Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2

PeerJ. 2022 Jul 5:10:e13680. doi: 10.7717/peerj.13680. eCollection 2022.

Abstract

Background: The COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions.

Methods: To gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein's receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics-generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant.

Results: Though mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex. Interaction at a key viral hotspot and hydrophobic contacts at ACE2's N-terminus were preserved, but intermolecular hydrogen bonds and polar contacts in the S-ACE2 interface were lower than in the original SARS-CoV-2 interface.

Keywords: Angiotensin-converting enzyme 2; B.1.1.529; Molecular dynamics; Omicron; SARS-CoV-2; Spike protein.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Angiotensin-Converting Enzyme 2 / genetics
  • COVID-19*
  • Humans
  • Pandemics
  • SARS-CoV-2* / genetics

Substances

  • Angiotensin-Converting Enzyme 2
  • ACE2 protein, human

Supplementary concepts

  • SARS-CoV-2 variants

Grants and funding

This research was funded by a UPAR grant number 12S006 to Ranjit Vijayan from the United Arab Emirates University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.