Distal protein-protein interactions contribute to nirmatrelvir resistance
Abstract SARS-CoV-2 main protease, Mpro, is responsible for processing the viral polyproteins into individual proteins, including the protease itself. Mpro is a key target of anti-COVID-19 therapeutics such as nirmatrelvir (the active component of Paxlovid). Resistance mutants identified clinically...
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| Format: | Article |
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Nature Portfolio
2025-02-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-56651-x |
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| author | Eric M. Lewandowski Xiujun Zhang Haozhou Tan Aiden Jaskolka-Brown Navita Kohaal Aliaksandra Frazier Jesper J. Madsen Lian M. C. Jacobs Jun Wang Yu Chen |
| author_facet | Eric M. Lewandowski Xiujun Zhang Haozhou Tan Aiden Jaskolka-Brown Navita Kohaal Aliaksandra Frazier Jesper J. Madsen Lian M. C. Jacobs Jun Wang Yu Chen |
| author_sort | Eric M. Lewandowski |
| collection | DOAJ |
| description | Abstract SARS-CoV-2 main protease, Mpro, is responsible for processing the viral polyproteins into individual proteins, including the protease itself. Mpro is a key target of anti-COVID-19 therapeutics such as nirmatrelvir (the active component of Paxlovid). Resistance mutants identified clinically and in viral passage assays contain a combination of active site mutations (e.g., E166V, E166A, L167F), which reduce inhibitor binding and enzymatic activity, and non-active site mutations (e.g., P252L, T21I, L50F), which restore the fitness of viral replication. To probe the role of the non-active site mutations in fitness rescue, here we use an Mpro triple mutant (L50F/E166A/L167F) that confers nirmatrelvir drug resistance with a viral fitness level similar to the wild-type. By comparing peptide and full-length Mpro protein as substrates, we demonstrate that the binding of Mpro substrate involves more than residues in the active site. Particularly, L50F and other non-active site mutations can enhance the Mpro dimer-dimer interactions and help place the nsp5-6 substrate at the enzyme catalytic center. The structural and enzymatic activity data of Mpro L50F, L50F/E166A/L167F, and others underscore the importance of considering the whole substrate protein in studying Mpro and substrate interactions, and offers important insights into Mpro function, resistance development, and inhibitor design. |
| format | Article |
| id | doaj-art-7c450a6c8e034bb6b99ef582a3e3d59a |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-7c450a6c8e034bb6b99ef582a3e3d59a2025-02-02T12:33:04ZengNature PortfolioNature Communications2041-17232025-02-011611810.1038/s41467-025-56651-xDistal protein-protein interactions contribute to nirmatrelvir resistanceEric M. Lewandowski0Xiujun Zhang1Haozhou Tan2Aiden Jaskolka-Brown3Navita Kohaal4Aliaksandra Frazier5Jesper J. Madsen6Lian M. C. Jacobs7Jun Wang8Yu Chen9Department of Molecular Medicine, Morsani College of Medicine, University of South FloridaDepartment of Molecular Medicine, Morsani College of Medicine, University of South FloridaDepartment of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New JerseyDepartment of Molecular Medicine, Morsani College of Medicine, University of South FloridaDepartment of Molecular Medicine, Morsani College of Medicine, University of South FloridaDepartment of Molecular Medicine, Morsani College of Medicine, University of South FloridaDepartment of Molecular Medicine, Morsani College of Medicine, University of South FloridaDepartment of Molecular Medicine, Morsani College of Medicine, University of South FloridaDepartment of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New JerseyDepartment of Molecular Medicine, Morsani College of Medicine, University of South FloridaAbstract SARS-CoV-2 main protease, Mpro, is responsible for processing the viral polyproteins into individual proteins, including the protease itself. Mpro is a key target of anti-COVID-19 therapeutics such as nirmatrelvir (the active component of Paxlovid). Resistance mutants identified clinically and in viral passage assays contain a combination of active site mutations (e.g., E166V, E166A, L167F), which reduce inhibitor binding and enzymatic activity, and non-active site mutations (e.g., P252L, T21I, L50F), which restore the fitness of viral replication. To probe the role of the non-active site mutations in fitness rescue, here we use an Mpro triple mutant (L50F/E166A/L167F) that confers nirmatrelvir drug resistance with a viral fitness level similar to the wild-type. By comparing peptide and full-length Mpro protein as substrates, we demonstrate that the binding of Mpro substrate involves more than residues in the active site. Particularly, L50F and other non-active site mutations can enhance the Mpro dimer-dimer interactions and help place the nsp5-6 substrate at the enzyme catalytic center. The structural and enzymatic activity data of Mpro L50F, L50F/E166A/L167F, and others underscore the importance of considering the whole substrate protein in studying Mpro and substrate interactions, and offers important insights into Mpro function, resistance development, and inhibitor design.https://doi.org/10.1038/s41467-025-56651-x |
| spellingShingle | Eric M. Lewandowski Xiujun Zhang Haozhou Tan Aiden Jaskolka-Brown Navita Kohaal Aliaksandra Frazier Jesper J. Madsen Lian M. C. Jacobs Jun Wang Yu Chen Distal protein-protein interactions contribute to nirmatrelvir resistance Nature Communications |
| title | Distal protein-protein interactions contribute to nirmatrelvir resistance |
| title_full | Distal protein-protein interactions contribute to nirmatrelvir resistance |
| title_fullStr | Distal protein-protein interactions contribute to nirmatrelvir resistance |
| title_full_unstemmed | Distal protein-protein interactions contribute to nirmatrelvir resistance |
| title_short | Distal protein-protein interactions contribute to nirmatrelvir resistance |
| title_sort | distal protein protein interactions contribute to nirmatrelvir resistance |
| url | https://doi.org/10.1038/s41467-025-56651-x |
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