Effects of the G48M mutant on the dynamics properties and binding mechanism of PR with SQV and ATV

The resistance of HIV-1 protease (PR) mutations seriously affects the efficiency of current drugs in the clinical treatment of AIDS. Therefore, it is important to understand the resistance mechanism of mutated residues for the development of PR inhibitors. In this work, the mechanism of G48M mutant PR to inhibitors Saquinavir and Atazanavir was studied by using molecular dynamics simulation combined with free energy prediction. The analysis results showed that, compared with the WT PR, the distance of the flap tip from the protease catalytic binding site and the dihedral angles in the flap regions in the mutant type complexes was changed. These changes resulted in a significant reduction in the occupancy of most of the hydrogen bonds in the mutant complex and the interaction energy of key residues with the inhibitor, which is the main reason for the resistance of the mutation to these inhibitors. This study can provide important guidance for the design of effective inhibitors against HIV-1 PR.