Elucidating the Dynamic Determinants of HIV-1 Protease Inhibition: An Integrative Molecular Dynamics Analysis

Abstract

Background: Human immunodeficiency virus type 1 (HIV-1) protease is essential for viral maturation and remains one of the most important therapeutic targets in antiretroviral therapy. Darunavir (DRV), a potent second-generation protease inhibitor, serves as a reference compound due to its high binding affinity and broad activity against resistant viral strains. However, drug resistance among newer strains continues to challenge therapeutic optimization. Objectives: In this study, four DRV-like inhibitors with different stereochemical configurations and substituents were investigated to elucidate the dynamic determinants of inhibitory potency. Methods: Molecular docking established the binding orientations of the inhibitors within the protease active site, while 200 ns all-atom molecular dynamics (MD) simulations provided detailed insights into conformational stability, flap flexibility, and secondary structure remodeling. Results: Analyses of root mean square deviation (RMSD), root mean square fluctuation (RMSF), solvent-accessible surface area (SASA), define secondary structure of proteins (DSSP), principal component analysis (PCA), and radius of gyration (Rg) revealed that high-potency inhibitors induce more pronounced conformational rearrangements, increased flap mobility, and adaptive secondary structure transitions. These dynamic features correlate strongly with experimentally obtained inhibitory constant (Ki) values. Conclusions: Overall, the findings deliver atomistic and mechanistic insights into inhibitor recognition and potency, offering predictive guidance for the rational design of next-generation HIV-1 protease inhibitors with enhanced efficacy and resistance resilience.