SIRP polypeptide compositions and methods of use

• US 9,845,345 B2
• Filed: 05/17/2016
• Issued: 12/19/2017
• Est. Priority Date: 05/18/2015
• Status: Active Grant

• Current Assignee: AB Initio Biotherapeutics Inc. (Ligand Pharmaceuticals, Inc.)
• Original Assignee: AB Initio Biotherapeutics Inc. (Ligand Pharmaceuticals, Inc.)
• Inventors: Ring, Aaron Michael, Maute, Roy Louis, Kruse, Andrew Curtis, Manglik, Aashish, Lin, Kenneth S.
• Primary Examiner(s): KAUFMAN, CLAIRE M
• Application Number:
  US15/157,291
• Publication Number:
  US 20160340397A1
• Time in Patent Office: 581 Days
• Field of Search: None
• CPC Class Codes: A61P 11/06 Antiasthmatics
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 37/06 Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 37/08 Antiallergic agents antiasthmatic agents A61P11/06; ophthalmic antiallergics A61P27/14
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: A61P 7/06 Antianaemics
• CPC Class Codes: A61P 9/10 for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
• CPC Class Codes: C07K 14/55 IL-2
• CPC Class Codes: C07K 14/70503 Immunoglobulin superfamily
• CPC Class Codes: C07K 14/70596 Molecules with a "CD"-designation not provided for elsewhere
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C07K 2319/21 containing a His-tag
• CPC Class Codes: C07K 2319/24 containing a MBP (maltose binding protein)-tag
• CPC Class Codes: C07K 2319/30 Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
• CPC Class Codes: C07K 2319/50 containing protease site

Abstract

Provided herein are SIRP-gamma, SIRP-beta or SIRP-beta2 decoy polypeptides for immunotherapy and/or treatment of cancer, anemia, transplant, asthma, allergy, auto-immune disease, and viral infection.

Claims

1. A polypeptide comprising a SIRP-gamma polypeptide consisting of the sequence EEELQX₁IQPEKLLLVTVGKTATLHCTX₂TSX₃X₄PX₅GPX₆X₇WFRGX₈GPGRX₉LIYNX₁₀X₁₁X₁₂GX₁₃FPRVTTVSDX₁₄X₁₅KRNNMDFSIRISSITPADVGTYYCX₁₆KFRKGX₁₇PEX₁₈VEFK SGPGTEMALGAKPS (SEQ ID NO:

2), wherein X₁ is M, I, L or F;

X₂ is F, I, or L;

X₃ is L, I, V, H, N or D;

X₄ is F, I, L or V;

X₅ is V, I, L, P, T or A;

X₆ is V or I;

X₇ is L or Q;

X₈ is V or A;

X₉ is E or V;

X₁₀ is Q, P, L, V, A or E;

X₁₁ is K or R;

X₁₂ is E, D, K, N, Q or H;

X₁₃ is H, P or R;

X₁₄ is L, I, V, P, T, A, R, S or G;

X₁₅ is T, I, N, F, S, Y, V, A or D;

X₁₆ is V or I;

X₁₇ is S, R, N, K, T, I or M; and

X₁₈ is N, K, D, E, H or Q, and wherein the SIRP-gamma polypeptide binds CD47.

2. The polypeptide of claim 1, wherein the SIRP-gamma polypeptide comprises a sequence selected from one of

3. The polypeptide of claim 1, wherein the polypeptide blocks binding of CD47 to a ligand.

4. The polypeptide of claim 3, wherein the ligand is SIRP-alpha, SIRP-gamma, or thrombospondin-1.

5. The polypeptide of claim 1, wherein the polypeptide binds to a cell which expresses CD47.

6. The polypeptide of claim 5, wherein the cell is a tumor cell, virally infected cell, bacterially infected cell, damaged red blood cell, arterial plaque cell, fibrotic tissue cell, a healthy normal cell such as hematopoietic stem cell, a healthy myeloid or lymphoid precursor cell, or a healthy differentiated hematopoietic cell type such as T, B, plasma, or NK cell.

7. The polypeptide of claim 1, wherein the polypeptide further comprises an opsonizing antibody to enable phagocytosis or ADCC of a cell expressing CD47, wherein the cell is a tumor cell, virally infected cell, bacterially infected cell, damaged red blood cell, arterial plaque cell, fibrotic tissue cell, healthy normal cell such as hematopoietic stem cell, healthy myeloid or lymphoid precursor cell or healthy differentiated hematopoietic cell type such as T, B, plasma, or NK cells.

8. The polypeptide of claim 1, wherein the SIRP-gamma polypeptide is multimeric.

9. The polypeptide of claim 1, wherein the SIRP-gamma polypeptide is monomeric.

10. The polypeptide of claim 1, wherein the polypeptide further comprises a detectable label.

11. The polypeptide of claim 1, wherein the polypeptide has increased occupancy relative to a wildtype SIRP-gamma.

12. The polypeptide of claim 1, wherein the polypeptide has increased persistence relative to a wildtype SIRP-gamma.

13. The polypeptide of claim 1, wherein the SIRP-gamma polypeptide comprises the sequence EEELQIIQPEKLLLVTVGKTATLHCTITSLFPVGPIQWFRGVGPGRVLIYNQREGPFPRVTT VSDGTKRNNMDFSIRISSITPADVGTYYCVKFRKGSPEDVEFKSGPGTEMALGAKPS (SEQ ID NO:

13).

14. The polypeptide of claim 1, wherein the SIRP-gamma polypeptide comprises one of the following sequences:

15. The polypeptide of claim 1, wherein the SIRP-gamma polypeptide is a fusion or chimeric polypeptide, and wherein the SIRP-gamma polypeptide is fused to a polypeptide sequence comprising an immune checkpoint inhibitor or a co-stimulatory molecule through a linker sequence.

16. The polypeptide of claim 15, wherein the linker sequence comprises GGGGSGGGGS (SEQ ID NO:

29).

17. The polypeptide of claim 15, wherein the SIRP-gamma polypeptide is located either N-terminal or C-terminal of the polypeptide sequence comprising an immune checkpoint inhibitor or co-stimulatory molecule.

18. The polypeptide of claim 15, wherein the immune checkpoint inhibitor polypeptide comprises a sequence of a PD-1 or PD-L1 antagonist, a BTLA or CD160 antagonist, or a phosphatidylserine antagonist, e.g., MFGE8, TIM1, TIM3 or TIM4.

19. The polypeptide of claim 15, wherein the co-stimulatory molecule polypeptide comprises a sequence of a CD40 agonist, a 41BBL or CD137 agonist.

20. The polypeptide of claim 15, wherein the fusion or chimeric polypeptide comprises a sequence selected from:

21. The polypeptide of claim 1, wherein the SIRP-gamma polypeptide is a fusion or chimeric polypeptide, wherein the SIRP-gamma polypeptide is fused to a polypeptide sequence comprising a cytokine or an attenuated cytokine through a linker sequence, and wherein the cytokine or the attenuated cytokine is a cytokine polypeptide comprising a sequence of an IL2.

22. The polypeptide of claim 21, wherein the IL2 comprises a polypeptide sequence comprising mutations D20T and F42A.

23. The polypeptide of claim 21, wherein the SIRP-gamma polypeptide is located either N-terminal or C-terminal of the polypeptide sequence comprising the cytokine or the attenuated cytokine.