Integrated High-Throughput Virtual Screening and Molecular Dynamics Approach to Identify Potential PD-1 Inhibitors for Cancer Immunotherapy

Programmed cell death 1 (PD-1) is a key immune checkpoint receptor that plays a pivotal role in maintaining immune tolerance by suppressing T cell activation. However, cancer cells frequently exploit the interaction between PD-1 and its ligand PD-L1, to evade immune surveillance. Although monoclonal antibodies targeting the PD-1/PD-L1 pathway have achieved considerable clinical success, their limitations such as high cost, immunogenicity, and limited tissue penetration highlight the need for alternative therapeutic strategies. In this study, a structure-based virtual screening strategy integrated with molecular docking and molecular dynamics (MD) simulations was employed to identify potential small-molecule inhibitors of human PD-1. An initial library of over 8.526 million compounds from the ZINC20 database was filtered for drug-likeness, toxicity, and pharmacokinetic properties, resulting in 18 lead compounds. Among these, four candidates, ZINC000009779862, ZINC000012821448, ZINC000095472904, and ZINC000102699623, exhibited superior binding affinities and interaction profiles with the PD-1 binding pocket. MD simulations confirmed the structural stability of PD-1/ligand complexes, while steered molecular dynamics (SMD) and umbrella sampling analyses revealed the mechanical and thermodynamic robustness of the interactions. Notably, ZINC000095472904 demonstrated the strongest binding strength and the highest binding free energy, making it the most promising candidate. Collectively, these findings suggest that the identified compounds, particularly ZINC000095472904, may interfere with PD-1/PD-L1 interaction and represent viable lead structures for the development of next-generation immune checkpoint inhibitors.