Investigation of Unprecedented Sites and Proposition of New Ligands for Programmed Cell Death Protein I through Molecular Dynamics with Probes and Virtual Screening

Cancer immunotherapy has attracted increasing attention over the last few years. Programmed cell death protein 1 (PD-1) promotes self-tolerance and inhibits immune responses by modulating the T-cell function. The interaction between PD-1 and programmed cell death ligand-1 (PD-L1) leads to immune exhaustion, protecting cancer cells from destruction. Here, we computationally designed a novel ligand named 1508 that binds to an unprecedented PD-1 cavity identified by MixMD and defined by amino acid residues Lys78 to Val97. We showed through a set of MD simulations totaling 12.5 μs that ligand 1508 establishes frequent cation-π and hydrogen bonding interactions with amino acid residues Lys78 and Arg86, respectively, and stabilizes the PD-1 C'D loop in a conformation that does not favor PD-1-PD-L1 complex formation. This study highlights the power of MixMD in exposing new cavities prone to protein-protein complex inhibition and establishes the basis for the design of new molecules that target the PD-1 C'D cavity as an alternative for exploring the modulation of the PD-1-PD-L1 complex in cancer therapy.