Evaluating QM/MM Free Energy Surfaces for Ranking Cysteine Protease Covalent Inhibitors
Clauber Henrique Souza da Costa, Vinícius Bonatto, Alberto Santos, Jerônimo Lameira, Andrei Leitão, Carlos A. Montanari
Abstract
One tactic for cysteine protease inhibition is to form a covalent bond between an electrophilic atom of the inhibitor and the thiol of the catalytic cysteine. In this study, we evaluate the reaction free energy obtained from a hybrid quantum mechanical/molecular mechanical (QM/MM) free energy profile as a predictor of affinity for reversible, covalent inhibitors of rhodesain. We demonstrate that the reaction free energy calculated with the PM6/MM potential is in agreement with the experimental data and suggest that the free energy profile for covalent bond formation in a protein environment may be a useful tool for the inhibitor design.