tetano
Editor, Senior Moderator
Sci Adv
. 2025 Jun 6;11(23):eadv8875.
doi: 10.1126/sciadv.adv8875. Epub 2025 Jun 6. Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease
Grace Neilsen[SUP] 1 2 [/SUP], Shuiyun Lan[SUP] 1 2 [/SUP], Ryan L Slack[SUP] 1 2 [/SUP], Zachary C Lorson[SUP] 1 2 [/SUP], Andres Emanuelli Castaner[SUP] 1 2 [/SUP], Rachel Lee[SUP] 1 2 [/SUP], Kristin G Edwards[SUP] 1 2 [/SUP], Huanchun Zhang[SUP] 1 2 [/SUP], Jasper Lee[SUP] 1 2 [/SUP], William A Cantara[SUP] 1 2 [/SUP], Maria E Cilento[SUP] 1 2 [/SUP], Hongwang Zhang[SUP] 1 2 [/SUP], Ramyani De[SUP] 1 2 [/SUP], Franck Amblard[SUP] 1 2 [/SUP], Philip R Tedbury[SUP] 1 2 [/SUP], Karen A Kirby[SUP] 1 2 [/SUP], Raymond F Schinazi[SUP] 1 2 [/SUP], Stefan G Sarafianos[SUP] 1 2 [/SUP]
Affiliations
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 tert-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.
. 2025 Jun 6;11(23):eadv8875.
doi: 10.1126/sciadv.adv8875. Epub 2025 Jun 6. Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease
Grace Neilsen[SUP] 1 2 [/SUP], Shuiyun Lan[SUP] 1 2 [/SUP], Ryan L Slack[SUP] 1 2 [/SUP], Zachary C Lorson[SUP] 1 2 [/SUP], Andres Emanuelli Castaner[SUP] 1 2 [/SUP], Rachel Lee[SUP] 1 2 [/SUP], Kristin G Edwards[SUP] 1 2 [/SUP], Huanchun Zhang[SUP] 1 2 [/SUP], Jasper Lee[SUP] 1 2 [/SUP], William A Cantara[SUP] 1 2 [/SUP], Maria E Cilento[SUP] 1 2 [/SUP], Hongwang Zhang[SUP] 1 2 [/SUP], Ramyani De[SUP] 1 2 [/SUP], Franck Amblard[SUP] 1 2 [/SUP], Philip R Tedbury[SUP] 1 2 [/SUP], Karen A Kirby[SUP] 1 2 [/SUP], Raymond F Schinazi[SUP] 1 2 [/SUP], Stefan G Sarafianos[SUP] 1 2 [/SUP]
Affiliations
- PMID: 40479048
- PMCID: PMC12143351
- DOI: 10.1126/sciadv.adv8875
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 tert-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.