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Molecular recognition of SARS-CoV-2 spike protein with three essential partners: exploring possible immune escape

Yan Cheng1, Dan Zheng1, Derong Zhang2

  • 1Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China.

Journal of Molecular Modeling
|March 25, 2023
PubMed
Abstract

Insights

New SARS-CoV-2 variants like Delta and Omicron exhibit increased transmissibility and immune escape. Molecular simulations reveal their enhanced binding to host cells and resistance to antibodies, guiding future vaccine development.

Area of Science:

  • Virology
  • Molecular Biology
  • Computational Biology

Background:

  • The COVID-19 pandemic continues globally, driven by emerging SARS-CoV-2 variants (e.g., Delta, Omicron).
  • Understanding viral lifecycle and host-pathogen interactions is crucial for developing effective countermeasures and vaccines.

Purpose of the Study:

  • To analyze molecular recognition and conformational changes in SARS-CoV-2 spike protein mutants (Delta, Mu, Omicron).
  • To compare interactions with host cell receptor hACE2, protease TMPRSS2, and antibody C121.

Main Methods:

  • Molecular simulations were employed to analyze key interactions.
  • Binding free energy and water basin calculations were performed.

Main Results:

  • Mutants demonstrated higher affinity for hACE2, indicating increased transmission potential.
  • TMPRSS2 cleavage efficiency varied among mutants, with Omicron showing inefficient utilization and potential endosomal entry.
  • Antibody C121 exhibited reduced binding to Omicron due to structural flexibility and altered binding angles.

Conclusions:

  • Future SARS-CoV-2 evolution may favor high infectivity, immune escape, and potentially lower virulence.
  • This study provides insights into mutant resistance mechanisms and theoretical guidance for drug design targeting the spike protein.
Keywords:
AntibodyMolecular dynamics simulationSARS-CoV-2TMPRSS2hACE2

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