RELATIVE BINDING FREE-ENERGIES OF PEPTIDE INHIBITORS OF HIV-1 PROTEASE - THE INFLUENCE OF THE ACTIVE-SITE PROTONATION STATE

Hydrogen bonding plays an important role in the stabilization of complexes between HIV-1 protease (HIV-1 PR) and its inhibitors. The adequate treatment of the protease active site protonation state is important for accurate molecular simulations of the protease-inhibitor complexes. We have applied the free energy simulation/thermodyamic cycle approach to evaluate the relative binding affinities of the S vs R isomers of the U85548E inhibitor of the protease. Several mono- and diprotonation states of the catalytic aspartic acid residues of the protease active site were considered in the course of molecular simulations. The calculated difference in binding free: energy of the S vs R isomers strongly depended on the location of proton(s), but in all cases the binding free energy of the S inhibitor was higher. On the basis of our calculations, we propose that in the HIV-1 PR-inhibitor complex only one catalytic aspartic acid residue is protonated and that the binding free energy of the S isomer is ca. 2.8 kcal/mol higher than that of the R isomer. The accuracy of these predictions shall be evaluated when binding affinities of both isomers become available.