Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease
E166V in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nsp5 protease confers strong resistance to the antiviral component of Paxlovid, nirmatrelvir (NIR), in passaging and clinical samples. In SARS-CoV-2 replicons, E166V drastically decreased Washington (WA1) but not Omicron (BA.1) fitness (20- versus 2-fold), suggesting a lower barrier to resistance in the BA.1 strain and consistent with observed differences in respective nsp5 dimerization affinities. Crystal structures reveal a steric clash between the rigid, bulky NIR <i>tert</i>-butyl group and the β-branched Val<sup>166</sup>, disrupting the covalent binding of NIR to the catalytic Cys<sup>145</sup> and leading to high resistance in BA.1 and WA1 replicons. NIR-resistant replicons remained susceptible to GC376, which can still covalently bind Cys<sup>145</sup> by avoiding a steric clash with Val<sup>166</sup> through "wiggling and jiggling." Hence, strategic flexibility is a strategy that will help design second-generation antivirals against NIR-resistant viruses.
Authors
- Maria E. Cilento (ORCID: https://orcid.org/0000-0001-7597-1248)
- Hongwang Zhang (ORCID: https://orcid.org/0000-0002-0032-9004)
- Ryan L. Slack (ORCID: https://orcid.org/0000-0002-5928-6205)
- Franck Amblard (ORCID: https://orcid.org/0009-0002-6235-4050)
- Karen A. Kirby (ORCID: https://orcid.org/0000-0003-2468-4796)
- Kristin Shirey Edwards (ORCID: https://orcid.org/0000-0002-2168-8241)
- William A. Cantara (ORCID: https://orcid.org/0000-0002-3214-7635)
- Jasper Lee (ORCID: https://orcid.org/0000-0003-0472-827X)
- Zachary C. Lorson (ORCID: https://orcid.org/0009-0002-1404-9086)
- Grace Neilsen (ORCID: https://orcid.org/0000-0001-9344-1160)
- Stefan G. Sarafianos (ORCID: https://orcid.org/0000-0002-5840-154X)
- Huanchun Zhang
- Andres Emanuelli Castaner (ORCID: https://orcid.org/0009-0005-1275-9684)
- Ramyani De (ORCID: https://orcid.org/0000-0001-5534-0705)
- Raymond F. Schinazi (ORCID: https://orcid.org/0000-0002-6688-3614)
- Philip R. Tedbury (ORCID: https://orcid.org/0000-0001-8151-4967)
- Shuiyun Lan (ORCID: https://orcid.org/0009-0002-4101-9894)
- Rachel Lee
Institutions
- Emory University (US)
- Children's Healthcare of Atlanta (US)
Publication Details
- Journal
- Science Advances
- Published
- 2025-06-06
- DOI
- https://doi.org/10.1126/sciadv.adv8875
- Citations
- 6
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 8.38