TY - JOUR
T1 - A comprehensive study of SARS-CoV-2 mfigain protease (Mpro) inhibitor-resistant mutants selected in a VSV-based system
AU - Costacurta, Francesco
AU - Dodaro, Andrea
AU - Bante, David
AU - Schöppe, Helge
AU - Peng, Ju Yi
AU - Sprenger, Bernhard
AU - He, Xi
AU - Moghadasi, Seyed Arad
AU - Egger, Lisa Maria
AU - Fleischmann, Jakob
AU - Pavan, Matteo
AU - Bassani, Davide
AU - Menin, Silvia
AU - Rauch, Stefanie
AU - Krismer, Laura
AU - Sauerwein, Anna
AU - Heberle, Anne
AU - Rabensteiner, Toni
AU - Ho, Joses
AU - Harris, Reuben S.
AU - Stefan, Eduard
AU - Schneider, Rainer
AU - Dunzendorfer-Matt, Theresia
AU - Naschberger, Andreas
AU - Wang, Dai
AU - Kaserer, Teresa
AU - Moro, Stefano
AU - von Laer, Dorothee
AU - Heilmann, Emmanuel
N1 - Publisher Copyright:
© 2024 Costacurta et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2024/9
Y1 - 2024/9
N2 - Nirmatrelvir was the first protease inhibitor 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 protease inhibitors (nirmatrelvir and ensitrelvir) with cell-based, biochemical and SARS-CoV-2 replicon 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, thereby informing treatment decisions.
AB - Nirmatrelvir was the first protease inhibitor 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 protease inhibitors (nirmatrelvir and ensitrelvir) with cell-based, biochemical and SARS-CoV-2 replicon 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, thereby informing treatment decisions.
UR - http://www.scopus.com/inward/record.url?scp=85203595435&partnerID=8YFLogxK
U2 - 10.1371/journal.ppat.1012522
DO - 10.1371/journal.ppat.1012522
M3 - Article
C2 - 39259728
AN - SCOPUS:85203595435
SN - 1553-7366
VL - 20
JO - PLOS Pathogens
JF - PLOS Pathogens
IS - 9
M1 - e1012522
ER -