Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors

Kovalevsky, Andrey; Aniana, Annie; Ghirlando, Rodolfo; Coates, Leighton; Drago, Victoria N.; Wear, Lauren; Gerlits, Oksana; Nashed, Nashaat T.; Louis, John M.

doi:10.1021/acs.jmedchem.4c01781

Title: Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors

Journal Article · 07 October 2024 · Journal of Medicinal Chemistry

DOI: https://doi.org/10.1021/acs.jmedchem.4c01781 · OSTI ID:2475721

^[1]; Aniana, Annie ^[2];

^[2];

^[1]; Drago, Victoria N. ^[1]; Wear, Lauren ^[3]; Gerlits, Oksana ^[3]; Nashed, Nashaat T. ^[2];

^[2]

Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
National Institutes of Health (NIH), Bethesda, MD (United States)
Tennessee Wesleyan University, Athens, TN (United States)

SARS-CoV-2 propagation under nirmatrelvir and ensitrelvir pressure selects for main protease (MPro) drug-resistant mutations E166V (DRM2), L50F/E166V (DRM3), E166A/L167F (DRM4), and L50F/E166A/L167F (DRM5). DRM2-DRM5 undergoes N-terminal autoprocessing to produce mature MPro with dimer dissociation constants (K_dimer) 2–3 times larger than that of the wildtype. Co-selection of L50F restores catalytic activity of DRM2 and DRM4 from ~10 to 30%, relative to that of the wild-type enzyme, without altering K_dimer. Binding affinities and thermodynamic profiles that parallel the drug selection pressure, exhibiting significant decreases in affinity through entropy/enthalpy compensation, were compared with GC373. Reorganization of the active sites due to mutations observed in the inhibitor-free DRM3 and DRM4 structures as compared to MPro^WT may account for the reduced binding affinities, although DRM2 and DRM3 complexes with ensitrelvir are almost identical to MPro^WT-ensitrelvir. In conclusion, chemical reactivity changes of the mutant active sites due to differences in electrostatic and protein dynamics effects likely contribute to losses in binding affinities.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 2475721

Journal Information:: Journal of Medicinal Chemistry, Journal Name: Journal of Medicinal Chemistry Journal Issue: 20 Vol. 67; ISSN 0022-2623

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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