Fibronectin binding domains with reduced immunogenicity

Patent metadata

Field	Value
Publication number	US-9416170-B2
Application number	US-201313757664-A
Country	US
Kind code	B2
Filing date	Feb 1, 2013
Priority date	Oct 31, 2011
Publication date	Aug 16, 2016
Grant date	Aug 16, 2016

Abstract

Fibronectin type III ( 10 Fn3) binding domains having novel designs that are associated with reduced immunogenicity are provided. The application describes alternative 10 Fn3 binding domains in which certain immunogenic regions are not modified when producing a binder in order to maintain recognition as a self antigen by the host organism. The application also describes 10 Fn3 binding domains in which HLA anchor regions have been destroyed thereby reducing the immunogenic contribution of the adjoining region. Also provided are 10 Fn3 domains having novel combinations of modified regions that can bind to a desired target with high affinity.

First claim

The invention claimed is:

1. A polypeptide comprising a human fibronectin type 3 tenth ( 10 Fn3) domain, which comprises AB, BC, CD, DE, EF, and FG loops and β-strands A, B, C, D, E, F, and G, wherein the 10 Fn3 domain comprises modifications only in the amino acid sequence of the FG loop relative to the FG loop of the wild-type human 10 Fn3 domain as set forth in SEQ ID NO: 6, and in the amino acid sequence of the CD loop relative to the corresponding loop of the wild-type human 10 Fn3 domain as set forth in SEQ ID NO: 6, wherein the modifications contribute to binding a target.

2. A library comprising the polypeptide of claim 1 .

3. A method treating or diagnosing a disease or disorder in a subject in need thereof comprising administering to the subject the polypeptide of claim 1 .

4. The polypeptide of claim 1 , wherein the CD loop is 3 to 11 residues long and the FG loop is 1 to 10 residues long.

5. The polypeptide of claim 1 , wherein the modification in the CD loop is in the amino acid residues corresponding to amino acids 39 to 45 of the wild-type human 10 Fn3 domain as set forth in SEQ ID NO: 6.

6. The polypeptide of claim 1 , wherein the modification in the FG loop is in the amino acid residues corresponding to amino acids 77 to 83 of the wild-type human 10 Fn3 domain as set forth in SEQ ID NO: 6.

7. The polypeptide of claim 5 , wherein the modification in the FG loop is in the amino acid residues corresponding to amino acids 77 to 83 of the wild-type human 10 Fn3 domain as set forth in SEQ ID NO: 6.

8. The polypeptide of claim 1 , wherein the modification in the CD loop is in the amino acid residues corresponding to amino acids 37 to 45 of the wild-type human 10 Fn3 domain as set forth in SEQ ID NO: 6.

9. The polypeptide of claim 1 , wherein the modification in the FG loop is in the amino acid residues corresponding to amino acids 76 to 86 of the wild-type human 10 Fn3 domain as set forth in SEQ ID NO: 6.

10. The polypeptide of claim 8 , wherein the modification in the PG loop is in the amino acid residues corresponding to amino acids 76 to 86 of the wild-type human 10 Fn3 domain as set forth in SEQ ID NO: 6.

11. The polypeptide of claim 1 or 4 , wherein the modifications are insertions, substitutions, or deletions.

12. The polypeptide of claim 5 , wherein the modifications are insertions, substitutions, or deletions.

13. The polypeptide of claim 6 , wherein the modifications are insertions substitutions, or deletions.

14. The polypeptide of claim 7 , wherein the modifications are insertions, substitutions, or deletions.

15. The polypeptide of claim 8 , wherein the modifications are insertions, substitutions, or deletions.

16. The polypeptide of claim 9 , wherein the modifications are insertions, substitutions, or deletions.

17. The polypeptide of claim 10 , wherein the modifications are insertions, substitutions, or deletions.

18. The polypeptide of claim 1 or 4 , wherein the modifications are substitutions.

19. The polypeptide of claim 5 , wherein the modifications are substitutions.

20. The polypeptide of claim 6 , wherein the modifications are substitutions.

21. The polypeptide of claim 7 , wherein the modifications are substitutions.

22. The polypeptide of claim 8 , wherein the modifications are substitutions.

23. The polypeptide of claim 9 , wherein the modifications are substitutions.

24. The polypeptide of claim 10 , wherein the modifications are substitutions.

25. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain binds to the target with a K d of less than 500 nM.

26. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain binds to the target with a K d of less than 100 nM.

27. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain binds to the target with a K d of less than 50 nM.

28. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain binds to the target with a K d of less than 1 nM.

29. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain binds to the target with a K d of less than 500 pM.

30. The polypeptide of any one of claims 1 and 4 to 7 , wherein the target is a human protein.

31. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain binds to tumor necrosis factor alpha (TNF-alpha), delta-like protein 4 (DLL4), interleukin 17 (IL-17), or pregnane X receptor (PXR).

32. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain binds to TNF-alpha.

33. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain binds to DLL4.

34. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain binds to IL-17.

35. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain binds to PXR.

36. The polypeptide of any one of claims 1 and 4 to 7 , wherein the 10 Fn3 domain further comprises a pharmacokinetic moiety.

37. The polypeptide of claim 36 , wherein the pharmacokinetic moiety is selected from a polyoxyalkylene moiety, a human serum albumin binding protein, a sialic acid, a human serum albumin, a transferrin, an IgG, an IgG binding protein, and an Fc fragment.

38. The polypeptide of claim 36 , wherein the pharmacokinetic moiety reduces a clearance rate of the polypeptide in a mammal relative to an unmodified polypeptide.

39. The polypeptide of claim 38 , wherein the clearance rate is reduced by greater than three-fold relative to the unmodified polypeptide.

40. A library comprising the polypeptide of any one of claims 4 to 7 .

41. A molecule comprising two or more polypeptides of any one of claims 1 and 4 to 7 .

42. The molecule of claim 41 , wherein each of the polypeptides are connected by a polypeptide linker selected from any one of SEQ ID NOs: 32-43.

43. The molecule of claim 41 , wherein each of the polypeptides binds to a single target molecule.

44. The molecule of claim 43 , wherein two or more of the polypeptides bind to different target molecules.

45. A method of treating or diagnosing a disease or disorder in a subject in need thereof comprising administering to the subject the polypeptide of any one of claims 1 and 4 to 7 .

Assignees

• Bristol Myers Squibb Co

Inventors

• Davis Jonathan
• Lipovsek Dasa
• Camphausen Ray

Classifications

• A61K38/00

  Medicinal preparations containing peptides (peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00) · CPC title

• C12N15/1062 Primary

  mRNA-Display, e.g. polypeptide and encoding template are connected covalently · CPC title

• C07K16/28

  against receptors, cell surface antigens or cell surface determinants · CPC title

• C07K16/244

  Interleukins [IL] · CPC title

• C07K16/2833

  against MHC-molecules, e.g. HLA-molecules · CPC title