Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Cysteine Protease Inhibition by Peptidyl-2,3-epoxyketones.
Cysteine proteases are the most abundant proteases in parasitic protozoa and they are essential enzymes to the life cycle of several of them, thus becoming attractive therapeutic targets for the development of new inhibitors. In this paper a computational study of the inhibition mechanism of cysteine protease by the dipeptidyl-2,3-epoxyketone Cbz-Phe-Hph-(S), a recently proposed inhibitor, has been carried out by means of molecular dynamics (MD) simulations with hybrid QM/MM potentials. The computed free energy surfaces of the inhibition mechanism of cysteine proteases by peptidyl epoxyketones showing how the activation of the epoxide ring and the attack of Cys25 to either C2 or C3 atoms take place in a concerted manner. According to our results, the acid species responsible of the protonation of the oxygen atom of the ring would be the conserved His159, in contrast to previous studies that proposed a water molecule as the activating species. The low activation free energies for the reaction where Cys25 attacks the C2 atom of the epoxide ring (12.1 kcal·mol-1) or to the C3 atom (15.4 kcal·mol-1), together with the high negative reaction energies suggest that derivatives of peptidyl-2,3-epoxyketones can be used to develop new potent inhibitors for the treatment of Chagas disease.