EP-4735614-A1 - ADENO-ASSOCIATED VIRUS COMPOSITIONS HAVING INCREASED BRAIN ENRICHMENT

EP4735614A1EP 4735614 A1EP4735614 A1EP 4735614A1EP-4735614-A1

Abstract

Described herein are compositions and kits comprising recombinant adeno-associated viruses (rAAVs) with increased transduction enrichment in the brain. The rAAV compositions described herein encapsidate a transgene, such as a therapeutic nucleic acid. Gene therapy using the rAAVs is described. Also described are methods of treating brain-related diseases and conditions.

Inventors

GOERTSEN, David G.
GROSS, Sean M.
XIAOJING, Shi
SANDBERG, TROY E.
WHEELER, BRANDON G.
FLYTZANIS, Nicholas C.
GOEDEN, Nicholas S.

Assignees

Capsida Biotherapeutics, Inc.

Dates

Publication Date: 20260506
Application Date: 20240628

Claims (1)

Patent Application CAPS-031/01WO 35847/121 CLAIMS WHAT IS CLAIMED IS: 1. An AAV capsid protein comprising an amino acid substitution and/or insertion sequence at position 588 having at least 80% identity to a sequence provided in Table 1 and/or Table 3. 2. An AAV capsid protein comprising an amino acid substitution and/or insertion sequence at position 587-597 having at least 80% identity to a sequence provided in Table 1 and/or Table 3. 3. An AAV capsid protein comprising an amino acid substitution and/or insertion sequence at position 452-458 having at least 80% identity to a sequence as provided in Table 2 and/or Table 3. 4. An AAV capsid protein comprising an amino acid substitution and/or insertion sequence of Formula I at position 587-597 X 1 -X 2 -X 3- X 4 -X 5 -X 6 -X 7 -X 8 -X 9 -X 10 -X 11 (I) wherein: X 1 is an amino acid selected from A, Q, H, K, T, S, N, and M, and preferably selected from A or Q; X 2 is an amino acid selected from Q, R, T, Y and M, and preferably from Q, R, and T; X 3 is an amino acid selected from R, E, L, and T, and is preferably R; X 4 is an amino acid selected from D, N, and S, and preferably from D and N; X 5 is an amino acid selected from G and H, and is preferably G; X 6 is an amino acid selected from L, V, A, and Q, and preferably from L and V; X 7 is an amino acid selected from I, H, and R, and is preferably I; X 8 is an amino acid selected from L, F, and S, and is preferably L; X 9 is an amino acid selected from I, K, V, Q, and A, and is preferably I; X 10 is an amino acid selected from A, S, E, Q, and T, and is preferably A; and Patent Application CAPS-031/01WO 35847/121 X 11 is an amino acid selected from Q, P, and K. 5. The AAV capsid protein of Claim 4, wherein X 1 is A or Q. 6. The AAV capsid protein of Claim 4 wherein X 2 is Q, R, or T. 7. The AAV capsid protein of Claim 4 wherein X 3 is R. 8. The AAV capsid protein of Claim 4 wherein X 4 is D or N. 9. The AAV capsid protein of Claim 4 wherein X 5 is G. 10. The AAV capsid protein of Claim 4 wherein X 6 is L or V. 11. The AAV capsid protein of Claim 4 wherein X 7 is I. 12. The AAV capsid protein of Claim 4 wherein X 8 is L. 13. The AAV capsid protein of Claim 4 wherein X 9 is I. 14. The AAV capsid protein of Claim 4 wherein X 10 is A. 15. The AAV capsid protein of Claim 4 wherein X 11 is Q or P. 16. An AAV capsid protein comprising an insertion sequence of Formula II at position 452-458 X 12 -X 13 -X 14 -X 15 -X 16 -X 17 -X 18 (II) wherein: X 12 is an amino acid selected from E, T, A, V, and N; X 13 is an amino acid selected from N, E, T, and P; X 14 is an amino acid selected E, N, and Q; X 15 is an amino acid selected from Q, S, T, G, N, and A; X 16 is an amino acid selected from R, G, K, and Q; X 17 is an amino acid selected from S, P, T, K, R, and N; and X 18 is an amino acid selected from Q, K, M, and T. 17. The AAV capsid protein of Claim 16, wherein X 12 is E. Patent Application CAPS-031/01WO 35847/121 18. The AAV capsid protein of Claim 16, wherein X 13 is N. 19. The AAV capsid protein of Claim 16, wherein X 14 is E. 20. The AAV capsid protein of Claim 16, wherein X 15 is Q. 21. The AAV capsid protein of Claim 16, wherein X 16 is R. 22. The AAV capsid protein of Claim 16, wherein X 17 is S. 23. The AAV capsid protein of Claim 16, wherein X 18 is Q. 24. An AAV capsid protein comprising: (i) an amino acid substitution and/or insertion sequence at position 587-597 having at least 80% identity to a sequence provided in Table 1 and/or Table 3; and (ii) an amino acid substitution and/or insertion sequence at position 452-458 having at least 80% identity to a sequence as provided in Table 2 and/or Table 3. 25. An AAV capsid protein comprising: an insertion sequence of Formula I at position 587-597 X 1 -X 2 -X 3- X 4 -X 5 -X 6 -X 7 -X 8 -X 9 -X 10 -X 11 (I) wherein: X 1 is an amino acid selected from A, Q, H, K, T, S, N, and M, and preferably selected from A or Q; X 2 is an amino acid selected from Q, R, T, Y and M, and preferably from Q, R, and T; X 3 is an amino acid selected from R, E, L, and T, and is preferably R; X 4 is an amino acid selected from D, N, and S, and preferably from D and N; X 5 is an amino acid selected from G and H, and is preferably G; X 6 is an amino acid selected from L, V, A, and Q, and preferably from L and V; X 7 is an amino acid selected from I, H, and R, and is preferably I; X 8 is an amino acid selected from L, F, and S, and is preferably L; X 9 is an amino acid selected from I, K, V, Q, and A, and is preferably I; X 10 is an amino acid selected from A, S, E, Q, and T, and is preferably A; and X 11 is an amino acid selected from Q, P, and K; and Patent Application CAPS-031/01WO 35847/121 an insertion sequence of Formula II at position 452-458 X 12 -X 13 -X 14 -X 15 -X 16 -X 17 -X 18 (II) wherein: X 12 is an amino acid selected from E, T, A, V, and N; X 13 is an amino acid selected from N, E, T, and P; X 14 is an amino acid selected E, N, and Q; X 15 is an amino acid selected from Q, S, T, G, N, and A; X 16 is an amino acid selected from R, G, K, and Q; X 17 is an amino acid selected from S, P, T, K, R, and N; and X 18 is an amino acid selected from Q, K, M, and T. 26. An AAV capsid protein comprising an insertion sequence of Formula III at position 583-599: X1-X2-X3-X4-X5-X6-X7-X8-X9-X10-X11-X12-X13-X14-X15-X16-X17 (III) wherein: X 1 is an amino acid selected from N, S, G, and T, and preferably N; X2 is an amino acid selected from H, N, A, and S, and preferably from H; X3 is amino acid Q; X 4 is an amino acid selected from S, A, T, G, and M, and preferably from S, M, or G; X5 is an amino acid selected from A, Q, N, S, M, Y, and E, and preferably from A, Q, or S; X 6 is an amino acid selected from T, V, Q, S, M and L, and preferably from T, V, or S; X7 is an amino acid selected from R, K, L, M, and I, and is preferably R or K; X 8 is an amino acid selected from N, D, G, and S, and is preferably N or D; X9 is an amino acid selected from G, S, Q, A, and N, and is preferably G; X10 is an amino acid selected from E, H, Q, A, and N, and is preferably E or H; X 11 is an amino acid selected from V, I, T, and L, and is preferably V or I; X 12 is an amino acid selected from F, L, Y, M, and H, and is preferably F, L, or Y; X13 is an amino acid selected from I, Y, V, and F, and is preferably I or Y; Patent Application CAPS-031/01WO 35847/121 X14 is an amino acid selected from A, and S, and is preferably A; X 15 is an amino acid selected from Q, M, S, G, N, T, A and V, and is preferably Q, M, S, or N; X16 is an amino acid selected from A or S, and is preferably A; and X 17 is an amino acid selected from Q, A, or G, and is preferably Q. 27. The AAV capsid protein of claim 26, wherein X 1 is N. 28. The AAV capsid protein of claim 26, wherein X2 is H. 29. The AAV capsid protein of claim 26, wherein X3 is Q. 30. The AAV capsid protein of claim 26, wherein X 4 is S or G. 31. The AAV capsid protein of claim 26, wherein X 5 is A or S. 32. The AAV capsid protein of claim 26, wherein X6 is T or S. 33. The AAV capsid protein of claim 26, wherein X7 is R or K. 34. The AAV capsid protein of claim 26, wherein X 8 is N or D. 35. The AAV capsid protein of claim 26, wherein X9 is G. 36. The AAV capsid protein of claim 26, wherein X10 is E or H. 37. The AAV capsid protein of claim 26, wherein X 11 is V or I. 38. The AAV capsid protein of claim 26, wherein X 12 is F, L, or Y. 39. The AAV capsid protein of claim 26, wherein X13 is I or Y. 40. The AAV capsid protein of claim 26, wherein X 14 is A. 41. The AAV capsid protein of claim 26, wherein X 15 is Q, M, or N. 42. The AAV capsid protein of claim 26, wherein X16 is A or S. Patent Application CAPS-031/01WO 35847/121 43. The AAV capsid protein of claim 26, wherein X 17 is Q 44. The AAV capsid protein of any of claims 1-43 wherein the AAV is AAV9. 45. The AAV capsid protein of any of claims 1-44 wherein the AAV is provided in SEQ ID NO: 1. 46. The AAV capsid protein of any one of claims 1-45, wherein 60 copies of the AAV capsid protein are assembled into the AAV capsid. 47. The AAV capsid protein of any of claims 1-46, wherein the AAV capsid protein is present in VP1, VP2, and VP3 of the AAV capsid. 48. The AAV capsid protein of any of claims 1-47, wherein the AAV capsid protein is characterized by at least one of an increased transduction enrichment when measured in a brain in a subject when delivered to the subject systemically. 49. The AAV capsid protein any of claims 1-48, wherein the AAV capsid protein further comprises an amino acid substitution comprising A589N or Q590P. 50. An AAV capsid comprising an AAV capsid protein of any of claims 1-49. 51. The AAV capsid of claim 50, wherein the AAV capsid is chimeric. 52. The AAV capsid of any of claims 50-51 that is isolated and purified. 53. The AAV capsid of any of claims 50-52 formulated as a pharmaceutical formulation for systemic administration to treat a disease or a condition of the brain, the pharmaceutical formulation further comprising a pharmaceutically acceptable carrier. 54. The AAV capsid protein of any of claims 1-50, wherein the capsid protein is expressed in the brain. 55. The AAV capsid protein of claim 54, wherein the brain comprises a cell-type selected from a neuron, an oligodendrocyte, an astrocyte, and a brain vascular cell. Patent Application CAPS-031/01WO 35847/121 56. The AAV capsid protein of any one of claims 54-55, wherein the brain comprises a tissue that is selected from brain, thalamus, cortex, putamen, lateral ventricles, medulla, the pons, the amygdala, the motor cortex, caudate, hypothalamus, striatum, ventral midbrain, neocortex, basal ganglia, hippocampus, thalamus, cerebrum, cerebellum, brain stem, and spinal cord. 57. A nucleic acid sequence encoding the peptide of any of claims 1-49. 58. A nucleic acid sequence encoding a peptide sequence as provided in Tables 1, 2, 3, 4, 5, or 6. 59. A recombinant vector comprising a nucleic acid encoding the AAV capsid protein of any one of claims 1-49. 60. A kit comprising: a) a first vector comprising the recombinant vector of claim 59; b) a second vector encoding a helper virus protein; and c) a third vector comprising a therapeutic nucleic acid encoding a therapeutic gene expression product. 61. A method of treating a disease or condition in a subject comprising administering a therapeutically effective amount of a pharmaceutical formulation comprising the AAV capsid protein of any one of claims 1-49. 62. The method of claim 61, wherein the disease or the condition is a disease or a condition of a brain of the subject. 63. A method of manufacturing a recombinant AAV particle from the AAV capsid of any one of claims 1-44, the method comprising: a. introducing into a cell a nucleic acid comprising: Patent Application CAPS-031/01WO 35847/121 i. a first nucleic acid sequence encoding a therapeutic gene expression product; ii. a second nucleic acid sequence encoding a recombinant viral genome comprising a capsid (Cap) gene modified to express the AAV capsid of any one of claims 1-44; and iii. a third nucleic acid sequence encoding an AAV helper virus genome; and b. assembling the recombinant AAV particle, the recombinant AAV particle comprising the AAV capsid encapsidating the first nucleic acid. 64. The AAV capsid protein of any of claims 1-49 wherein the AAV capsid protein is characterized by an increased transduction enrichment when measured in a tissue in a subject when delivered to the subject systemically. 65. The AAV capsid protein of any of claims 1-49 wherein the tissue is brain tissue. 66. An AAV particle comprising an AAV capsid protein of any of claims 1-49 and a viral genome.

Description

Patent Application CAPS-031/01WO 35847/121 ADENO-ASSOCIATED VIRUS COMPOSITIONS HAVING INCREASED BRAIN ENRICHMENT BACKGROUND [001] Recombinant adeno-associated viruses (rAAVs) are widely used as vectors for gene delivery in therapeutic applications because of their ability to transduce both dividing and non-dividing cells, their long-term persistence as episomal DNA in infected cells, and their low immunogenicity. These characteristics make them appealing for applications in therapeutic applications, such as gene therapy. However, there is a need to significantly improve the performance of existing AAV serotypes to selectively and efficiently express in distinct cell-types, upon systemic delivery to a subject. This need is especially acute when the AAV must be expressed in the brain. REFERENCE TO SEQUENCE LISTING [002] The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file named CAPS-031-01WO.xml, created on June 28, 2024, which is 4,255 kilobytes in size. The information in the electronic format of the Sequence Listing is incorporated herein by reference in its entirety. SUMMARY OF THE INVENTION [003] Disclosed herein are rAAVs with engineered transduction into the capsid structure through iterative rounds of selection in non-human primates (NHPs), yielding variants having increased transduction when measured in the brain. [004] The present invention provides rAAVs with widespread transduction to the brain. [005] The present disclosure provides an AAV capsid protein comprising an amino acid substitution and/or insertion sequence at position 588 having at least 80% identity to a sequence provided in Table 1 and/or Table 3. In certain aspects, the present disclosure provides an AAV capsid protein comprising an amino acid substitution and/or insertion sequence at position 587-597 having at least 80% identity to a sequence provided in Table 1 and/or Table 3. In certain aspects, the present disclosure provides a protein comprising an amino acid substitution and/or insertion sequence at position 452-458 having at least 80% identity to a sequence as provided in Table 2 and/or Table 3. Patent Application CAPS-031/01WO 35847/121 [006] The present disclosure provides an AAV capsid protein comprising an amino acid insertion and/or substitution sequence of Formula I at position 587-597 X1-X2-X3-X4-X5-X6-X7-X8-X9-X10-X11 (I) wherein: X1 is an amino acid selected from A, Q, H, K, T, S, N, and M, and preferably selected from A or Q; X2 is an amino acid selected from Q, R, T, Y and M, and preferably from Q, R, and T; X3 is an amino acid selected from R, E, L, and T, and is preferably R; X4 is an amino acid selected from D, N, and S, and preferably from D and N; X5 is an amino acid selected from G and H, and is preferably G; X6 is an amino acid selected from L, V, A, and Q, and preferably from L and V; X7 is an amino acid selected from I, H, and R, and is preferably I; X8 is an amino acid selected from L, F, and S, and is preferably L; X9 is an amino acid selected from I, K, V, Q, and A, and is preferably I; X10 is an amino acid selected from A, S, E, Q, and T, and is preferably A; and X11 is an amino acid selected from Q, P, and K. [007] In certain embodiments, in the AAV capsid protein comprising an amino acid insertion and/or substitution sequence of Formula I at position 587-597, X1 may be a substitution or the parental amino acid at 587, X2 may be a substitution or parental amino acid at position 588, X3, X4, X5, X6, X7, X8, and X9 may be insertions, X10 may be a substitution or parenteral amino acid at position 589 (i.e., now at position 596 in view of the insertion), and X11 and may be a substitution or the parental amino acid at position 590 (i.e., now at position at 597 in view of the insertion). [008] In certain aspects, the present disclosure provides an AAV capsid protein comprising an amino acid substitution and/or insertion sequence of Formula II at position 452-458 X12-X13-X14-X15-X16-X17-X18 (II) wherein: X12 is an amino acid selected from E, T, A, V, and N; X13 is an amino acid selected from N, E, T, and P; X14 is an amino acid selected E, N, and Q; X15 is an amino acid selected from Q, S, T, G, N, and A; X16 is an amino acid selected from R, G, K, and Q; X17 is an amino acid selected from S, P, T, K, R, and N; and X18 is an amino acid selected from Q, K, M, and T. [009] The present disclosure provides an AAV capsid protein comprising: (i) an amino acid substitution and/or insertion sequence at position 587-597 having at least 80% identity to a sequence provided in Table 1 and/or Table 3; and (ii) an amino acid substitution and/or Patent Application CAPS-031/01WO 35847/121 insertion sequence at position 452-458 having at least 80% identity to a sequence as provided in Table 2 and/or Table 3. [010] In certain aspects, the present disclosure provides rAAVs with high expression level in the brain. [011] In certain aspects, the