Antiviral Peptides as Promising Therapeutics against SARS-CoV-2

J Phys Chem B. 2020 Nov 5;124(44):9785-9792. doi: 10.1021/acs.jpcb.0c05621. Epub 2020 Oct 23.

Abstract

Over 50 peptides, which were known to inhibit SARS-CoV-1, were computationally screened against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. Based on the binding affinity and interaction, 15 peptides were selected, which showed higher affinity compared to the α-helix of the human ACE2 receptor. Molecular dynamics simulation demonstrated that two peptides, S2P25 and S2P26, were the most promising candidates, which could potentially block the entry of SARS-CoV-2. Tyr489 and Tyr505 residues present in the "finger-like" projections of the RBD were found to be critical for peptide interaction. Hydrogen bonding and hydrophobic interactions played important roles in prompting peptide-protein binding and interaction. Structure-activity relationship indicated that peptides containing aromatic (Tyr and Phe), nonpolar (Pro, Gly, Leu, and Ala), and polar (Asn, Gln, and Cys) residues were the most significant contributors. These findings can facilitate the rational design of selective peptide inhibitors targeting the spike protein of SARS-CoV-2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antiviral Agents / chemistry
  • Antiviral Agents / metabolism*
  • Betacoronavirus / chemistry*
  • Binding Sites
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Molecular Structure
  • Peptides / chemistry
  • Peptides / metabolism*
  • Protein Binding
  • Protein Domains
  • SARS-CoV-2
  • Spike Glycoprotein, Coronavirus / chemistry
  • Spike Glycoprotein, Coronavirus / metabolism*
  • Structure-Activity Relationship

Substances

  • Antiviral Agents
  • Peptides
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2