Immunological reagents
This disclosure relates to binding agents with specificity for programmed cell death 1 (PD-1) and to methods for using the same to treat, prevent and/or ameliorate an infectious disease (e.g., human immunodeficiency virus (HIV)), cancer and/or autoimmunity. In addition, this disclosure identifies a novel binding patch (“P2”) on PD-1 that is linked with a previously unidentified functional activity of PD-1 that is distinct from the interaction site involved with either the PD-L1 or PD-L2 ligands. Furthermore, we demonstrate that antibodies that interact with this region of PD-1 are able to act as antagonists of PD-1 and that this antagonism is further enhanced with the addition of antibodies that act through the blockade of the PD-1/PD-L1/L2 interaction.
1. A humanized antibody or fragment thereof that binds human PD-1 and comprises a heavy chain variable region (VH) comprising the amino acid sequence set forth in SEQ ID NO: 176 and a light chain variable region (VL) comprising the amino acid sequence set forth in SEQ ID NO: 190.
2. A composition comprising the humanized antibody or fragment thereof of claim 1 and at least one pharmaceutically acceptable carrier.
3. A method of inducing internalization of PD-1 from the surface of a T cell by contacting the T cell with the composition of claim 2 .
4. The method of claim 3 , wherein the T cell is a human T cell infected with human immunodeficiency virus (HIV).
5. A method of relieving functional exhaustion and increasing proliferation of antigen-specific CD8 T cells by contacting the CD8 T cells with the composition of claim 2 .
6. The method of claim 5 , wherein the T cells are specific for human immunodeficiency virus (HIV).
7. The method of claim 3 or 5 , wherein the method further comprises contacting the T cells with the anti-PD-1 antibody pembrolizumab.
8. A method of treating cancer in a human patient, the method comprising administering to the patient with the cancer an effective amount of the composition of claim 2 .
9. The method of claim 8 , wherein the method further comprises administering pembrolizumab to the patient.
10. The fragment of claim 1 , wherein the fragment is an F ab , F ab2 , Fab′, single chain antibody, or F v fragment.
11. A composition comprising the fragment of claim 10 and at least one pharmaceutically acceptable carrier.
12. A composition comprising the humanized antibody or fragment thereof of claim 1 and the anti-PD-1 antibody pembrolizumab.
13. A binding agent that comprises the humanized antibody or fragment thereof of claim 1 and a second binding specificity against a different antigen.
14. A composition comprising the binding agent of claim 13 and a pharmaceutically acceptable carrier.
15. A derivative of the humanized antibody or fragment thereof of claim 1 , wherein the derivative comprises the humanized antibody or fragment thereof of claim 1 and a detectable label or an effector moiety fixably attached thereto.
16. A composition comprising the derivative of claim 15 and a pharmaceutically acceptable carrier.
17. An isolated polynucleotide encoding a humanized antibody or fragment thereof that binds human PD-1 and comprises a heavy chain variable region (VH) comprising the amino acid sequence set forth in SEQ ID NO: 176 and a light chain variable region (VL) comprising the amino acid sequence set forth in SEQ ID NO: 190.
18. An isolated polynucleotide comprising the nucleic acid sequence set forth in SEQ ID NO: 229 or SEQ ID NO: 243.
19. An expression vector comprising one or more polynucleotide of claim 17 or 18 .
20. A host cell comprising the expression vector of claim 19 .
21. A host cell comprising one or more polynucleotide of claim 17 or 18 .
22. A humanized antibody or fragment thereof that binds human PD-1 and comprises a combination of a heavy chain variable region (VH) and a light chain variable region (VL), wherein the humanized antibody comprises:
(a) a VH comprising an amino acid sequence as set forth in one of SEQ ID NOS: 147-150 and a VL comprising an amino acid sequence set forth in one of SEQ ID NOS: 159-163; or
(b) a VH comprising an amino acid sequence as set forth in one of SEQ ID NOS: 172-177 and a VL comprising an amino acid sequence as set forth in one of SEQ ID NOS: 186-190.
23. A composition comprising the humanized antibody or fragment thereof of claim 22 and a pharmaceutically acceptable carrier.
24. A composition comprising the humanized antibody or fragment thereof of claim 22 and the anti-PD-1 antibody pembrolizumab.
25. A method of treating cancer in a human patient, the method comprising administering to the patient with the cancer an effective amount of the composition of claim 22 .
26. The method of claim 25 , wherein the method further comprises administering pembrolizumab to the patient.
27. An isolated polynucleotide encoding a humanized antibody or fragment that binds human PD-1 and comprises a combination of a heavy chain variable region (VH) and a light chain variable region (VL), wherein the humanized antibody comprises:
(a) a VH encoded by a nucleic acid sequence as set forth in one of SEQ ID NOS: 200-203 and a VL encoded by a nucleic acid sequence as set forth in one of SEQ ID NOS: 212-216;
or
(b) a VH encoded by a nucleic acid sequence as set forth in one of SEQ ID NOS: 225-230 and a VL encoded by a nucleic acid sequence as set forth in one of SEQ ID NOS: 239-243.
28. A vector comprising the polynucleotide of claim 27 .
29. A host cell comprising the vector of claim 28 .