Phosphinate pseudopeptide enhances binding free energy in HIV-1 protease by driving flap closure and suppressing global flexibility

HIV-1 protease (HIV-1 PR) is a critical therapeutic target for HIV treatment, yet the development of novel inhibitors with improved efficacy remains a significant challenge. This study investigates the molecular mechanisms underlying the binding of three diastereoisomers of the novel phosphinate pseudopeptide inhibitor PAC-Phe-Val (SSSS, SRSS, SRRS) to HIV-1 PR in comparison with Darunavir, a clinically approved inhibitor. Using molecular dynamics simulations and MM/PBSA calculations, we characterized protein stability, flap dynamics, and allosteric communication networks within the protease-inhibitor complexes. Our results revealed that the SRSS isomer conferred superior structural stabilization comparable to Darunavir by suppressing global protein flexibility and maintaining a closed, catalytically inactive flap conformation. Importantly, SRSS disrupted key allosteric communication pathways within the protease. MM/PBSA analysis indicated that SRSS exhibited the highest binding affinity (−11.76 kcal/mol) among the designed inhibitors, driven primarily by a strong salt bridge interaction with the Arg8 residue. However, a substantial solvation penalty limited its overall binding affinity relative to Darunavir (−15.75 kcal/mol). These findings identify SRSS as a promising lead compound for HIV-1 PR inhibitor development. Our work provides atomic-level mechanistic insights into inhibitor binding and suggests that future optimization strategies should focus on reducing ligand polarity to minimize desolvation penalties and enhance binding affinity.