IP Library › Granted Patent US 10,882,914
Granted Patent B2
US 10,882,914 · App. 15/488,409 · Granted Jan 5, 2021

ICOS ligand variant immunomodulatory proteins and uses thereof

Inventors: Ryan Swanson (Seattle, WA); Michael Kornacker (Seattle, WA)
Assignee: ALPINE IMMUNE SCIENCES, INC.
C07K16/2896C07K14/70532C07K16/461C07K2317/40C07K2319/01
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Quick Facts
Patent No.
US 10,882,914
App. No.
15/488,409
Granted
Jan 5, 2021
Kind
B2
Abstract

Provided herein are immunomodulatory proteins comprising ICOSL variants and nucleic acids encoding such proteins. The immunomodulatory proteins provide therapeutic utility for a variety of immunological and oncological conditions. Compositions and methods for making and using such proteins are provided.

Claims (57)

1. A variant ICOS Ligand (ICOSL) polypeptide, comprising one or more amino acid substitutions in the amino acid sequence of an unmodified ICOSL at one or more amino acid positions corresponding to amino acid position(s) selected from the group consisting of 52, 57, 100, 110, 115, 172, and 198 with reference to amino acid positions set forth in SEQ ID NO:32, wherein corresponding amino acid positions are identified by alignment of the unmodified ICOSL polypeptide with the polypeptide set forth in SEQ ID NO:32, wherein:

the one or more amino acid substitutions are selected from the group consisting of N52H, N52D, N52S, N52Y, N52K, N57D, N57Y, Q100R, Q100K, Q100P, V110D, V110N, V110A, H115R, H115Q, F172S, and C198R; and

the unmodified ICOSL comprises (i) the sequence of amino acids set forth in SEQ ID NO:32, or (ii) a portion of the sequence of (i) comprising an immunoglobulin superfamily (IgSF) domain which is one or both of an IgV domain or IgC domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5 and the IgC domain is amino acids 141-227 of SEQ ID NO:5.

2. The variant ICOSL polypeptide of claim 1 , wherein the variant ICOSL comprises up to 9 amino acid substitution compared to the unmodified ICOSL polypeptide.

3. The variant ICOSL polypeptide of claim 1 , wherein the unmodified ICOSL consists of (i) the sequence of amino acids set forth in SEQ ID NO:32, or (ii) a portion of the sequence of (i) comprising an immunoglobulin superfamily (IgSF) domain which is one or both of an IgV domain or IgC domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5 and the IgC domain is amino acids 141-227 of SEQ ID NO:5.

4. The variant ICOSL polypeptide of claim 1 , wherein the one or more amino acid substitutions are selected from the group consisting of N52H/N57Y/Q100P, N52H/C198R, N57Y/Q100P, N52S/C198R, N52H/N57Y/Q100R/V110D, N52H/N57Y/Q100R, N52H/Q100R, N52H/N57Y/Q100R/F172S, N52H/N57Y, N52H/N57Y/Q100R/V110D/C198R, N52H/N57Y/Q100R/V110D/F172S/C198R, N52H/N57Y/Q100R/V110D/H115R/C198R, N52H/N57Y/Q100R/C198R, N52D, N57Y/Q100R/C198R, N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/Q100R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/C198R, N52H/N57Y/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/H115R, N52H/N57Y/Q100R/H115R, N52H/N57Y/Q100R/H115R/F172S, N52H/N57Y/Q100R/F172S, N52H/N57Y/Q100P/H115R/F172S, N52Y/N57Y/Q100P/F172S, N52S/H115R/F172S/C198R, N52H/N57Y/Q100P/C198R, N52H/N57Y/Q100P/H115R/F172S/C198R, N52H/N57Y/Q100P/F172S/C198R, N52H/N57Y/Q100P/H115R, N52H/N57Y/Q100P/H115R/C198R, N52H/Q100R/C198R, N52H/Q100R/H115R/F172S, N52H/Q100R/F172S/C198R, N52H/Q100R/H115R/F172S/C198R, and N52H/N57Y/Q100R/F172S/C198R.

5. The variant ICOSL polypeptide of claim 3 , wherein the one or more amino acid substitutions are selected from the group consisting of N52H/N57Y/Q100P, N52H/C198R, N57Y/Q100P, N52S/C198R, N52H/N57Y/Q100R/V110D, N52H/N57Y/Q100R, N52H/Q100R, N52H/N57Y/Q100R/F172S, N52H/N57Y, N52H/N57Y/Q100R/V110D/C198R, N52H/N57Y/Q100R/V110D/F172S/C198R, N52H/N57Y/Q100R/V110D/H115R/C198R, N52H/N57Y/Q100R/C98R, N52D, N52Q/N84Q, N52Q/N119Q, N57Y/Q100R/C198R, N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/Q100R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/C198R, N52H/N57Y/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/H115R, N52H/N57Y/Q100R/H115R, N52H/N57Y/Q100R/H115R/F172S, N52H/N57Y/Q100R/F172S, N52H/N57Y/Q100P/H115R/F172S, N52Y/N57Y/Q100P/F172S, N52S/H115R/F172S/C198R, N52H/N57Y/Q100P/C198R, N52H/N57Y/Q100P/H115R/F172S/C198R, N52H/N57Y/Q100P/F172S/C198R, N52H/N57Y/Q100P/H115R, N52H/N57Y/Q100P/H115R/C198R, N52H/Q100R/C198R, N52H/Q100R/H115R/F172S, N52H/Q100R/F172S/C198R, N52H/Q100R/H115R/F172S/C198R, and N52H/N57Y/Q100R/F172S/C198R.

6. The variant ICOSL polypeptide of claim 1 , wherein the one or more amino acid substitutions are selected from the group consisting of N52H, N52D, N52S, N52K, N52Y, N57Y, Q100P, Q100R, V110A, V110D, and C198R.

7. The variant ICOSL polypeptide of claim 5 , wherein the one or more amino acid substitutions are N52H/N57Y/Q100R/C198R, N52H/N57Y/Q100R, N52H/Q100R, N52H/N57Y/Q100P, or N52H/N57Y/Q100R/C198R.

8. The variant ICOSL polypeptide of claim 1 , comprising:

the sequence of amino acids set forth in any of SEQ ID NOS: 109-111, 113, 115, 120, 121, 122, 125, 281, 283, 285, 288, 291, 292, 302, 315, 320, 365, 427, 430, 435, 436, 437, 442, 443, 444, 445, 447, 448, 450, 451, and 460-470; or

the sequence of amino acids set forth in any of SEQ ID NOS: 197-201, 204-206, 209, 327, 329, 331, 333, 334, and 434.

9. The variant ICOSL polypeptide of claim 1 , wherein the variant ICOSL polypeptide specifically binds to the ectodomain of human CD28 with increased affinity compared to the binding of the unmodified ICOSL polypeptide to the ectodomain of human CD28.

10. The variant ICOSL polypeptide of claim 9 , wherein the variant ICOSL polypeptide specifically binds to the ectodomain of human ICOS and the ectodomain of human CD28 each with increased affinity compared to the binding of the unmodified ICOSL polypeptide to the ectodomain of human ICOS and human CD28.

11. The variant ICOSL polypeptide of claim 9 , wherein the affinity to the ectodomain of human CD28 is increased more than 5-fold.

12. The variant ICOSL polypeptide of claim 3 , wherein the variant ICOSL polypeptide is linked to an Fc domain.

13. The variant ICOSL polypeptide of claim 1 , wherein the variant ICOSL polypeptide is soluble and lacks a transmembrane domain.

14. The variant ICOSL polypeptide of claim 1 , wherein the unmodified ICOSL consists of a portion of the sequence of amino acids set forth in SEQ ID NO:32 comprising the IgV domain but not comprising the IgC domain.

15. A fusion protein comprising the variant ICOSL polypeptide of claim 13 linked to an Fc domain.

16. A nucleic acid molecule encoding a sequence of amino acids comprising the variant ICOSL polypeptide of claim 1 .

17. The fusion protein of claim 15 , wherein the Fc domain is a variant human IgG1 Fc with reduced effector function.

18. A fusion protein comprising the variant ICOSL polypeptide of claim 1 linked to an Fc domain.

19. The fusion protein of claim 18 , wherein the Fc domain is a variant human IgG1 Fc with reduced effector function.

20. A fusion protein comprising the variant ICOSL polypeptide of claim 4 linked to an Fc domain.

21. The fusion protein of claim 20 , wherein the Fc domain is a variant human IgG1 Fc with reduced effector function.

22. A variant ICOSL-Fc fusion, comprising a variant ICOSL polypeptide linked to an Fc domain, wherein the variant ICOSL polypeptide comprises the amino acid substitutions N52H/N57Y/Q100P in the amino acid sequence set forth in SEQ ID NO:32 or a portion thereof comprising an IgV domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5.

23. The variant ICOSL-Fc fusion of claim 22 , wherein the Fc domain is a variant human IgG1 Fc with reduced effector function.

24. A variant ICOSL-Fc fusion, comprising a variant ICOSL polypeptide linked to an Fc domain, wherein the variant ICOSL polypeptide comprises the amino acid substitutions N52H/N57Y/Q100R in the amino acid sequence set forth in SEQ ID NO:32 or a portion thereof comprising an IgV domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5.

25. The variant ICOSL-Fc fusion of claim 24 , wherein the Fc domain is a variant human IgG1 Fc with reduced effector function.

26. A variant ICOSL-Fc fusion, comprising a variant ICOSL polypeptide linked to an Fc domain, wherein the variant ICOSL polypeptide comprises the amino acid substitutions N52H/Q100R in the amino acid sequence set forth in SEQ ID NO:32 or a portion thereof comprising an IgV domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5.

27. The variant ICOSL-Fc fusion of claim 26 , wherein the Fc domain is a variant human IgG1 Fc with reduced effector function.

28. A variant ICOSL-Fc fusion, comprising a variant ICOSL polypeptide linked to an Fc domain, wherein the variant ICOSL polypeptide comprises the amino acid substitution N52D in the amino acid sequence set forth in SEQ ID NO:32 or a portion thereof comprising an IgV domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5.

29. The variant ICOSL-Fc fusion of claim 28 , wherein the Fc domain is a variant human IgG1 Fc with reduced effector function.

30. A variant ICOSL-Fc fusion, comprising a variant ICOSL polypeptide linked, via a linker, to an Fc domain, wherein:

(i) the variant ICOSL polypeptide comprises the amino acid substitutions N52H/N57Y/Q100P in the amino acid sequence set forth in SEQ ID NO:32 or a portion thereof comprising an IgV domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5; and

(ii) the Fc domain is a variant human IgG1 Fc with reduced effector function.

31. A variant ICOSL-Fc fusion, comprising a variant ICOSL polypeptide linked, via a linker, to an Fc domain, wherein:

(i) the variant ICOSL polypeptide comprises the amino acid substitutions N52H/N57Y/Q100R in the amino acid sequence set forth in SEQ ID NO:32 or a portion thereof comprising an IgV domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5; and

(ii) the Fc domain is a variant human IgG1 Fc with reduced effector function.

32. A variant ICOSL-Fc fusion, comprising a variant ICOSL polypeptide linked, via a linker, to an Fc domain, wherein:

(i) the variant ICOSL polypeptide comprises the amino acid substitutions N52H/Q100R in the amino acid sequence set forth in SEQ ID NO:32 or a portion thereof comprising an IgV domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5; and

(ii) the Fc domain is a variant human IgG1 Fc with reduced effector function.

33. A variant ICOSL-Fc fusion, comprising a variant ICOSL polypeptide linked, via a linker, to an Fc domain, wherein:

(i) the variant ICOSL polypeptide comprises the amino acid substitution N52D in the amino acid sequence set forth in SEQ ID NO:32 or a portion thereof comprising an IgV domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5; and

(ii) the Fc domain is a variant human IgG1 Fc with reduced effector function.

34. The variant ICOSL polypeptide of claim 1 , wherein the one or more amino acid substitution are N52H/N57Y/Q100P.

35. The variant ICOSL polypeptide of claim 1 , wherein the one or more amino acid substitutions are N52H/N57Y/Q100R.

36. The variant ICOSL polypeptide of claim 1 , wherein the one or more amino acid substitutions are N52H/Q100R.

37. The variant ICOSL polypeptide of claim 1 , wherein the one or more amino acid substitution is N52D.

38. The variant ICOSL polypeptide of claim 9 , wherein the variant ICOSL polypeptide is linked to an Fc domain.

39. The fusion protein of claim 18 , wherein the unmodified ICOSL polypeptide consists of (i) the sequence of amino acids set forth in SEQ ID NO:32, or (ii) a portion of the sequence of (i) comprising an immunoglobulin superfamily (IgSF) domain which is one or both of an IgV domain or IgC domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5 and the IgC domain is amino acids 141-227 of SEQ ID NO:5.

40. The fusion protein of claim 39 , wherein the unmodified ICOSL polypeptide consists of a portion of the sequence of amino acids set forth in SEQ ID NO:32 comprising the IgV domain but not comprising the IgC domain.

41. The fusion protein of claim 40 , wherein Fc domain is a variant human IgG1 Fc with reduced effector function.

42. The fusion protein of claim 41 , wherein the one or more amino acid substitutions comprise N52H.

43. The fusion protein of claim 41 , wherein the one or more amino acid substitutions comprise N57Y.

44. The fusion protein of claim 41 , wherein the one or more amino acid substitutions comprise Q100R.

45. The fusion protein of claim 41 , wherein the one or more amino acid substitutions are N52H/N57Y/Q100R.

Assignments (2)
CORRECTIVE ASSIGNMENT TO CORRECT THE THE STREET ADDRESS FOR THE INVENTORS PREVIOUSLY RECORDED AT REEL: 044441 FRAME: 0904. ASSIGNOR(S) HEREBY CONFIRMS THE ASSIGNMENT. Recorded Sep 21, 2020
From: SWANSON, RYAN; KORNACKER, MICHAEL
To: ALPINE IMMUNE SCIENCES, INC.
Reel/Frame 053839/0556 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Dec 19, 2017
From: SWANSON, RYAN; KORNACKER, MICHAEL
To: ALPINE IMMUNE SCIENCES, INC.
Reel/Frame 044441/0904 →
Continuity (6)
Provisional Application 62475162 · Mar 22, 2017
Provisional Application 62472568 · Mar 16, 2017
Provisional Application 62410842 · Oct 20, 2016
Provisional Application 62394745 · Sep 14, 2016
Provisional Application 62323608 · Apr 15, 2016
Related Publication 20170320959A1 · Nov 9, 2017
Cited By (8)
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