Thermodynamics of the Interaction between the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus-2 and the Receptor of Human Angiotensin-Converting Enzyme 2. Effects of Possible Ligands

J Phys Chem Lett. 2020 Nov 5;11(21):9272-9281. doi: 10.1021/acs.jpclett.0c02203. Epub 2020 Oct 21.

Abstract

Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 1000000 deaths all over the world and still lacks a medical treatment despite the attention of the whole scientific community. Human angiotensin-converting enzyme 2 (ACE2) was recently recognized as the transmembrane protein that serves as the point of entry of SARS-CoV-2 into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the protein complex. Moreover, the free energy of binding between ACE2 and the active receptor binding domain of the SARS-CoV-2 spike protein is evaluated quantitatively, providing for the first time the thermodynamics of virus-receptor recognition. Furthermore, the action of different ACE2 ligands is also examined in particular in their capacity to disrupt SARS-CoV-2 recognition, also providing via a free energy profile the quantification of the ligand-induced decreased affinity. These results improve our knowledge on molecular grounds of the SARS-CoV-2 infection and allow us to suggest rationales that could be useful for the subsequent wise molecular design for the treatment of COVID-19 cases.

MeSH terms

  • Angiotensin-Converting Enzyme 2
  • Betacoronavirus / metabolism*
  • Binding Sites
  • COVID-19
  • Coronavirus Infections / pathology
  • Coronavirus Infections / virology
  • Diosmin / chemistry
  • Diosmin / metabolism
  • Humans
  • Ligands*
  • Molecular Dynamics Simulation
  • Pandemics
  • Peptidyl-Dipeptidase A / chemistry
  • Peptidyl-Dipeptidase A / metabolism*
  • Plicamycin / chemistry
  • Plicamycin / metabolism
  • Pneumonia, Viral / pathology
  • Pneumonia, Viral / virology
  • Protein Binding
  • Protein Domains
  • SARS-CoV-2
  • Spike Glycoprotein, Coronavirus / chemistry
  • Spike Glycoprotein, Coronavirus / metabolism*
  • Thermodynamics

Substances

  • Ligands
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2
  • Diosmin
  • Peptidyl-Dipeptidase A
  • ACE2 protein, human
  • Angiotensin-Converting Enzyme 2
  • Plicamycin