Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants

The SARS-CoV-2 spike protein binds to the angiotensin-converting enzyme 2 (ACE2) receptor to mediate viral entry, with mutations in different variants influencing binding affinity and conformational dynamics. Using large-scale molecular dynamics simulations, we analyzed the Spike-ACE2 complex in the wild-type (WT), Beta, and Delta variants. Our findings reveal significant conformational rearrangements at the interface in Beta and Delta compared to WT, leading to distinct interaction networks and changes in complex stability. Binding free energy analysis further highlights variant-specific differences in ACE2 affinity, with alternative binding modes emerging over the simulation. The results enhance our understanding of spike-ACE2 stoichiometry across variants, providing implications for viral infectivity and therapeutic targeting.

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Publication Details

Journal
Computational and Structural Biotechnology Journal
Published
2025-01-01
DOI
https://doi.org/10.1016/j.csbj.2025.07.034
Citations
1
Primary Topic
SARS-CoV-2 and COVID-19 Research
Type
article
Field-Weighted Citation Impact
1.40

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Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants

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Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants

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article en
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Abstract

The SARS-CoV-2 spike protein binds to the angiotensin-converting enzyme 2 (ACE2) receptor to mediate viral entry, with mutations in different variants influencing binding affinity and conformational dynamics. Using large-scale molecular dynamics simulations, we analyzed the Spike-ACE2 complex in the wild-type (WT), Beta, and Delta variants. Our findings reveal significant conformational rearrangements at the interface in Beta and Delta compared to WT, leading to distinct interaction networks and changes in complex stability. Binding free energy analysis further highlights variant-specific differences in ACE2 affinity, with alternative binding modes emerging over the simulation. The results enhance our understanding of spike-ACE2 stoichiometry across variants, providing implications for viral infectivity and therapeutic targeting.

Computational and Structural Biotechnology JournalVol. 27
Centre National de la Recherche Scientifique (FR), Université de Montpellier (FR), Laboratoire Lorrain de Recherche en Informatique et ses Applications (FR), Institut de Recherche en Infectiologie de Montpellier (FR), Université Grenoble Alpes (FR), Université de Lorraine (FR)
Agence Nationale de la Recherche, Grand Équipement National De Calcul Intensif
Affordable and clean energy
Openalex Percentile: Top 17%
SARS-CoV-2 and COVID-19 Research
1.40
DOIOpen Access PDFOpenAlex
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