Inhibition activities of catechol diether based non-nucleoside inhibitors against the HIV reverse transcriptase variants: Insights from molecular docking and ONIOM calculations

Abstract

The therapeutic effectiveness of the catechol diether analogs against both the wild-type and drug-resistant reverse transcriptase (RT) mutants of HIV strains are investigated by performing molecular docking and hybrid ONIOM calculations. The docking protocol has been used to predict the binding modes of the non-nucleoside inhibitors inside the active site cavity of the viral enzymes. For each enzyme-inhibitor adduct, the predicted docked poses are assessed by employing different scoring function based programs. However, the docking protocol fails to explain satisfactorily the antiviral activities of the drug molecules. Two-layered ONIOM calculations have been carried out to compute the relative binding affinities of the catechol diether derivatives to the binding pockets of RT variants. The binding efficacies of the inhibitors are significantly suppressed by the Y181C and K103N mutations, as revealed by the computed interaction energies at the ONIOM [B3LYP/6-31G(d,p):PM6] level of theory. Deformation energies for each bound ligand conformer are also estimated. The nature of interactions between the drug molecules and the active site residues are analyzed from the reduced density gradient (RDG) isosurfaces. The simulated ECD spectra support the conformational adaption upon inhibitor binding in the binding pockets of HIV strains.