9BOA

Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.

(2025) ACS Bio Med Chem Au 5: 215-226

• PubMed: 39990941 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1021/acsbiomedchemau.4c00109
• Primary Citation of Related Structures:  
  9BNT, 9BNU, 9BNV, 9BNW, 9BNX, 9BNY, 9BNZ, 9BO0, 9BO1, 9BO2, 9BO3, 9BO4, 9BO5, 9BO6, 9BO7, 9BO8, 9BO9, 9BOA, 9BOB, 9BOC, 9BOD, 9BOE, 9CDK, 9CDL, 9CDM


• PubMed Abstract: 
  

  SARS-CoV-2 M ^pro inhibitors, such as nirmatrelvir, have proven efficacy in clinical use. Nirmatrelvir was developed in a target-based approach against wild-type M ^pro , with the anticipation that prolonged usage may cause enrichment of drug-resistant mutations and persistence of COVID infections. Although globally prevalent drug-resistant mutations have not yet been observed, individual cases have recently been reported among patients following treatment with Paxlovid-a formulation of nirmatrelvir. Mutations E166V and E166A have been detected in these drug-resistant clinical isolates, consistent with predictions from in vitro viral passage experiments and therefore necessitate ongoing drug development. In this study, we selected seven M ^pro variants (T21I, L50F, E166V, A173V, T190I, E166V/L50F, and A173V/L50F), which have been repeatedly found in viral passage experiments. We investigated their kinetic and structural properties, as well as resistance level to M ^pro inhibitors: nirmatrelvir, GC376-a similar peptidomimetic for feline COVID infections, and our in-house-developed nonpeptidomimetic inhibitor Mpro61. Mpro61 maintains potency against the single variants (except for E166V) and the A173/L50F double variant, with K _i values similar to those of the wild type. In contrast, while nirmatrelvir and GC376 were still effective against the A173V/L50F double variant, their K _i values significantly increased up to 10-fold. None of the inhibitors appeared to be potent against E166V-containing variants. Our structural analysis revealed a significant movement of Ser1 residue in all E166V-containing variants in the presence or absence of an inhibitor. The new orientation of the Ser1 suggested potential strategies for medicinal chemistry modifications of Mpro61 to enhance hydrogen-bonding interactions between these variants and Mpro61 derivatives. These studies provide critical insights into guiding the future design of additional Mpro61 derivatives that would potentially inhibit variants with the pan-drug-resistant E166V mutation.

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Organizational Affiliation: 

Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States.