Study of the Binding Free Energies between HIV-1 Protease and Its Inhibitors

HIV-1 protease is an important target of AIDS chemotherapy Molecular dynamics simulations followed by MM-PBSA analyses were performed to study the binding of inhibitors BE4, BE5 and BE6 to HIV-1 protease The results show that positioning of the fluorine atoms on the benzyloxy group of P-1/P-1 of the inhibitors affects their binding free energies Inhibitor-residue interactions calculated provide some insights into the mechanisms of enzyme-inhibitor binding Our results indicate that the three inhibitors bind to HIV-1 protease in a very similar mode The calculated data agree well with experimental findings