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Identification of naturally occurring drug-resistant mutations of SARS-CoV-2 papain-like protease

Author

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  • Haozhou Tan

    (Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey)

  • Qianru Zhang

    (College of Veterinary Medicine, Oklahoma State University)

  • Kyriakos Georgiou

    (National and Kapodistrian University of Athens)

  • Siyu Zhang

    (College of Veterinary Medicine, Oklahoma State University)

  • Kan Li

    (Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey)

  • George Lambrinidis

    (National and Kapodistrian University of Athens)

  • Antonios Kolocouris

    (National and Kapodistrian University of Athens)

  • Xufang Deng

    (College of Veterinary Medicine, Oklahoma State University
    Oklahoma State University)

  • Jun Wang

    (Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey)

Abstract

The SARS-CoV-2 papain-like protease (PLpro) is a cysteine protease that cleaves viral polyproteins and antagonizes the host immune response during viral replication. Jun12682 and PF-07957472 are the first-in-class PLpro inhibitors showing potent in vivo antiviral efficacy in mouse models. In this study, we characterize naturally occurring mutations at residues located at the drug-binding site of Jun12682. The results reveal several PLpro mutants showing significant drug resistance while maintaining comparable enzymatic activity as the wild-type PLpro. The physiological relevance of the identified drug-resistant mutants, including E167G and Q269H, is validated through independent serial viral passage experiments. Molecular dynamics simulations and perturbative free energy calculations show that drug-resistant PLpro mutants weaken hydrogen bonding and π-π stacking interactions. Collectively, this study identifies E167, Y268, and Q269 as drug-resistant hotspots for PLpro inhibitors that bind to the BL2 loop and groove region, which are valuable in informing the design of the next-generation PLpro inhibitors.

Suggested Citation

  • Haozhou Tan & Qianru Zhang & Kyriakos Georgiou & Siyu Zhang & Kan Li & George Lambrinidis & Antonios Kolocouris & Xufang Deng & Jun Wang, 2025. "Identification of naturally occurring drug-resistant mutations of SARS-CoV-2 papain-like protease," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59922-9
    DOI: 10.1038/s41467-025-59922-9
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