Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations. Insights for Improved Designs

We present the results of classical and QM/MM simulations for inhibition SARS-CoV-2 3CL protease by a hydroxymethylketone inhibitor, PF-00835231. In noncovalent complex carbonyl oxygen atom warhead is placed in oxyanion hole formed residues 143 to 145, while P1–P3 groups are accommodated active site with interactions similar those observed peptide substrate. According alchemical free energy calculations, P1′ hydroxymethyl group also contributes binding energy. Covalent enzyme triggered proton transfer from Cys145 His41. This step followed nucleophilic attack Sγ on carbon inhibitor His41 mediated hydroxyl group. Computational show that addition chloromethyl substituent may lower activation covalent