2. Academic Validation
  3. Structure-Based Design of Covalent SARS-CoV‑2 Main Protease Inhibitors Targeting the Nirmatrelvir-Resistant E166 Mutants

Structure-Based Design of Covalent SARS-CoV‑2 Main Protease Inhibitors Targeting the Nirmatrelvir-Resistant E166 Mutants

  • JACS Au. 2026 Jan 12;6(1):233-244. doi: 10.1021/jacsau.5c01178.
Zhengjun Cai 1,  Navita Kohaal 2,  Kyriakos Georgiou 3,  Xueying Liang 4,  Xiang Chi 4,  Haozhou Tan 1,  Bin Tan 1,  Kan Li 1,  Guangjin Fan 1,  George Lambrinidis 3,  Antonios Kolocouris 3,  Xufang Deng 4 5,  Yu Chen 2,  Jun Wang 1
Affiliations

Affiliations

  • 1 Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States.
  • 2 Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States.
  • 3 Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece.
  • 4 Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, United States.
  • 5 Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma 74078, United States.
PMID: 41614164 DOI: 10.1021/jacsau.5c01178
Abstract

The COVID-19 pandemic spurred the rapid development of nirmatrelvir, a main protease (Mpro) inhibitor now widely prescribed as part of Paxlovid (nirmatrelvir plus ritonavir). However, increasing use has raised concerns about drug resistance. Resistance Selection studies have identified multiple Mpro mutations, with E166V emerging as a particularly resistant variant. Sequencing data from COVID-19 patients confirms E166V as a clinically relevant mutation, and importantly, this substitution also confers cross-resistance to several next-generation Mpro inhibitors under development. In response, this study reports the rational design of inhibitors active against nirmatrelvir-resistant E166V/A mutants. The lead candidate, Jun13698, shows potent inhibition of both wild-type Mpro and the E166V/A mutants. Structural studies and molecular dynamics simulations reveal that Jun13698 forms stable complexes with wild-type and mutant proteases, consistent with its potent enzymatic and Antiviral activity. Together, these findings position Jun13698 as a promising next-generation Mpro inhibitor capable of overcoming clinically relevant nirmatrelvir resistance.

Keywords

E166V; SARS-CoV-2; antiviral; drug resistance; main protease.

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