Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 Mpro† † Electronic supplementary information (ESI) available: Includes a movie describing a representative binding process, the minimum distance between the non-hydrogen atoms of PF-07321332 and the non-hydrogen atoms of the catalytic dyad, the minimum distance dSγ–CN between the nitrile group of PF-07321332 and the sulfur atom of the Cys145 residue, the binding pathway of PF-07321332 to SARS-CoV-2 Mpro over the trajectories 0 and 20, the optimization starting from the ion pair Cys145−–His41H+, the optimized transition state for the hydrolysis of Int-3, and energy and Cartesian coordinates. See DOI: 10.1039/d1ra08752e

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic, resulting in several million deaths being reported. Numerous investigations have been carried out to discover a compound that can inhibit the biological activity of the SARS-CoV-2 main protease, which is an enzyme related to the viral replication. Among these, PF-07321332 (Nirmatrelvir) is currently under clinical trials for COVID-19 therapy. Therefore, in this work, atomistic and electronic simulations were performed to unravel the binding and covalent inhibition mechanism of the compound to Mpro. Initially, 5 μs of steered-molecular dynamics simulations were carried out to evaluate the ligand-binding process to SARS-CoV-2 Mpro. The successfully generated bound state between the two molecules showed the important role of the PF-07321332 pyrrolidinyl group and the residues Glu166 and Gln189 in the ligand-binding process. Moreover, from the MD-refined structure, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to unravel the reaction mechanism for the formation of the thioimidate product from SARS-CoV-2 Mpro and the PF-07321332 inhibitor. We found that the catalytic triad Cys145–His41–Asp187 of SARS-CoV-2 Mpro plays an important role in the activation of the PF-07321332 covalent inhibitor, which renders the deprotonation of Cys145 and, thus, facilitates further reaction. Our results are definitely beneficial for a better understanding of the inhibition mechanism and designing new effective inhibitors for SARS-CoV-2 Mpro. The catalytic triad Cys145–His41–Asp187 of SARS-CoV-2 Mpro plays an important role in the activation of the PF-07321332 covalent inhibitor.