Heteroclitic neoepitope vaccines

HK40137857APending Publication Date: 2026-09-18JOHNS HOPKINS UNIVERSITY
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Patent Information

Application Number
HK62026126736
Authority / Receiving Office
HK · HK
Patent Type
Applications
Current Assignee / Owner
Priority Date
2023-04-14
Filing Date
2026-07-28
Publication Date
2026-09-18
Estimated Expiration
2044-04-13

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Abstract

Compositions of peptides modified to improve HLA binding or T cell recognition while conserving reactivity to the target neoepitope, enhance activation of neoantigen-specific T cells. Methods of use include treating cancer by administering one or more of these peptides generated by computer modeling.
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Description

Abstract: Modified peptide compositions, wherein the peptides are modified to enhance HLA binding or T cell recognition while preserving responsiveness to target novel epitopes, thereby increasing the activation of neoantigen-specific T cells. Application methods include treating cancer by administering one or more of these peptides generated by computer modeling.

Claims

What is claimed:

1. A method of identifying heteroclitic neoepitopes having improved immunogenicity, the method comprising: modeling a library of peptides onto a human leukocyte antigen (HLA) to form an HLA- peptide structure, wherein the modeling comprises identifying positional sequence similarity of peptide epitopes that bind to one or a plurality of HLA haplotypes; (a) selecting the HLA-peptide structure having a sequence identity similar to a parental epitope being modeled; (b) modeling heteroclitic neoepitopes into an HLA cleft by introducing amino acid rotamers with the lowest energy confirmation at each position; (c) generating HLA-heteroclitic neoepitope complexes; (d) validating the HLA-heteroclitic neoepitope complexes using a root-mean-square deviation analysis (Cα-RMSD); and (e) performing a high-resolution Monte Carlo simulation with minimization docking of the heteroclitic neoepitope to the HLA cleft to identify the lowest full-atom energy conformation; thereby identifying the heteroclitic neoepitopes having improved immunogenicity.

2. The method of claim 1, wherein the modeling of the peptides onto the HLA comprises aligning peptide sequences with a consensus binding motif of HLA molecules.

3. The method of claim 2, wherein the consensus binding motif comprises a consensus binding motif for 8-mer, 9-mer, 11-mer, 12-mer, 13-mer, 14-mer, 15-mer, 16-mer, 17-mer, 18- mer, 19-mer, 20-mer, 21-mer, 22-mer, 23-mer, 24-mer, or 25-mer epitopes.

4. The method of claim 3, wherein the consensus binding motif for the 8-mer, 9-mer, 11-mer, 12-mer, 13-mer, 14-mer, 15-mer, 16-mer, 17-mer, 18-mer, 19-mer, 20-mer, 21-mer, 22-mer, 23- mer, 24-mer, or 25-mer epitopes comprises distinct anchor residue binding motifs subdivided into hydrophobic, hydrophilic, or neutral binding anchors.

5. The method of any one of claims 1-4 , wherein the root-mean-square deviation analysis is conducted to identify unstable structural changes of an HLA cleft. 81 73617376. The method of any one of claims 1-5, wherein anchor energetic-optimized structures are selected to identify anchor residue modifications.

7. The method of any one of claims 1-6, wherein the peptides are generated comprising combinations of anchor residue amino acids for each HLA class and subgroups thereof.

8. The method of claim any one of claims 1-7, wherein the HLA comprises an HLA type, wherein the HLA type comprise class I, II and subgroups thereof.

9. The method of claim any one of claims 1-8, wherein the peptides are derived from tumor cells or antigenic derivatives thereof.

10. The method of any one of claims 1-9, wherein the peptides comprise a tumor antigen.

11. The method of claim 10, wherein the tumor antigen comprises Kirsten rat sarcoma viral (KRAS), BRAF, FBWX7, FGFR3, IDH1, MUC4, NRAS, PIK3CA, PPP2R1A, PTEN, or TP53.

12. The method of claim 11, wherein the tumor antigen comprises one or more mutations.

13. The method of claim 12, wherein the one or more mutations is selected from KRAS G12D, KRAS G12V, KRAS G12R, or KRAS G12C.

14. The method of claim 12, wherein the one or more mutations is selected from BRAF V600E or BRAF V600M.

15. The method of claim 12, wherein the one or more mutation is FBXW7 R465C or FBXW7 R465Q.

16. The method of claim 12, wherein the one or more mutations is FGFR3 S249Q.

17. The method of claim 12, wherein the one or more mutations is IDH1 R132C.

18. The method of claim 12, wherein the one or more mutations is MUC4 D3157N.

19. The method of claim 12, wherein the one or more mutations is NRAS Q61K or NRAS G545R.

20. The method of claim 12, wherein the one or more mutations is PIK3CA G545K, PIK3CA H1047R, or PIK3CA R88Q.

21. The method of claim 12, wherein the one or more mutations is PPP2R1A P179R. 82 736173722. The method of claim 12, wherein the one or more mutations is PTEN R130G or PTEN R130Q.

23. The method of claim 12, wherein the one or more mutations is TP53 R175H, TP53 R248Q, TP53 R273H, TP53 R248Q, TP53 R273H, TP53 R282W, or TP53 R241Y.

24. The method of any one of claims 1-23, wherein the HLA is HLA-A, HLA-B, or HLA-C.

25. The method of claim 24, wherein the HLA-A is HLA-A*02:01, HLA-A*03:01, HLA- A*11:01, HLA-A*30:01, or HLA-A*68:

01.

26. The method of claim 24, wherein the HLA-B is HLA-B*07:

02.

27. The method of claim 24, wherein the HLA-C is HLA-C*01:02, HLA-C*03:03, HLA- C*03:04, or HLA-C*08:

02.

28. The method of any one of claims 1-27, wherein the identity greater than the sequence identity similar to the parental epitope comprises at least 85%, 90%, 95%, 97%, 99% sequence identity.

29. A method of generating a library of immunogenic peptides, comprising: modeling a peptide onto a human leukocyte antigen (HLA), wherein the modeling comprises identifying positional sequence similarity of peptide epitopes that bind to one or a plurality of HLA haplotypes; selecting an HLA-peptide structure having a sequence identity similar to a parental epitope being modeled; modeling a heteroclitic neoepitope into an HLA cleft by introducing amino acid rotamers with the lowest energy confirmation at each position to form HLA-heteroclitic neoepitope complexes; validating the resulting HLA-heteroclitic neoepitope complexes using a root-mean-square deviation analysis (Cα-RMSD); and performing a high-resolution Monte Carlo simulation with minimization docking of the heteroclitic neoepitope to the HLA cleft to identify the lowest full-atom energy conformation; thereby generating the library of immunogenic peptides.

30. The method of claim 29, wherein the modeling the heteroclitic neoepitope into an HLA cleft comprises introducing amino acid rotamers with a lowest energy confirmation at each position. 83 736173731. The method of any one of claims 29-30, wherein the root-mean-square deviation analysis is conducted to identify unstable structural changes of the HLA cleft.

32. The method of any one of claims 29-31, wherein the peptides comprise peptides isolated from tumor cells or antigenic derivatives thereof.

33. The method of any one of claims 29-32, wherein the peptides comprise tumor antigens.

34. The method of claim 33, wherein the tumor antigen comprises Kirsten rat sarcoma viral (KRAS), BRAF, FBWX7, FGFR3, IDH1, MUC4, NRAS, PIK3CA, PPP2R1A, PTEN, or TP53.

35. The method of claim 34, wherein the tumor antigen comprises one or more mutations.

36. The method of claim 35, wherein the one or more mutations is selected from the group consisting of G12D, G12V, G12R, and G12C.

37. The method of claim 35, wherein the one or more mutations is selected from BRAF V600E or BRAF V600M.

38. The method of claim 35, wherein the one or more mutation is FBXW7 R465C or FBXW7 R465Q.

39. The method of claim 35, the one or more mutations is FGFR3 S249Q.

40. The method of claim 35, wherein the one or more mutations is IDH1 R132C.

41. The method of claim 35, wherein the one or more mutations is MUC4 D3157N.

42. The method of claim 35, wherein the one or more mutations is NRAS Q61K or NRAS G545R.

43. The method of claim 35, wherein the one or more mutations is PIK3CA G545K, PIK3CA H1047R, or PIK3CA R88Q.

44. The method of claim 35, wherein the one or more mutations is PPP2R1A P179R.

45. The method of claim 35, wherein the one or more mutations is PTEN R130G or PTEN R130Q.

46. The method of claim 35, wherein the one or more mutations is TP53 R175H, TP53 R248Q, TP53 R273H, TP53 R248Q, TP53 R273H, TP53 R282W, or TP53 R241Y. 84 736173747. The method of any one of claims 29-46, wherein a KRAS peptide sequence is positionally aligned with 8-mer, 9-mer, 11-mer, 12-mer, 13-mer, 14-mer, 15-mer, 16-mer, 17-mer, 18-mer, 19- mer, 20-mer, 21-mer, 22-mer, 23-mer, 24-mer, or 25-mer epitopes that bind HLA molecules.

48. The method of claim 47, wherein the 8-mer, 9-mer, 11-mer, 12-mer, 13-mer, 14-mer, 15- mer, 16-mer, 17-mer, 18-mer, 19-mer, 20-mer, 21-mer, 22-mer, 23-mer, 24-mer, or 25-mer epitopes comprises distinct anchor residue binding motifs subdivided into hydrophobic, hydrophilic, or neutral binding anchors.

49. The method of any one of claims 29-48, wherein a HLA-KRAS peptide comprising the greatest sequence similarity is selected for modeling into an HLA cleft.

50. The method of any one of claims 29-49, wherein anchor energetic-optimized HLA-KRAS structures are selected to identify anchor residue modifications.

51. The method of any one of claims 29-50, wherein a library of KRAS peptides is generated comprising combinations of anchor residue amino acid for each HLA class and subgroups thereof.

52. The method of claim 51, wherein the KRAS peptides comprise heteroclitic epitopes.

53. The method of claim 51, wherein contacting the KRAS peptides comprising heteroclitic epitopes with a population of immune cells leads to a higher percentage of expansion of the population of immune cells as compared to a corresponding peptide that is otherwise same but does not comprise the heteroclitic epitopes.

54. The method of claim 51, wherein contacting the KRAS peptides comprising heteroclitic epitopes with a population of immune cells leads to higher activation of the population of immune cells as compared to a corresponding peptide that is otherwise same but does not comprise the heteroclitic epitopes.

55. The method of claim 54, wherein the activation comprises IFNg secretion.

56. The method of any one of claims 29-55, wherein the HLA comprises an HLA type, wherein the HLA-types comprise class I, II and subgroups thereof.

57. The method of any one of claims 29-56, wherein the HLA is HLA-A, HLA-B, or HLA-C.

58. The method of claim 57, wherein the HLA-A is HLA-A*02:01, HLA-A*03:01, HLA- A*11:01, HLA-A*30:01, or HLA-A*68:

01. 85 736173759. The method of claim 57, wherein the HLA-B is HLA-B*07:

02.

60. The method of claim 57, wherein the HLA-C is HLA-C*01:02, HLA-C*03:03, HLA- C*03:04, or HLA-C*08:

02.

61. A method of treating cancer comprising administering to subject in need thereof, one or more peptide comprising one or more heteroclitic epitopes.

62. The method of claim 61, wherein the peptide is generated by the method of any one of claims 1-59.

63. The method of claim 61 or 62, wherein the peptide comprises an amino acid sequence having at least 75% sequence identity to any one or more of SEQ ID NOs: 1-838.

64. The method of claim 63, wherein the peptide comprises any one or more of SEQ ID NOs: 2, 3, 5-12, 14-21, 23-30, 32-39, 41-48, 50-57, 59-66, 68-75, 77-84, 86-93, 85-99, 101-105, 107- 111, 113-117, 119-123, 125-129, 131-135, 137-141, 143-146, 148-152, 154-162, 164-168, 170- 179, 181-185, 187-196, 198-202, 204-213, 215-219, 221-230, 232-236, 238-244, 246-252, 254- 260, 262-268, 270-276, 278-284, 286-292, 294-300, 302-308, 310-316, 318-324, 326-332, 334- 340, 342-348, 350-356, 358-364, 366-372, 374-380, 382-388, 390-396, 398-404, 406-412, 414- 420, 422-428, 430-436, 438-443, 445-450, 452-457, 459-464, 466-471, 473-478, 480-485, 487- 492, 494-499, 501-506, 508-512, 514-518, 520-524, 526-530, 532-536, 538-542, 544-548, 550- 554, 556-560, 562-566, 568-573, 585-580, 582-587, 589-594, 596-601, 603-607, 609-613, 615- 619, 621-625, 627-631, 633-638, 340-644, 646-651, 653-657, 659-664, 666-670, 672-677, 679- 683, 685-690, 692-696, 698-703, 705-711, 713-718, 720-726, 728-733, 735-741, 743-748, 750- 756, 758-763, 765-771, 773-777, 779-783, 785-789, 791-795, 797-801, 803-807, 809-813, 815- 819, 821-825, 827-831, 833, or 834.

65. The method of claim 63 or 64, wherein the peptide comprises the amino acid sequence of SEQ ID NO: 2 or SEQ ID NO:

833.

66. The method of claim 63 or 64, wherein the peptide comprises the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO:

834.

67. The method of any one of claims 61-66, further comprising administering an adjuvant to the subject. 86 736173768. The method of any one of claims 61-67, further comprising administering one or more therapeutics to the subject.

69. A cancer vaccine comprising one or more peptide, wherein the peptide comprise at least one heteroclitic neoepitope.

70. The cancer vaccine of claim 69, wherein the peptide is a tumor antigen.

71. The cancer vaccine of claim 70, wherein the tumor antigen comprises Kirsten rat sarcoma viral (KRAS), BRAF, FBWX7, FGFR3, IDH1, MUC4, NRAS, PIK3CA, PPP2R1A, PTEN, or TP53.

72. The cancer vaccine of claim 71, wherein the tumor antigen comprises one or more mutations.

73. The cancer vaccine of claim 72, wherein the one or more mutations is selected from KRAS G12D, KRAS G12V, KRAS G12R, or KRAS G12C.

74. The cancer vaccine of claim 72, wherein the one or more mutations is selected from BRAF V600E or BRAF V600M.

75. The cancer vaccine of claim 72, wherein the one or more mutation is FBXW7 R465C or FBXW7 R465Q.

76. The cancer vaccine of claim 72, the one or more mutations is FGFR3 S249Q.

77. The cancer vaccine of claim 72, wherein the one or more mutations is IDH1 R132C.

78. The cancer vaccine of claim 72, wherein the one or more mutations is MUC4 D3157N.

79. The cancer vaccine of claim 72, wherein the one or more mutations is NRAS Q61K or NRAS G545R.

80. The cancer vaccine of claim 72, wherein the one or more mutations is PIK3CA G545K, PIK3CA H1047R, or PIK3CA R88Q.

81. The cancer vaccine of claim 72, wherein the one or more mutations is PPP2R1A P179R.

82. The cancer vaccine of claim 72, wherein the one or more mutations is PTEN R130G or PTEN R130Q. 87 736173783. The cancer vaccine of claim 72, wherein the one or more mutations is TP53 R175H, TP53 R248Q, TP53 R273H, TP53 R248Q, TP53 R273H, TP53 R282W, or TP53 R241Y.

84. The cancer vaccine of any one of claims 69-83, wherein the peptide is displayed on a surface of an antigen presenting cell (APC) via an HLA antigen presentation pathway and a tumor specific immune response is induced.

85. The cancer vaccine of any one of claims 69-84, wherein the peptide is immunogenic specifically for the subject’s HLA type.

86. The cancer vaccine of claim 85, wherein the HLA is HLA-A, HLA-B, or HLA-C.

87. The cancer vaccine of claim 86, wherein the HLA-A is HLA-A*02:01, HLA-A*03:01, HLA-A*11:01, HLA-A*30:01, or HLA-A*68:

01.

88. The cancer vaccine of claim 86, wherein the HLA-B is HLA-B*07:

02.

89. The cancer vaccine of claim 86, wherein the HLA-C is HLA-C*01:02, HLA-C*03:03, HLA-C*03:04, or HLA-C*08:

02.

90. The cancer vaccine of any one of claims 69-89, wherein the peptide is generated by the method of any one of claims 1-60 91. The cancer vaccine of any one of claims 69-90, wherein the peptide comprises an amino acid sequence having at least 75% sequence identity to any one or more of SEQ ID NOs: 1-838.

92. The cancer vaccine of any one of claims 69-91, wherein the peptide comprises any one or more of SEQ ID NOs: 1-838.

93. The cancer vaccine of any one of claims 91-92, wherein the peptide comprises any one or more of SEQ ID NOs: 2, 3, 5-12, 14-21, 23-30, 32-39, 41-48, 50-57, 59-66, 68-75, 77-84, 86-93, 85-99, 101-105, 107-111, 113-117, 119-123, 125-129, 131-135, 137-141, 143-146, 148-152, 154- 162, 164-168, 170-179, 181-185, 187-196, 198-202, 204-213, 215-219, 221-230, 232-236, 238- 244, 246-252, 254-260, 262-268, 270-276, 278-284, 286-292, 294-300, 302-308, 310-316, 318- 324, 326-332, 334-340, 342-348, 350-356, 358-364, 366-372, 374-380, 382-388, 390-396, 398- 404, 406-412, 414-420, 422-428, 430-436, 438-443, 445-450, 452-457, 459-464, 466-471, 473- 478, 480-485, 487-492, 494-499, 501-506, 508-512, 514-518, 520-524, 526-530, 532-536, 538- 542, 544-548, 550-554, 556-560, 562-566, 568-573, 585-580, 582-587, 589-594, 596-601, 603- 88 7361737607, 609-613, 615-619, 621-625, 627-631, 633-638, 340-644, 646-651, 653-657, 659-664, 666- 670, 672-677, 679-683, 685-690, 692-696, 698-703, 705-711, 713-718, 720-726, 728-733, 735- 741, 743-748, 750-756, 758-763, 765-771, 773-777, 779-783, 785-789, 791-795, 797-801, 803- 807, 809-813, 815-819, 821-825, 827-831, 833, or 834.

94. The cancer vaccine of claim 93, wherein the peptide comprises the amino acid sequence of SEQ ID NO: 2 or SEQ ID NO:

833.

95. The cancer vaccine of claim 93, wherein the peptide comprises the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO:

834.

96. An expression vector encoding one or more peptide generated by the method of any one of claims 1-60 or a peptide comprising the amino acid sequence of any one of SEQ ID NOs: 1-838.

97. The expression vector of claim 96, wherein the peptide comprises the amino acid sequence of any one of SEQ ID NOs: 2, 3, 5-12, 14-21, 23-30, 32-39, 41-48, 50-57, 59-66, 68-75, 77-84, 86-93, 85-99, 101-105, 107-111, 113-117, 119-123, 125-129, 131-135, 137-141, 143-146, 148- 152, 154-162, 164-168, 170-179, 181-185, 187-196, 198-202, 204-213, 215-219, 221-230, 232- 236, 238-244, 246-252, 254-260, 262-268, 270-276, 278-284, 286-292, 294-300, 302-308, 310- 316, 318-324, 326-332, 334-340, 342-348, 350-356, 358-364, 366-372, 374-380, 382-388, 390- 396, 398-404, 406-412, 414-420, 422-428, 430-436, 438-443, 445-450, 452-457, 459-464, 466- 471, 473-478, 480-485, 487-492, 494-499, 501-506, 508-512, 514-518, 520-524, 526-530, 532- 536, 538-542, 544-548, 550-554, 556-560, 562-566, 568-573, 585-580, 582-587, 589-594, 596- 601, 603-607, 609-613, 615-619, 621-625, 627-631, 633-638, 340-644, 646-651, 653-657, 659- 664, 666-670, 672-677, 679-683, 685-690, 692-696, 698-703, 705-711, 713-718, 720-726, 728- 733, 735-741, 743-748, 750-756, 758-763, 765-771, 773-777, 779-783, 785-789, 791-795, 797- 801, 803-807, 809-813, 815-819, 821-825, 827-831, 833, or 834.

98. A method of treating cancer in a subject diagnosed with the cancer comprising: isolating cells from a biological sample of the subject; culturing the isolated cells with one or more peptide generated by the method of any one of claims 1-60, isolating T cells, NK cells, and / or antigen presenting cells cultured with the one or more peptide and expanding the T cells, NK cells, and / or antigen presenting cells to produce a 89 7361737therapeutically effective composition of tumor antigen specific T cells, NK cells, and / or antigen presenting cells; adoptively transferring the tumor antigen specific T cells, NK cells, and / or antigen presenting cells into the subject, thereby treating the subject diagnosed with cancer.

99. The method of claim 96, wherein the peptide comprise one or more heteroclitic neoepitopes.

100. A cell comprising one or more peptide generated by the method of any one of claims 1-60, or a peptide comprising the amino acid sequence of any one of SEQ ID NOs: 1-838.

101. The cell of claim 100, wherein the peptide comprises the amino acid sequence of any one of SEQ ID NOs: 2, 3, 5-12, 14-21, 23-30, 32-39, 41-48, 50-57, 59-66, 68-75, 77-84, 86-93, 85-99, 101-105, 107-111, 113-117, 119-123, 125-129, 131-135, 137-141, 143-146, 148-152, 154-162, 164-168, 170-179, 181-185, 187-196, 198-202, 204-213, 215-219, 221-230, 232-236, 238-244, 246-252, 254-260, 262-268, 270-276, 278-284, 286-292, 294-300, 302-308, 310-316, 318-324, 326-332, 334-340, 342-348, 350-356, 358-364, 366-372, 374-380, 382-388, 390-396, 398-404, 406-412, 414-420, 422-428, 430-436, 438-443, 445-450, 452-457, 459-464, 466-471, 473-478, 480-485, 487-492, 494-499, 501-506, 508-512, 514-518, 520-524, 526-530, 532-536, 538-542, 544-548, 550-554, 556-560, 562-566, 568-573, 585-580, 582-587, 589-594, 596-601, 603-607, 609-613, 615-619, 621-625, 627-631, 633-638, 340-644, 646-651, 653-657, 659-664, 666-670, 672-677, 679-683, 685-690, 692-696, 698-703, 705-711, 713-718, 720-726, 728-733, 735-741, 743-748, 750-756, 758-763, 765-771, 773-777, 779-783, 785-789, 791-795, 797-801, 803-807, 809-813, 815-819, 821-825, 827-831, 833, or 834.

102. A pharmaceutical composition comprising one or more peptide generated by the method of any one of claims 1-60, the cancer vaccine of any one of claims 69-95, the cell of claim 100 or 101, the expression vector of claim 96 or 97, or a peptide comprising the amino acid sequence of any one of SEQ ID NOs: 1-838 and a pharmaceutically acceptable excipient or carrier.

103. The pharmaceutical composition of claim 102, wherein the peptide comprises the amino acid sequence of any one of SEQ ID NOs: 2, 3, 5-12, 14-21, 23-30, 32-39, 41-48, 50-57, 59-66, 68-75, 77-84, 86-93, 85-99, 101-105, 107-111, 113-117, 119-123, 125-129, 131-135, 137-141, 143-146, 148-152, 154-162, 164-168, 170-179, 181-185, 187-196, 198-202, 204-213, 215-219, 90 7361737221-230, 232-236, 238-244, 246-252, 254-260, 262-268, 270-276, 278-284, 286-292, 294-300, 302-308, 310-316, 318-324, 326-332, 334-340, 342-348, 350-356, 358-364, 366-372, 374-380, 382-388, 390-396, 398-404, 406-412, 414-420, 422-428, 430-436, 438-443, 445-450, 452-457, 459-464, 466-471, 473-478, 480-485, 487-492, 494-499, 501-506, 508-512, 514-518, 520-524, 526-530, 532-536, 538-542, 544-548, 550-554, 556-560, 562-566, 568-573, 585-580, 582-587, 589-594, 596-601, 603-607, 609-613, 615-619, 621-625, 627-631, 633-638, 340-644, 646-651, 653-657, 659-664, 666-670, 672-677, 679-683, 685-690, 692-696, 698-703, 705-711, 713-718, 720-726, 728-733, 735-741, 743-748, 750-756, 758-763, 765-771, 773-777, 779-783, 785-789, 791-795, 797-801, 803-807, 809-813, 815-819, 821-825, 827-831, 833, or 834.

104. Use of a one or more peptides generated by the method of any one of claims 1-60, the cancer vaccine of any one of claims 69-95, the expression vector of claim 96 or 97, the cell of claim 100 or 101, the pharmaceutical composition of claim 102 or 103 or a peptide comprising the amino acid sequence of any one of SEQ ID NOs: 1-838 in the manufacture of a medicament for treatment in a subject.

105. The use of claim 104, wherein the peptide comprises the amino acid sequence of any one of SEQ ID NOs: 2, 3, 5-12, 14-21, 23-30, 32-39, 41-48, 50-57, 59-66, 68-75, 77-84, 86-93, 85-99, 101-105, 107-111, 113-117, 119-123, 125-129, 131-135, 137-141, 143-146, 148-152, 154-162, 164-168, 170-179, 181-185, 187-196, 198-202, 204-213, 215-219, 221-230, 232-236, 238-244, 246-252, 254-260, 262-268, 270-276, 278-284, 286-292, 294-300, 302-308, 310-316, 318-324, 326-332, 334-340, 342-348, 350-356, 358-364, 366-372, 374-380, 382-388, 390-396, 398-404, 406-412, 414-420, 422-428, 430-436, 438-443, 445-450, 452-457, 459-464, 466-471, 473-478, 480-485, 487-492, 494-499, 501-506, 508-512, 514-518, 520-524, 526-530, 532-536, 538-542, 544-548, 550-554, 556-560, 562-566, 568-573, 585-580, 582-587, 589-594, 596-601, 603-607, 609-613, 615-619, 621-625, 627-631, 633-638, 340-644, 646-651, 653-657, 659-664, 666-670, 672-677, 679-683, 685-690, 692-696, 698-703, 705-711, 713-718, 720-726, 728-733, 735-741, 743-748, 750-756, 758-763, 765-771, 773-777, 779-783, 785-789, 791-795, 797-801, 803-807, 809-813, 815-819, 821-825, 827-831, 833, or 834.

106. A peptide comprising an amino acid sequence having at least 75%, 80%, 90%, 95%, 98% sequence identity to any one or more of SEQ ID NOs: 1-838. 91 7361737107. The peptide of claim 106, wherein the peptide comprises an amino acid sequence having at least 75%, 80%, 90%, 95%, 98% sequence identity to SEQ ID NO: 2 or SEQ ID NO:

833.

108. The peptide of claim 107, wherein the peptide comprises an amino acid sequence having at least 75%, 80%, 90%, 95%, 98% sequence identity to SEQ ID NO: 3 or SEQ ID NO:

834.

109. A peptide comprising the amino acid sequence of SEQ ID NOs: 2, 3, 5-12, 14-21, 23-30, 32-39, 41-48, 50-57, 59-66, 68-75, 77-84, 86-93, 85-99, 101-105, 107-111, 113-117, 119-123, 125-129, 131-135, 137-141, 143-146, 148-152, 154-162, 164-168, 170-179, 181-185, 187-196, 198-202, 204-213, 215-219, 221-230, 232-236, 238-244, 246-252, 254-260, 262-268, 270-276, 278-284, 286-292, 294-300, 302-308, 310-316, 318-324, 326-332, 334-340, 342-348, 350-356, 358-364, 366-372, 374-380, 382-388, 390-396, 398-404, 406-412, 414-420, 422-428, 430-436, 438-443, 445-450, 452-457, 459-464, 466-471, 473-478, 480-485, 487-492, 494-499, 501-506, 508-512, 514-518, 520-524, 526-530, 532-536, 538-542, 544-548, 550-554, 556-560, 562-566, 568-573, 585-580, 582-587, 589-594, 596-601, 603-607, 609-613, 615-619, 621-625, 627-631, 633-638, 340-644, 646-651, 653-657, 659-664, 666-670, 672-677, 679-683, 685-690, 692-696, 698-703, 705-711, 713-718, 720-726, 728-733, 735-741, 743-748, 750-756, 758-763, 765-771, 773-777, 779-783, 785-789, 791-795, 797-801, 803-807, 809-813, 815-819, 821-825, 827-831, 833, or 834.

110. The peptide of claim 110, wherein the peptide comprises the amino acid sequence of SEQ ID NO: 2 or SEQ ID NO:

833.

111. The peptide of claim 110, wherein the peptide comprises the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO:

834.

112. The method of any preceding claims, further comprising quantifying differences in structural features between the peptide being modeled and the parental epitope.

113. The method of claim 112, wherein the features comprises contacts between the peptide and HLA cleft residues, solvent-assessable surface area (SASA), peptide rigidity as a measure of CαRMSD of the top 10 predicted structural models for each peptide-HLA complex, surface hydrophobicity, or electrostatic potential.

114. The method of any one of claims 112 or 108, fu13her comprising in vitro co-culturing of heteroclitic peptides with HLA-matched lymphocytes to validate which heteroclitic peptides 92 7361737induce the greatest T cell expansion and activation as compared to parental peptides, as assessed by IFN-gamma ELISpot assay.

115. A kit comprising: (a) One or more peptides generated by the method of any one of claims 1-68, the cancer vaccine of any one of claims 69-95, the expression vector of claim 96 or 97, the cell of claim 100 or 101, the pharmaceutical composition of claim 102 or 103, or the peptide of any one of claims 106-111 and (b) an information material containing instructions for administering a dosage of the one or more peptides, the cancer vaccine, the cell, or a dosage form of the pharmaceutical composition to a subject. 93 7361737