Molecular mechanism of ensitrelvir inhibiting SARS-CoV-2 main protease and its variants

SARS-CoV-2 poses an unprecedented threat to the world as the causative agent of the COVID-19 pandemic. Among a handful of therapeutics developed for the prevention and treatment of SARS-CoV-2 infection, ensitrelvir is the first noncovalent and nonpeptide oral inhibitor targeting the main protease (M^pro) of SARS-CoV-2, which recently received emergency regulatory approval in Japan. Here we determined a 1.8-Å structure of M^pro in complex with ensitrelvir, which revealed that ensitrelvir targets the substrate-binding pocket of M^pro, specifically recognizing its S1, S2, and S1' subsites. Further, our comprehensive biochemical and structural data have demonstrated that even though ensitrelvir and nirmatrelvir (an FDA-approved drug) belong to different types of M^pro inhibitors, both of them remain to be effective against M^pros from all five SARS-CoV-2 variants of concern, suggesting M^pro is a bona fide broad-spectrum target. The molecular mechanisms uncovered in this study provide basis for future inhibitor design.