Activatable binding polypeptides and methods of identification and use thereof

• US 8,518,404 B2
• Filed: 03/02/2012
• Issued: 08/27/2013
• Est. Priority Date: 08/22/2007
• Status: Active Grant

• Current Assignee: CytomX Therapeutics, Inc, Regents of the University of California (University of California)
• Original Assignee: CytomX Therapeutics, Inc, Regents of the University of California (University of California)
• Inventors: Daugherty, Patrick, Stagliano, Nancy, Thomas, Jerry, Kamath, Kathryn, West, James W., Khare, Sanjay, Sagert, Jason
• Primary Examiner(s): HUYNH, PHUONG N
• Application Number:
  US13/411,409
• Publication Number:
  US 20120244154A1
• Time in Patent Office: 543 Days
• Field of Search: None
• US Class Current: 424/134.1
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: A61P 9/00 Drugs for disorders of the cardiovascular system
• CPC Class Codes: C07K 16/22 against growth factors ; against growth regulators
• CPC Class Codes: C07K 16/24 against cytokines, lymphokines or interferons
• CPC Class Codes: C07K 16/2818 against CD28 or CD152
• CPC Class Codes: C07K 16/2836 against CD106
• CPC Class Codes: C07K 16/42 against immunoglobulins
• CPC Class Codes: C07K 2317/34 Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
• CPC Class Codes: C07K 2317/622 Single chain antibody (scFv)
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• 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
• CPC Class Codes: C12N 15/1034 Isolating an individual clone by screening libraries
• CPC Class Codes: C12N 15/1044 Preparation or screening of libraries displayed on scaffold proteins

Abstract

Activatable binding polypeptides (ABPs), which contain a target binding moiety (TBM), a masking moiety (MM), and a cleavable moiety (CM) are provided. Activatable antibody compositions, which contain a TBM containing an antigen binding domain (ABD), a MM and a CM are provided. Furthermore, ABPs which contain a first TBM, a second TBM and a CM are provided. The ABPs exhibit an “activatable” conformation such that at least one of the TBMs is less accessible to target when uncleaved than after cleavage of the CM in the presence of a cleaving agent capable of cleaving the CM. Further provided are libraries of candidate ABPs, methods of screening to identify such ABPs, and methods of use. Further provided are ABPs having TBMs that bind VEGF, CTLA-4, or VCAM, ABPs having a first TBM that binds VEGF and a second TBM that binds FGF, as well as compositions and methods of use.

Claims

1. An activatable binding polypeptide (ABP) that in an activated state binds Cytotoxic T-Lymphocyte Antigen 4 (CTLA 4), the ABP comprising, in an N- to C-terminal direction or in a C- to N-terminal direction:

an antigen binding domain (ABD) that specifically binds to CTLA-4,

a cleavable moiety (CM), and

a masking moiety (MM), wherein the MM is a peptide that inhibits binding of the ABD to CTLA-4, wherein the MM comprises an amino acid sequence selected from the group consisting of MILLCAAGRTWVEACANGR (SEQ ID NO;

     63), AERLCAWAGRFCGS (SEQ ID NO;

     65), WADVMPGSGVLPWTS (SEQ ID NO;

     67) and SDGRMGSLELCALWGRFCGS (SEQ ID NO;

69, and wherein the CM is positioned in the ABP such that in an uncleaved state the MM interferes with specific binding of the ABD to CTLA-4 and in a cleaved state the MM does not interfere with specific binding of the ABD to CTLA-4.

2. The ABP of claim 1, wherein the MM is a peptide of no more than about 40 amino acids in length.

3. The ABP of claim 1, wherein the ABP comprises a linker peptide between the MM and the CM.

4. The ABP of claim 1, wherein the ABP comprises a linker peptide between the CM and the ABD.

5. The ABP of claim 1, wherein the ABP comprises a Fab fragment, ScFv, or single chain antibody (SCAB) comprising the ABD.

6. The ABP of claim 1, wherein the ABD is from ipilimumab or tremelimumab.

7. The ABP of claim 1, wherein the CM is positioned in the ABP in an uncleaved state N-terminal to the ABD.

8. The ABP of claim 1, wherein the CM is positioned in the ABP in an uncleaved state C-terminal to the ABD.

9. The ABP of claim 7, wherein the CM is positioned in the ABP in an uncleaved state N-terminal to a variable light (VL) chain of the ABD.

10. The ABP of claim 1, wherein the ABD is positioned at the N-terminus of the ABP.

11. The ABP of claim 1, wherein the ABD is positioned at the C-terminus of the ABP.

12. The ABP of claim 1, wherein the MM, CM and ABD are positioned in an N- to C-terminal direction of the ABP in an uncleaved state.

13. The ABP of claim 1, wherein the CM is a substrate for an enzyme selected from the group consisting of MMP-1, MMP-2, MMP-3, MMP-8, MMP-9, MMP-14, plasmin, PSA, PSMA, CATHEPSIN D, CATHEPSIN K, CATHEPSIN S, ADAM10, ADAM12, ADAMTS, Caspase-1, Caspase-2, Caspase-3, Caspase-4, Caspase-5, Caspase-6, Caspase-7, Caspase-8, Caspase-9, Caspase10, Caspase-11, Caspase-12, Caspase-13, Caspase-14, and TACE.

14. The ABP of claim 1, wherein the CM is a substrate for an enzyme selected from the group consisting of an MMP and a CATHEPSIN.

15. The ABP of claim 1, wherein the ABP comprises a detectable moiety.

16. The ABP of claim 15, wherein the detectable moiety is a diagnostic agent.

17. The ABP of claim 1, wherein the ABP comprises a first linker peptide (L₁) and a second linker peptide (L₂), wherein the first linker peptide is positioned between the MM and the CM and the second linker peptide is positioned between the ABD and the CM.

18. The ABP of claim 17, wherein each of L₁ and L₂ is a peptide of about 1 to 20 amino acids in length, and wherein each of L₁ and L₂ need not be the same linker.

19. The ABP of claim 17, wherein one or both of L₁ and L₂ comprise a glycine-serine polymer.

20. The ABP of claim 17, wherein both of L₁ and L₂ comprise a glycine-serine polymer.

21. The ABP of claim 17, wherein at least one of L₁ and L₂ comprises an amino acid sequence selected from the group consisting of (GS)_n, GSGGS (SEQ ID NO:

1) and (GGGS)_n (SEQ ID NO;

     2), where n is an integer of at least one.

22. The ABP of claim 17, wherein at least one of L₁ and L₂ comprises an amino acid sequence having the formula (GGS)_n, where n is an integer of at least one.

23. The ABP of claim 17, wherein at least one of L₁ and L₂ comprises an amino acid sequence selected from the group consisting of GGSG (SEQ ID NO:

3), GGSGG (SEQ ID NO;

     4), GSGSG (SEQ ID NO;

     5), GSGGG (SEQ ID NO;

     6), GGGSG (SEQ ID NO;

     7), and GSSSG (SEQ ID NO;

     8).

24. The ABP of claim 17, wherein L₁ comprises the amino acid sequence (GGGS)₃ and L₂ comprises the amino acid sequence (GGS)₂.

25. A method of inhibiting Cytotoxic T-Lymphocyte Antigen 4 (CTLA-4) activity in a subject, comprising:

administering to the subject a therapeutically effective amount of a composition comprising an ABP according to claim 1 and a pharmaceutically acceptable excipient.