A comprehensive study of SARS-CoV-2 main protease (M pro ) inhibitor-resistant mutants selected in a VSV-based system.

Autor:	Costacurta F; Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria., Dodaro A; Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy., Bante D; Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria., Schöppe H; Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria., Sprenger B; Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria., Moghadasi SA; Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, United States., Fleischmann J; Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria.; Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria., Pavan M; Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy., Bassani D; Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy., Menin S; Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy., Rauch S; Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria., Krismer L; Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria., Sauerwein A; Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria., Heberle A; Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria., Rabensteiner T; Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria., Ho J; Bioinformatics Institute, Agency for Science Technology and Research, Singapore., Harris RS; 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., Stefan E; Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria.; Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria., Schneider R; Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria., Kaserer T; Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria., Moro S; Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy., von Laer D; Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria., Heilmann E; Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2023 Oct 04. Date of Electronic Publication: 2023 Oct 04.
DOI:	10.1101/2023.09.22.558628
Abstrakt:	Nirmatrelvir was the first protease inhibitor (PI) specifically developed against the SARS-CoV-2 main protease (3CL pro /M pro ) 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 M pro resistance mutations, we passaged a previously developed, chimeric vesicular stomatitis virus (VSV-M pro ) with increasing, yet suboptimal concentrations of nirmatrelvir. Using Wuhan-1 and Omicron M pro 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 M pro 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. Competing Interests: D.v.L. is founder of ViraTherapeutics GmbH. D.v.L serves as a scientific advisor to Boehringer Ingelheim and Pharma KG. E.H. and D.v.L have received an Austrian Science Fund (FWF) grant in the special call “SARS urgent funding”. E.H. is a registered consultant at Guidepoint. D. Bante holds stocks of Pfizer Inc. and Oxford Nanopore Technologies plc. S.A.M and R.S.H. are inventors on the patent application “Live cell assay for protease inhibition”, application number WO/2022/094463. All other authors declare they have no competing interests.
Databáze:	MEDLINE
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