Tweet
Proc Natl Acad Sci U S A
. 2025 Mar 11;122(10):e2419854122.
doi: 10.1073/pnas.2419854122. Epub 2025 Mar 4. Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr
Florian Kabinger 1 , Valerie Doze 1 , Jana Schmitzová 1 , Michael Lidschreiber 1 , Christian Dienemann 1 , Patrick Cramer 1
Affiliations
Targeting the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 with small molecules is a promising therapeutic strategy against COVID-19, but potent and safe inhibitors are lacking. HeE1-2Tyr, a nonnucleoside inhibitor of Dengue virus RdRp, was also shown to inhibit SARS-CoV-2 RdRp in vitro and to have antiviral activity in cells, but the underlying mechanism remains unclear. Here, we elucidate the molecular mechanism of HeE1-2Tyr-mediated SARS-CoV-2 RdRp inhibition. Biochemical assays confirm that HeE1-2Tyr inhibits RdRp with an IC50 of 5 µM and show that it competes with RNA binding to RdRp in vitro. Structural analysis using cryo-EM reveals that a stack of three HeE1-2Tyr molecules binds to the RNA binding site of RdRp. The identification of the conserved HeE1-2Tyr binding site and its intriguing inhibition mechanism of three stacked molecules that outcompete RNA may facilitate further development of pan-corona nonnucleoside inhibitors.
Keywords: RNA-dependent RNA polymerase; SARS-CoV-2; cryo-EM; non-nucleoside inhibitor.
. 2025 Mar 11;122(10):e2419854122.
doi: 10.1073/pnas.2419854122. Epub 2025 Mar 4. Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr
Florian Kabinger 1 , Valerie Doze 1 , Jana Schmitzová 1 , Michael Lidschreiber 1 , Christian Dienemann 1 , Patrick Cramer 1
Affiliations
- PMID: 40035759
- DOI: 10.1073/pnas.2419854122
Targeting the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 with small molecules is a promising therapeutic strategy against COVID-19, but potent and safe inhibitors are lacking. HeE1-2Tyr, a nonnucleoside inhibitor of Dengue virus RdRp, was also shown to inhibit SARS-CoV-2 RdRp in vitro and to have antiviral activity in cells, but the underlying mechanism remains unclear. Here, we elucidate the molecular mechanism of HeE1-2Tyr-mediated SARS-CoV-2 RdRp inhibition. Biochemical assays confirm that HeE1-2Tyr inhibits RdRp with an IC50 of 5 µM and show that it competes with RNA binding to RdRp in vitro. Structural analysis using cryo-EM reveals that a stack of three HeE1-2Tyr molecules binds to the RNA binding site of RdRp. The identification of the conserved HeE1-2Tyr binding site and its intriguing inhibition mechanism of three stacked molecules that outcompete RNA may facilitate further development of pan-corona nonnucleoside inhibitors.
Keywords: RNA-dependent RNA polymerase; SARS-CoV-2; cryo-EM; non-nucleoside inhibitor.