A Computational Comparison Between Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS-CoV-2 Main Protease. Implications for Resistance Mechanisms

This study investigates the binding mode and reaction mechanism between pomotrelvir and the SARS-CoV-2 main protease using a combination of molecular mechanics and hybrid quantum mechanics / molecular mechanics simulations. Alchemical transformations where each Pi group of pomotrelvir was transformed into its counterpart in nirmatrelvir were performed to unravel the individual contribution of each group of the inhibitor to the binding and reaction processes. We have shown that while a gamma-lactam ring is preferred at position P1, a delta-lactam ring could be an alternative to be incorporated at this position in the design of inhibitors designed against wild-type main protease and for variants presenting mutations at position 166. For the P2 position, tertiary amines are clearly preferred with respect to secondary amines, because the ability to act as a hydrogen bond donor seem to favour more the interaction with the solvent than with the protein, decreasing the affinity for the enzyme. In addition, flexible groups at P2 position disfavour the formation of the covalent complex because they can disrupt the preorganization of the active site, favouring the exploration of non-reactive conformations. The substitution of the P2 group of pomotrelvir by that of nirmatrelvir resulted in a compound, here named as C2, that presents a notable improvement in the binding energy and a higher population of reactive conformations in the Michaelis complex. Analysis of the chemical reaction to form the covalent complex has shown a similar reaction mechanism and activation free energies for pomotrelvir, nirmatrelvir and C2. We hope that these findings could be useful to design better inhibitors to fight present and future variants of SARS-CoV-2 virus.