Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2

The main protease (M-Pro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key enzyme, which extensively digests CoV replicase polyproteins essential for viral replication and transcription, making it an attractive target for antiviral drug development. However, the molecular mechanism of how M-Pro of SARS-CoV-2 digests replicase polyproteins, releasing the nonstructural proteins (nsps), and its substrate specificity remain largely unknown. Here, we determine the high-resolution structures of SARS-CoV-2 M-Pro in its resting state, precleavage state, and postcleavage state, constituting a full cycle of substrate cleavage. The structures show the delicate conformational changes that occur during polyprotein processing. Further, we solve the structures of the SARS-CoV-2 M-Pro mutant (H41A) in complex with six native cleavage substrates from replicase polyproteins, and demonstrate that SARS-CoV-2 M-Pro can recognize sequences as long as 10 residues but only have special selectivity for four subsites. These structural data provide a basis to develop potent new inhibitors against SARS-CoV-2.

Automated summary

This study determines the high-resolution structures of SARS-CoV-2 M-Pro in different states, revealing the conformational changes that occur during substrate processing. The study also demonstrates the enzyme's specificity for certain sequences and provides a foundation for the development of new anti-SARS-CoV-2 drugs.