Journal Article

A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery

Kim, Peter S., Tang, Shaogeng

2019

Overview

Immune checkpoint blockade of programmed death-1 (PD-1) by monoclonal antibody drugs has delivered breakthroughs in the treatment of cancer. Nonetheless, small-molecule PD-1 inhibitors could lead to increases in treatment efficacy, safety, and global access. While the ligand-binding surface of apo-PD-1 is relatively flat, it harbors a striking pocket in the murine PD-1/PD-L2 structure. An analogous pocket in human PD-1 may serve as a small-molecule drug target, but the structure of the human complex is unknown. Because the CC′ and FG loops in murine PD-1 adopt new conformations upon binding PD-L2, we hypothesized that mutations in these two loops could be coupled to pocket formation and alter PD-1’s affinity for PD-L2. Here, we conducted deep mutational scanning in these loops and used yeast surface display to select for enhanced PD-L2 binding. A PD-1 variant with three substitutions binds PD-L2 with an affinity two orders of magnitude higher than that of the wild-type protein, permitting crystallization of the complex. We determined the X-ray crystal structures of the human triple-mutant PD-1/PD-L2 complex and the apo triple-mutant PD-1 variant at 2.0 Å and 1.2 Å resolution, respectively. Binding of PD-L2 is accompanied by formation of a prominent pocket in human PD-1, as well as substantial conformational changes in the CC′ and FG loops. The structure of the apo triple-mutant PD-1 shows that the CC′ loop adopts the ligand-bound conformation, providing support for allostery between the loop and pocket. This human PD-1/PD-L2 structure provide critical insights for the design and discovery of small-molecule PD-1 inhibitors.

• Publisher: National Academy of Sciences
• Subject: Affinity / Allosteric Regulation / Amino Acid Substitution / B7-H1 Antigen - chemistry / B7-H1 Antigen - metabolism / BASIC BIOLOGICAL SCIENCES / Binding / Binding Sites / Biochemistry / Biological Sciences / Biophysics and Computational Biology / Crystal structure / Crystallization / Crystallography, X-Ray / Drug delivery systems / Drug Discovery / Humans / Immune checkpoint / Immunosuppressive agents / Inhibitors / Ligands / Models, Molecular / Molecular structure / Monoclonal antibodies / Multiprotein Complexes - chemistry / Mutation / PD-1 / PD-1 protein / PD-L2 / Physical Sciences / Programmed Cell Death 1 Ligand 2 Protein - chemistry / Programmed Cell Death 1 Ligand 2 Protein - metabolism / Programmed Cell Death 1 Receptor - antagonists & inhibitors / Programmed Cell Death 1 Receptor - chemistry / Programmed Cell Death 1 Receptor - genetics / Programmed Cell Death 1 Receptor - metabolism / Protein Conformation / Small Molecule Libraries - pharmacology / Yeast