Molecular dynamics reveals novel small-molecule inhibitors block PD-1/PD-L1 by promoting PD-L1 dimer stability

Abstract

In the field of cancer immunotherapy, the development of small-molecule inhibitors targeting the PD-1/PD-L1 signaling pathway has emerged as a pivotal research direction to overcome the clinical limitations of current antibody-based therapeutics. Based on the lead compound BMS-202, this study systematically elucidated the dynamic binding mechanisms of three novel inhibitors (BMS-202, LP23, A56) with the PD-L1 dimer through molecular dynamics simulations and multifaceted analysis. Results demonstrated that A56 exhibits superior binding stability and the strongest binding affinity among the three compounds, primarily due to its strong van der Waals (vdW) and electrostatic interactions with Chain B, whereas LP23 predominantly engages with Chain A via favorable electrostatic contributions. The alanine scanning method identified several key hotspot residues (Y56(B), M115(A/B), Y123(A), K124(A), etc.) that were crucial for inhibitor binding. Notably, the A56/PD-L1 system involved the most hotspot residues, which played an important role in enhancing binding affinity. Further analyses through dynamic cross-correlation matrix (DCCM) and principal component analysis (PCA) confirmed the highest structural rigidity and substantial correlated motions in the A56/PD-L1 complex, suggesting that A56 may achieve blockade of immune checkpoint signaling by stabilizing the closed conformation of the PD-L1 dimer and thereby dynamically occluding the PD-1/PD-L1 interaction interface. These findings elucidated the different binding mechanisms of novel small-molecule inhibitors to PD-L1 from both energy and conformational perspectives, providing a potential structural basis for the optimized design of immune checkpoint inhibitors.