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Costacurta F, Dodaro A, Bante D, Schöppe H, Sprenger B, Moghadasi SA, Fleischmann J, Pavan M, Bassani D, Menin S, Rauch S, Krismer L, Sauerwein A, Heberle A, Rabensteiner T, Ho J, Harris RS, Stefan E, Schneider R, Kaserer T, Moro S, von Laer D, Heilmann E. A comprehensive study of SARS-CoV-2 main protease (M pro) inhibitor-resistant mutants selected in a VSV-based system. bioRxiv 2023:2023.09.22.558628. [PMID: 37808638 PMCID: PMC10557589 DOI: 10.1101/2023.09.22.558628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Nirmatrelvir was the first protease inhibitor (PI) specifically developed against the SARS-CoV-2 main protease (3CLpro/Mpro) and licensed for clinical use. As SARS-CoV-2 continues to spread, variants resistant to nirmatrelvir and other currently available treatments are likely to arise. This study aimed to identify and characterize mutations that confer resistance to nirmatrelvir. To safely generate Mpro resistance mutations, we passaged a previously developed, chimeric vesicular stomatitis virus (VSV-Mpro) with increasing, yet suboptimal concentrations of nirmatrelvir. Using Wuhan-1 and Omicron Mpro variants, we selected a large set of mutants. Some mutations are frequently present in GISAID, suggesting their relevance in SARS-CoV-2. The resistance phenotype of a subset of mutations was characterized against clinically available PIs (nirmatrelvir and ensitrelvir) with cell-based and biochemical assays. Moreover, we showed the putative molecular mechanism of resistance based on in silico molecular modelling. These findings have implications on the development of future generation Mpro inhibitors, will help to understand SARS-CoV-2 protease-inhibitor-resistance mechanisms and show the relevance of specific mutations in the clinic, thereby informing treatment decisions.
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Affiliation(s)
- Francesco Costacurta
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Andrea Dodaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Bernhard Sprenger
- Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Jakob Fleischmann
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Silvia Menin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anne Heberle
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Toni Rabensteiner
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Joses Ho
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, United States
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, United States
| | - Eduard Stefan
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria
| | - Rainer Schneider
- Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
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Abstract
The clinical, angiographic and demographic characteristics of 42 patients with low-grade (less than 50%) residual stenosis at the infarct lesion after thrombolysis for acute myocardial infarction (MI) were assessed. The study group (group I) represented 21% of 198 consecutive patients receiving thrombolytic therapy over a 59-month period. Data on the 156 remaining patients were pooled for comparison (group II). Group I patients were predominantly men (86%) who were cigarette smokers (81%). Group II patients were predominantly men (75%, p greater than 0.10) but were significantly older (52 +/- 12 vs 56 +/- 10 years, p = 0.02). Prior acute MI or angina was unusual in group I. Sixty percent had no significant (greater than 50%) residual coronary artery disease while 25% had residual single artery disease. Average significant (greater than 50% diameter stenosis) residual vessel disease was 0.6 +/- 1.0 for group I and 1.9 +/- 0.9 for group II (p less than 0.001). In group I, average residual infarct lesion diameter stenosis was 36 +/- 7% in the right anterior oblique and 34 +/- 8% in the left anterior oblique views. Thirty-nine group I patients were discharged with medical therapy and 100% follow-up was obtained over a mean interval of 18 +/- 17 months. Fifteen patients experienced chest pain after acute MI accounting for 17 discrete events. Fifty-nine percent of group I had a benign course on follow-up. Eight events were classified as unstable angina, 4 as acute MI and 5 as atypical angina. Documented coronary vasospasm occurred in 3.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J C Marshall
- Division of Cardiology, Cooper Hospital/University Medical Center, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Camden
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