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

Haozhou Tan, Qianru Zhang, Kyriakos Georgiou, Siyu Zhang, Kan Li, George Lambrinidis, Antonios Kolocouris, Xufang Deng () and Jun Wang ()
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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
Jun Wang: Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-59922-9

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