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Nat Commun
. 2025 May 16;16(1):4548.
doi: 10.1038/s41467-025-59922-9. Identification of naturally occurring drug-resistant mutations of SARS-CoV-2 papain-like protease
Haozhou Tan # 1 , Qianru Zhang # 2 , Kyriakos Georgiou 3 , Siyu Zhang 2 , Kan Li 1 , George Lambrinidis 3 , Antonios Kolocouris 3 , Xufang Deng 4 5 , Jun Wang 6
Affiliations
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.
. 2025 May 16;16(1):4548.
doi: 10.1038/s41467-025-59922-9. Identification of naturally occurring drug-resistant mutations of SARS-CoV-2 papain-like protease
Haozhou Tan # 1 , Qianru Zhang # 2 , Kyriakos Georgiou 3 , Siyu Zhang 2 , Kan Li 1 , George Lambrinidis 3 , Antonios Kolocouris 3 , Xufang Deng 4 5 , Jun Wang 6
Affiliations
- PMID: 40379662
- PMCID: PMC12084387
- DOI: 10.1038/s41467-025-59922-9
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.