Receptor-based antagonists of the programmed cell death 1 (pd-1) pathway

Abstract

Provided herein are compositions and methods for alleviating cancer or infection in a subject by administering a therapeutically effective amount of a pharmaceutical composition comprising an isolated PD-1 variant polypeptide. The PD-1 variant polypeptide can inhibit the activity of PD-1 by, for example, competitive or non-competitive inhibition of the interaction between wild-type PD-1 and one or more of its ligands, PD-L1 and PD-L2.

1 - 29 . (canceled) 
     
     
         30 . An isolated PD-1 variant polypeptide, wherein the polypeptide lacks the PD-1 transmembrane and intracellular domains, and wherein the polypeptide comprises at least one amino acid modification at one or more positions selected from the group consisting of F37, N49, A50, S87, P89, Q99, N102, N116, G124, R139, A140, T145, and R147 relative to the wild-type PD-1 amino acid sequence set forth in SEQ ID NO:1. 
     
     
         31 . The polypeptide of  claim 30 , wherein the polypeptide is soluble. 
     
     
         32 . The polypeptide of  claim 30 , wherein the polypeptide comprises the amino acid sequence set forth in SEQ ID NO:2 and the at least one amino acid modification. 
     
     
         33 . The polypeptide of  claim 32 , wherein the polypeptide comprises a fragment of SEQ ID NO:2 and the at least one amino acid modification. 
     
     
         34 . The polypeptide of  claim 30 , wherein the at least one amino acid modification comprises from about 1 to about 15 amino acid modifications. 
     
     
         35 . The polypeptide of  claim 30 , wherein the at least one amino acid modification is one or more members selected from the group consisting of F37L, N49S, A50V, S87G, P89L or P89S, Q99A or Q99R, N102S, N116D or N116S, G124S, R139G, A140V, T145A or T145I, and R147K relative to SEQ ID NO:1. 
     
     
         36 . The polypeptide of  claim 30 , wherein the polypeptide further comprises at least one amino acid modification at one or more positions selected from the group consisting of M70, N74, T76, Q88, Q91, D92, H107, R115, A125, S127, K131, and A132 relative to SEQ ID NO:1. 
     
     
         37 . The polypeptide of  claim 36 , wherein the at least one amino acid modification is one or more members selected from the group consisting of M70V or M70I, N74D or N74S, T76A, Q88R, Q91R, D92A or D92G, H107R, R115G, A125V, S127F or S127L or S127V, K131R, and A132I or A132V relative to SEQ ID NO:1. 
     
     
         38 . The polypeptide of  claim 30 , wherein the at least one amino acid modification is at one or more positions selected from the group consisting of S87, P89, N116, G124, R139, and A140 relative to SEQ ID NO:1. 
     
     
         39 . The polypeptide of  claim 38 , wherein the at least one amino acid modification is at one or more positions selected from the group consisting of S87G, P89L or P89S, N116D or N116S, G124S, R139G, and A140V relative to SEQ ID NO:1. 
     
     
         40 . The polypeptide of  claim 30 , wherein the polypeptide comprises at least the amino acid modifications at positions S87, P89, N116, G124, S127, A132, and A140 relative to SEQ ID NO:1. 
     
     
         41 . The polypeptide of  claim 40 , wherein the amino acid modifications are S87G, P89L or P89S, N116D or N116S, G124S, S127F or S127L or S127V, A132I or A132V, and A140V relative to SEQ ID NO:1. 
     
     
         42 . The polypeptide of  claim 30 , wherein the polypeptide comprises the amino acid sequence set forth in any one of SEQ ID NOS:3-29. 
     
     
         43 . The polypeptide of  claim 30 , wherein the at least one amino acid modification increases the binding affinity of the polypeptide to a PD-1 ligand. 
     
     
         44 . The polypeptide of  claim 30 , wherein the polypeptide has a binding affinity of less than about 1×10 −8  M for a PD-1 ligand. 
     
     
         45 . The polypeptide of  claim 30 , wherein the polypeptide has a binding affinity for a PD-1 ligand that is at least about 10-fold stronger than that of the wild-type PD-1 polypeptide. 
     
     
         46 . The polypeptide of  claim 30 , wherein the polypeptide inhibits or prevents binding between the wild-type PD-1 polypeptide and a PD-1 ligand in vivo or in vitro. 
     
     
         47 . The polypeptide of  claim 43 , wherein the PD-1 ligand is PD-L1 and/or PD-L2. 
     
     
         48 . A nucleic acid comprising a nucleotide sequence encoding one or more polypeptides of  claim 30 . 
     
     
         49 . A pharmaceutical composition comprising a therapeutically effective amount of one or more polypeptides of  claim 30 , or a pharmaceutically acceptable salt thereof. 
     
     
         50 . The pharmaceutical composition of  claim 49 , further comprising a pharmaceutically acceptable carrier. 
     
     
         51 . The pharmaceutical composition of  claim 49 , further comprising a cytotoxic agent. 
     
     
         52 . A method of treating, reducing or preventing metastasis or invasion of a tumor in a subject with cancer, the method comprising administering to the subject a therapeutically effective dose of one or more polypeptides of  claim 30 . 
     
     
         53 . The method of  claim 52 , wherein the cancer is selected from the group consisting of melanoma, glioma, lymphoma, myeloma, head and neck cancer, esophageal cancer, kidney cancer, lung cancer, breast cancer, liver cancer, colorectal cancer, gallbladder cancer, gastric cancer, pancreatic cancer, prostate cancer, cervical cancer, uterine cancer, ovarian cancer, testicular cancer, and any other solid tumor cancer. 
     
     
         54 . A method of treating a subject with an infection, the method comprising administering to the subject a therapeutically effective dose of one or more polypeptides of  claim 30 . 
     
     
         55 . The method of  claim 54 , wherein the infection is a fungal infection, bacterial infection or viral infection. 
     
     
         56 . The method of  claim 55 , wherein the viral infection is selected from the group consisting of a hepatitis B virus infection, hepatitis C virus infection, human papilloma virus infection, human immunodeficiency virus (HIV) infection, human T-lymphotrophic virus (HTLV) infection, Epstein-Barr virus infection, herpes virus infection, cytomegalovirus infection, and any other chronic viral infection. 
     
     
         57 . The method of  claim 52 , wherein the effective dose of the one or more polypeptides inhibits, reduces, or modulates signal transduction mediated by the wild-type PD-1 polypeptide in the subject. 
     
     
         58 . The method of  claim 52 , wherein the effective dose of the one or more polypeptides increases a T cell response in the subject. 
     
     
         59 . A method of treating, reducing or preventing metastasis or invasion of a tumor in a subject with cancer, the method comprising administering to the subject a therapeutically effective dose of an isolated PD-1 variant polypeptide, wherein the polypeptide lacks the PD-1 transmembrane and intracellular domains, and wherein the polypeptide comprises at least one amino acid modification at one or more positions selected from the group consisting of N33, F37, T45, N49, A50, T59, S87, P89, C93, R96, T98, Q99, N102, R112, N116, G124, K135, R139, A140, T145, R147, and R148 relative to the wild-type PD-1 amino acid sequence set forth in SEQ ID NO:1. 
     
     
         60 . A method of treating a subject with an infection, the method comprising administering to the subject a therapeutically effective dose of an isolated PD-1 variant polypeptide, wherein the polypeptide lacks the PD-1 transmembrane and intracellular domains, and wherein the polypeptide comprises at least one amino acid modification at one or more positions selected from the group consisting of N33, F37, T45, N49, A50, T59, S87, P89, C93, R96, T98, Q99, N102, R112, N116, G124, K135, R139, A140, T145, R147, and R148 relative to the wild-type PD-1 amino acid sequence set forth in SEQ ID NO:1.