Crystal structures of main protease (M(pro)) mutants of SARS-CoV-2 variants bound to PF-07304814

There is an urgent need to develop effective antiviral drugs to prevent the viral infection caused by constantly circulating SARS-CoV-2 as well as its variants. The main protease (M(pro)) of SARS-CoV-2 is a salient enzyme that plays a vital role in viral replication and serves as a fascinating therapeutic target. PF-07304814 is a covalent inhibitor targeting SARS-CoV-2 M(pro) with favorable inhibition potency and drug-like properties, thus making it a promising drug candidate for the treatment of COVID-19. We previously solved the structure of PF-07304814 in complex with SARS-CoV-2 M(pro). However, the binding modes of PF-07304814 with M(pro)s from evolving SARS-CoV-2 variants is under-determined. In the current study, we expressed six M(pro) mutants (G15S, K90R, M49I, S46F, V186F, and Y54C) that have been identified in Omicron variants including the recently emerged XBB.1.16 subvariant and solved the crystal structures of PF-07304814 bound to M(pro) mutants. Structural analysis provided insight into the key molecular determinants responsible for the interaction between PF-07304814 and these mutant M(pro)s. Patterns for PF-07304814 to bind with these investigated M(pro) mutants and the wild-type M(pro) are generally similar but with some differences as revealed by detailed structural comparison. Structural insights presented in this study will inform the development of novel drugs against SARS-CoV-2 and the possible conformation changes of M(pro) mutants when bound to an inhibitor.