Methods related to a structure of high-affinity human pd-1/pd-l2 complex

Abstract

Variants of human PD-1 comprising one or more of amino acid substitutions in residues corresponding to N74, T76 and A132 of SEQ ID NO:1 are described. Also described are structures, obtained using X-ray crystallography, of the human PD-1/PD-L2 complex and mutant PD-1 variants. The structures of human PD-1 described in the present disclosure are useful in drug discovery, including small-molecule drug discovery. Accordingly, methods of using the structures in drug discovery are also described.

1 . An in silico method of identifying a compound that binds to PD-L2 binding pocket of human PD-1, the method comprising:
 (a) receiving, by a computer system, information on a three-dimensional structure of PD-L2 binding pocket of human PD-1 comprising a plurality of amino acids;   (b) receiving, by the computer system, information on a three-dimensional structure of a candidate compound;   (c) using the computer system and the information received into the computer system in steps (a) and (b), performing one or more of molecular dynamic simulations, kinetic Monte Carlo (KMC) simulations, direct simulations Monte Carlo (DSMC), or density functional theory (DFT) simulations to determine if the candidate compound binds to the PD-L2 binding pocket of human PD-1, thereby identifying the compound that binds to PD-L2 binding pocket of human PD-1.   
     
     
         2 . A protein comprising a ligand binding pocket with a three-dimensional structure corresponding to a structure of PD-L2 binding pocket of a variant of human PD-1 with one or more of amino acid substitutions in residues corresponding to N74, T76 or A132 of SEQ ID NO:1. 
     
     
         3 . A variant of human PD-1 comprising one or more of amino acid substitutions in residues corresponding to N74, T76 and A132 of SEQ ID NO:1.