Crystal structures of SARS-CoV-2 main protease and its complex with PBI-0451

The SARS-CoV-2 main protease (M^pro) has a pivotal role in mediating viral genome replication and transcription of the coronavirus, making it a prime target for antiviral drug development. This study presents four high-resolution crystal structures of SARS-CoV-2 M^pro in the apo state. Among these structures, we identify a previously unobserved, stable inactive conformation, characterized by a major displacement of the oxyanion loop (especially Phe140, Leu141 and Asn142), the rotation of some important residues (including His163 and His172) and the loss of many key interactions around the active site, which provides new insights into the conformational dynamics of the enzyme. We also report structures of M^pro in complex with the covalent inhibitor pomotrelvir (PBI-0451) for the wild-type enzyme and three clinical variant-associated mutants (G15S, K90R and P132H). PBI-0451 adopts a virtually identical mode when bound to wild-type M^pro and the K90R and G15S M^pro mutants. However, the crystal structure of PBI-0451 bound to SARS-CoV-2 M^pro P132H reveals a discernible shift of the Gln189-bearing loop and incomplete electron density for the Gln189 side chain, which may be responsible for the subtle modest reduction in PBI-0451 susceptibility. These findings expand the conformational landscape of M^pro and offer structural guidance for the design of M^pro-targeted antiviral drugs.