Topological analysis of SARS CoV-2 main protease

Chaos. 2020 Jun;30(6):061102. doi: 10.1063/5.0013029.

Abstract

There is an urgent necessity of effective medication against severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), which is producing the COVID-19 pandemic across the world. Its main protease (Mpro) represents an attractive pharmacological target due to its involvement in essential viral functions. The crystal structure of free Mpro shows a large structural resemblance with the main protease of SARS CoV (nowadays known as SARS CoV-1). Here, we report that average SARS CoV-2 Mpro is 1900% more sensitive than SARS CoV-1 Mpro in transmitting tiny structural changes across the whole protein through long-range interactions. The largest sensitivity of Mpro to structural perturbations is located exactly around the catalytic site Cys-145 and coincides with the binding site of strong inhibitors. These findings, based on a simplified representation of the protein as a residue network, may help in designing potent inhibitors of SARS CoV-2 Mpro.

MeSH terms

  • Amino Acid Sequence
  • Betacoronavirus / metabolism*
  • Binding Sites / drug effects
  • COVID-19
  • Catalytic Domain / drug effects*
  • Coronavirus 3C Proteases
  • Coronavirus Infections / drug therapy*
  • Crystallography, X-Ray
  • Cysteine Endopeptidases / drug effects
  • Cysteine Endopeptidases / metabolism*
  • Drug Design
  • Humans
  • Pandemics
  • Pneumonia, Viral / drug therapy*
  • Protease Inhibitors / pharmacology*
  • SARS-CoV-2
  • Severe acute respiratory syndrome-related coronavirus / metabolism
  • Viral Nonstructural Proteins / drug effects
  • Viral Nonstructural Proteins / metabolism*

Substances

  • Protease Inhibitors
  • Viral Nonstructural Proteins
  • Cysteine Endopeptidases
  • Coronavirus 3C Proteases