QM/MM simulations of the covalent inhibition of the SARS-CoV-2 main protease: Four compounds and three reaction mechanisms

B.L. Grigorenko, I. Polyakov, G. Giudetti, S. Faraji, A.I. Krylov, and A.V. Nemukhin
J. Am. Chem. Soc.  145, 13204 – 13214 (2023)

The search for efficient inhibitors of the SARS-CoV-2 enzymes remains important due to the continuing COVID-19 pandemic. We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have been shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work, derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of efficient chemical reactions with the catalytic cysteine residue in the MPro active site. The reactions of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. According to calculations, the reactions for all four compounds are exothermic, with sufficiently low barriers, suggesting efficient inhibition of the enzyme. From the chemical perspective, the four compounds react with MPro following three distinct mechanisms. In all cases, the reaction is initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand involves the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir, which has a reactive nitrile group, leads to the formation of the covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site.

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