claims 18-26, wherein the particle (e.g., particle comprising the variant capsid polypeptide) delivers the payload to the eye with increased transduction specificity in one or more regions of the eye as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1, wherein the increase in transduction is at least 1.5-times, 2-times, 4-times, 8-times, 16-times, or 19-times as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1, and wherein the increase in transduction is specific to macular tissue relative to non-macular retina tissue. 29. The variant capsid polypeptide of any of claims 1-11, the virus particle of any of claims 15-17 or the method of any one of claims 18-26, wherein the particle (e.g., particle comprising the variant capsid polypeptide) delivers the payload to the eye with increased transduction specificity in one or more regions of the eye as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1, wherein the increase in transduction is at least 1.5-times, 2-times, 4-times, 8-times, 16-times, or 19-times as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1, and wherein the increase in transduction is specific to macular tissue relative to trabecular meshwork tissue. 30. The variant capsid polypeptide of any of claims 1-11, the virus particle of any of claims 15-17 or the method of any one of claims 18-26, wherein the particle (e.g., particle comprising the variant capsid polypeptide) delivers the payload to the eye with increased transduction specificity in one or more regions of the eye as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1, wherein the increase in transduction is at least 1.5-times, 2-times, 4-times, 8-times, or 15-times as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1, and wherein the increase in transduction is specific to non-macular retina tissue relative to trabecular meshwork tissue. 31. The variant capsid polypeptide of any of claims 1-11, the virus particle of any of claims 15-17 or the method of any one of claims 18-26, wherein the particle (e.g., particle comprising the variant capsid polypeptide) delivers the payload to the eye with increased transduction specificity in one or more regions of the eye as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1, wherein the increase in transduction is at least 1.5-times, 2-times, 4-times, 8-times, 15-times, or 19-times as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1, and wherein the increase in transduction is specific to macular tissue and non-macular retina tissue relative to trabecular meshwork tissue. 32. The variant capsid polypeptide of any of claims 1-11, the virus particle of any of claims 15-17 or the method of any one of claims 18-26, wherein the particle (e.g., particle comprising the variant capsid polypeptide) delivers the payload to the eye with increased transduction specificity in one or more regions of the eye as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1 without increased biodistribution in one or more regions of the eye as compared to a virus particle comprising capsid polypeptides of SEQ ID NO: 1. 33. The method of any one of claims 18-26, wherein the administration to the subject is via an intravitreal injection, or an intracameral injection. 34. A method of treating a disease or condition in a subject, comprising administering to the subject a dependoparvovirus particle in an amount effective to treat the disease or condition, wherein the dependoparvovirus particle is a particle comprising a capsid polypeptide of any one of claims 1-11 and 27-32, or encoded by the nucleic acid of any one of claims 12-14, or is a virus particle of any one of claims 15-17. 35. A cell, cell-free system, or other translation system, comprising the capsid polypeptide, nucleic acid molecule, or virus particle of any one of claims 1-17 or 27-32. 36. A method of making a dependoparvovirus (e.g., an adeno-associated dependoparvovirus (AAV) particle, comprising: providing a cell, cell-free system, or other translation system, comprising a nucleic acid of any of claims 12-14; and cultivating the cell, cell-free system, or other translation system, under conditions suitable for the production of the dependoparvovirus particle, thereby making the dependoparvovirus particle. 37. The method of claim 36, wherein the cell, cell-free system, or other translation system comprises a second nucleic acid molecule and said second nucleic acid molecule is packaged in the dependoparvovirus particle. 38. The method of claim 37, wherein the second nucleic acid comprises a payload, e.g., a heterologous nucleic acid sequence encoding a therapeutic product. 39. The method of any one of claims 36-38, wherein the nucleic acid of any of claims 12-14 mediates the production of a dependoparvovirus particle which does not include said nucleic acid of any of claims 12-14. 40. The method of any one of claims 36-39, wherein the nucleic acid of any of claims 12-14 mediates the production of a dependoparvovirus particle at a level at least 10%, at least 20%, at least 50%, at least 100%, at least 200% or greater than the production level mediated by the nucleic acid of SEQ ID NO: 2. 41. A composition, e.g., a pharmaceutical composition, comprising a virus particle of any one of claims 15-17 or a virus particle produced by the method of any one of claims 18 or 36-40, and a pharmaceutically acceptable carrier. 42. The variant capsid polypeptide of any of claims 1-11 and 27-32, the nucleic acid molecule of any of claims 12-14, or the virus particle of any of claims 15-17 for use in treating a disease or condition in a subject. 43. The variant capsid polypeptide of any of claims 1-11 and 27-32, the nucleic acid molecule of any of claims 12-14, or the virus particle of any of claims 15-17 for use in the manufacture of a medicament for use in treating a disease or condition in a subject."
  ],
  "cpc": [
    "A61K 48/0058",
    "C07K 14/005",
    "C12N 15/86",
    "C12N 2750/14122",
    "C12N 2750/14143",
    "C12N 2750/14145",
    "C12N 2750/14152"
  ],
  "filing_date": "2023-09-13",
  "publication_date": "2026-04-16",
  "application_number": "US-202319111196-A"
}