1. Structural and virologic mechanism of the emergence of resistance to M pro inhibitors in SARS-CoV-2.
- Author
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Hattori SI, Bulut H, Hayashi H, Kishimoto N, Takamune N, Hasegawa K, Furusawa Y, Yamayoshi S, Murayama K, Tamamura H, Li M, Wlodawer A, Kawaoka Y, Misumi S, and Mitsuya H
- Subjects
- Humans, Chlorocebus aethiops, Animals, Vero Cells, Protease Inhibitors pharmacology, Protease Inhibitors chemistry, Protease Inhibitors metabolism, COVID-19 virology, Antiviral Agents pharmacology, Betacoronavirus drug effects, Crystallography, X-Ray, Lactams, Leucine, Nitriles, Proline, SARS-CoV-2 drug effects, Coronavirus 3C Proteases metabolism, Coronavirus 3C Proteases antagonists & inhibitors, Coronavirus 3C Proteases chemistry, Drug Resistance, Viral genetics
- Abstract
We generated SARS-CoV-2 variants resistant to three SARS-CoV-2 main protease (M
pro ) inhibitors (nirmatrelvir, TKB245, and 5h), by propagating the ancestral SARS-CoV-2WK521 WT in VeroE6TMPRSS2 cells with increasing concentrations of each inhibitor and examined their structural and virologic profiles. A predominant E166V-carrying variant (SARS-CoV-2WK521 E166V ), which emerged when passaged with nirmatrelvir and TKB245, proved to be resistant to the two inhibitors. A recombinant SARS-CoV-2E166V was resistant to nirmatrelvir and TKB245, but sensitive to 5h. X-ray structural study showed that the dimerization of Mpro was severely hindered by E166V substitution due to the disruption of the presumed dimerization-initiating Ser1'-Glu166 interactions. TKB245 stayed bound to Mpro E166V , whereas nirmatrelvir failed. Native mass spectrometry confirmed that nirmatrelvir and TKB245 promoted the dimerization of Mpro , and compromised the enzymatic activity; the Ki values of recombinant Mpro E166V for nirmatrelvir and TKB245 were 117±3 and 17.1±1.9 µM, respectively, indicating that TKB245 has a greater (by a factor of 6.8) binding affinity to Mpro E166V than nirmatrelvir. SARS-CoV-2WK521 WT selected with 5h acquired A191T substitution in Mpro (SARS-CoV-2WK521 A191T ) and better replicated in the presence of 5h, than SARS-CoV-2WK521 WT . However, no significant enzymatic or structural changes in Mpro A191T were observed. The replicability of SARS-CoV-2WK521 E166V proved to be compromised compared to SARS-CoV-2WK521 WT but predominated over SARS-CoV-2WK521 WT in the presence of nirmatrelvir. The replicability of SARS-CoV-2WK521 A191T surpassed that of SARS-CoV-2WK521 WT in the absence of 5h, confirming that A191T confers enhanced viral fitness. The present data should shed light on the understanding of the mechanism of SARS-CoV-2's drug resistance acquisition and the development of resistance-repellant COVID-19 therapeutics., Competing Interests: Competing interests statement:The authors declare no competing interest.- Published
- 2024
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