Polyacylated anthocyanins constructively network with catalytic dyad residues of 3CLpro of 2019-nCoV than monomeric anthocyanins: A structural-relationship activity study with 10 anthocyanins using in-silico approaches

J Mol Graph Model. 2020 Nov:100:107690. doi: 10.1016/j.jmgm.2020.107690. Epub 2020 Jul 24.

Abstract

Coronavirus epidemic 2019 (COVID-19), caused by novel coronavirus (2019-nCoV), is newly increasing worldwide and elevating global health concerns. Similar to SARS-CoV and MERS-CoV, the viral key 3-chymotrypsin-like cysteine protease enzyme (3CLPro), which controls 2019-nCoV duplications and manages its life cycle, could be pointed as a drug discovery target. Herein, we theoretically studied the binding ability of 10 structurally different anthocyanins with the catalytic dyad residues of 3CLpro of 2019-nCoV using molecular docking modelling. The results revealed that the polyacylated anthocyanins, including phacelianin, gentiodelphin, cyanodelphin, and tecophilin, were found to authentically bind with the receptor binding site and catalytic dyad (Cys145 and His41) of 2019-nCoV-3CLpro. Our analyses revealed that the top four hits might serve as potential anti-2019-nCoV leading molecules for further optimization and drug development process to combat COVID-19. This study unleashed that anthocyanins with specific structure could be used as effective anti-COVID-19 natural components.

Keywords: Anthocyanins; COVID-19; Molecular docking; Protease; Structural-relationship effects.

MeSH terms

  • Amino Acid Sequence
  • Anthocyanins / chemistry*
  • Antiviral Agents / chemistry*
  • Benzopyrans / chemistry*
  • Betacoronavirus / chemistry*
  • Betacoronavirus / enzymology
  • Binding Sites
  • Coronavirus 3C Proteases
  • Cysteine Endopeptidases / chemistry*
  • Glucosides / chemistry*
  • Molecular Docking Simulation
  • Protease Inhibitors / chemistry*
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Structure, Secondary
  • SARS-CoV-2
  • Sequence Alignment
  • Structure-Activity Relationship
  • Thermodynamics
  • Viral Nonstructural Proteins / antagonists & inhibitors
  • Viral Nonstructural Proteins / chemistry*

Substances

  • Anthocyanins
  • Antiviral Agents
  • Benzopyrans
  • Glucosides
  • Protease Inhibitors
  • Viral Nonstructural Proteins
  • gentiodelphin
  • Cysteine Endopeptidases
  • Coronavirus 3C Proteases