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SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study.

Hoang Linh Nguyen1,2, Thai Quoc Nguyen3,4, Mai Suan Li5

  • 1Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam.

The Journal of Physical Chemistry. B
|April 2, 2024
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Summary

Omicron variants of SARS-CoV-2 bind human ACE2 strongly, but binding affinities are similar across lineages. Viral evolution may prioritize immune evasion over increased ACE2 binding.

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Area of Science:

  • Virology
  • Biophysics
  • Computational Biology

Background:

  • Omicron (B.1.1.529) variant of SARS-CoV-2 increases COVID-19 pandemic severity due to high transmissibility.
  • Omicron exhibits stronger binding to human ACE2 than the wild-type virus.
  • Emerging Omicron lineages show potential for enhanced receptor binding and immune evasion.

Purpose of the Study:

  • Investigate the binding free energy between various Omicron lineages and human ACE2.
  • Determine if newer Omicron subvariants have improved binding affinity to ACE2.
  • Understand the forces governing the interaction between Omicron variants and human cells.

Main Methods:

  • All-atom molecular dynamics simulations.
  • Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations.
  • Analysis of binding free energy for multiple Omicron lineages (BA.2, BA.2.3.20, BA.3, BA4/BA5, BA.2.75, BA.2.75.2, BA.4.6, XBB.1, XBB.1.5, BJ.1, BN.1, BQ.1.1, CH.1.1) to human ACE2.

Main Results:

  • All investigated Omicron lineages demonstrated increased binding affinity to human ACE2 compared to the BA.1 lineage.
  • BA.2.75 and BA.2.75.2 subvariants showed the strongest binding to ACE2 among the studied Omicron lineages.
  • Binding affinities among Omicron lineages were generally not significantly different; electrostatic forces dominated interactions over van der Waals forces.

Conclusions:

  • While Omicron variants bind human ACE2 effectively, further significant improvements in binding affinity are not evident.
  • Viral evolution of SARS-CoV-2 may focus more on mechanisms of immune evasion rather than enhancing ACE2 binding.
  • Understanding these interactions is crucial for predicting viral spread and developing effective countermeasures.