On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

Virus Res. 2020 Aug;285:198021. doi: 10.1016/j.virusres.2020.198021. Epub 2020 May 15.


A new betacoronavirus named SARS-CoV-2 has emerged as a new threat to global health and economy. A promising target for both diagnosis and therapeutics treatments of the new disease named COVID-19 is the coronavirus (CoV) spike (S) glycoprotein. By constant-pH Monte Carlo simulations and the PROCEEDpKa method, we have mapped the electrostatic epitopes for four monoclonal antibodies and the angiotensin-converting enzyme 2 (ACE2) on both SARS-CoV-1 and the new SARS-CoV-2 S receptor binding domain (RBD) proteins. We also calculated free energy of interactions and shown that the S RBD proteins from both SARS viruses binds to ACE2 with similar affinities. However, the affinity between the S RBD protein from the new SARS-CoV-2 and ACE2 is higher than for any studied antibody previously found complexed with SARS-CoV-1. Based on physical chemical analysis and free energies estimates, we can shed some light on the involved molecular recognition processes, their clinical aspects, the implications for drug developments, and suggest structural modifications on the CR3022 antibody that would improve its binding affinities for SARS-CoV-2 and contribute to address the ongoing international health crisis.

Keywords: ACE2; Antibody development; Antigenic analysis; Binding affinity; Computer simulation; Coronavirus; Electrostatic interactions; Epitopes; Host-pathogen interaction; Protein-protein interaction; SARS-CoV-2; pH effect.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Angiotensin-Converting Enzyme 2
  • Antibodies, Monoclonal / immunology
  • Antibodies, Monoclonal / metabolism
  • Antibodies, Viral / immunology
  • Antibodies, Viral / metabolism
  • Betacoronavirus / chemistry*
  • Betacoronavirus / immunology
  • Computer Simulation
  • Epitope Mapping
  • Humans
  • Models, Molecular
  • Monte Carlo Method
  • Peptidyl-Dipeptidase A / chemistry
  • Peptidyl-Dipeptidase A / metabolism*
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Domains and Motifs
  • Protein Interaction Mapping
  • Receptors, Virus / chemistry
  • Receptors, Virus / metabolism*
  • SARS-CoV-2
  • Severe acute respiratory syndrome-related coronavirus / chemistry*
  • Severe acute respiratory syndrome-related coronavirus / immunology
  • Spike Glycoprotein, Coronavirus / chemistry
  • Spike Glycoprotein, Coronavirus / immunology
  • Spike Glycoprotein, Coronavirus / metabolism*
  • Thermodynamics


  • Antibodies, Monoclonal
  • Antibodies, Viral
  • Receptors, Virus
  • Spike Glycoprotein, Coronavirus
  • spike glycoprotein, SARS-CoV
  • spike protein, SARS-CoV-2
  • Peptidyl-Dipeptidase A
  • ACE2 protein, human
  • Angiotensin-Converting Enzyme 2