Monte Carlo calculations on HIV-1 reverse transcriptase complexed with thenon-nucleoside inhibitor 8-Cl TIBO: contribution of the L100I and Y181C variants to protein stability and biological activity

A computational model of the non-nucleoside inhibitor 8-Cl TIBO complexed w ith HIV-1 reverse transcriptase (RT) was constructed in order to determine the binding free energies. Using Monte Carlo simulations, both free energy perturbation and linear response calculations were carried out for the tran sformation of wild-type RT to two key mutants, Y181C and L100I. The newer l inear response method estimates binding free energies based on changes in e lectrostatic and van der Waals energies and solvent-accessible surface area s. In addition, the change in stability of the protein between the folded a nd unfolded states was estimated for each of these mutations, which are kno wn to emerge upon treatment with the inhibitor. Results from the calculatio ns revealed that there is a large hydrophobic contribution to protein stabi lity in the native, folded state. The calculated absolute free energies of binding from both the linear response, and also the more rigorous free ener gy perturbation method, gave excellent agreement with the experimental diff erences in activity. The success of the relatively rapid linear response me thod in predicting experimental activites holds promise for estimating the activity of the inhibitors not only against the wild-type RT, but also agai nst key protein variants whose emergence undermines the efficacy of the dru gs.