A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process

J Mol Biol. 2021 Sep 3;433(18):167118. doi: 10.1016/j.jmb.2021.167118. Epub 2021 Jun 24.


SARS-CoV-2 is the causative agent of COVID-19. The dimeric form of the viral Mpro is responsible for the cleavage of the viral polyprotein in 11 sites, including its own N and C-terminus. The lack of structural information for intermediary forms of Mpro is a setback for the understanding its self-maturation process. Herein, we used X-ray crystallography combined with biochemical data to characterize multiple forms of SARS-CoV-2 Mpro. For the immature form, we show that extra N-terminal residues caused conformational changes in the positioning of domain-three over the active site, hampering the dimerization and diminishing its activity. We propose that this form preludes the cis and trans-cleavage of N-terminal residues. Using fragment screening, we probe new cavities in this form which can be used to guide therapeutic development. Furthermore, we characterized a serine site-directed mutant of the Mpro bound to its endogenous N and C-terminal residues during dimeric association stage of the maturation process. We suggest this form is a transitional state during the C-terminal trans-cleavage. This data sheds light in the structural modifications of the SARS-CoV-2 main protease during its self-maturation process.

Keywords: COVID; M(pro); SARS-CoV-2; drug discovery; maturation.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Catalytic Domain / physiology
  • Crystallography, X-Ray / methods
  • Dimerization
  • Humans
  • Peptide Hydrolases / chemistry*
  • Peptide Hydrolases / metabolism*
  • SARS-CoV-2 / metabolism*
  • Viral Proteins / chemistry*
  • Viral Proteins / metabolism*


  • Viral Proteins
  • Peptide Hydrolases