Microscopic interactions between ivermectin and key human and viral proteins involved in SARS-CoV-2 infection

Phys Chem Chem Phys. 2021 Oct 20;23(40):22957-22971. doi: 10.1039/d1cp02967c.

Abstract

The identification of chemical compounds able to bind specific sites of the human/viral proteins involved in the SARS-CoV-2 infection cycle is a prerequisite to design effective antiviral drugs. Here we conduct a molecular dynamics study with the aim to assess the interactions of ivermectin, an antiparasitic drug with broad-spectrum antiviral activity, with the human Angiotensin-Converting Enzyme 2 (ACE2), the viral 3CLpro and PLpro proteases, and the viral SARS Unique Domain (SUD). The drug/target interactions have been characterized in silico by describing the nature of the non-covalent interactions found and by measuring the extent of their time duration along the MD simulation. Results reveal that the ACE2 protein and the ACE2/RBD aggregates form the most persistent interactions with ivermectin, while the binding with the remaining viral proteins is more limited and unspecific.

MeSH terms

  • Angiotensin-Converting Enzyme 2 / chemistry
  • Angiotensin-Converting Enzyme 2 / metabolism*
  • Antiviral Agents / chemistry
  • Antiviral Agents / metabolism*
  • Binding Sites
  • Coronavirus 3C Proteases / chemistry
  • Coronavirus 3C Proteases / metabolism*
  • Coronavirus Papain-Like Proteases / chemistry
  • Coronavirus Papain-Like Proteases / metabolism*
  • G-Quadruplexes
  • Humans
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Ivermectin / chemistry
  • Ivermectin / metabolism*
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Protein Binding
  • Protein Domains
  • RNA / genetics
  • RNA / metabolism
  • SARS-CoV-2

Substances

  • Antiviral Agents
  • RNA
  • Ivermectin
  • ACE2 protein, human
  • Angiotensin-Converting Enzyme 2
  • 3C-like proteinase, SARS-CoV-2
  • Coronavirus Papain-Like Proteases
  • papain-like protease, SARS-CoV-2
  • Coronavirus 3C Proteases