A Pathway Model to Understand the Evolution of Spike Protein Binding to ACE2 in SARS-CoV-2 Variants

Ludovico Pipitò, Christopher A. Reynolds, Juan Carlos Mobarec, Owen Vickery, Giuseppe Deganutti

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    Abstract

    After the SARS-CoV-2 Wuhan variant that gave rise to the pandemic, other variants named Delta, Omicron, and Omicron-2 sequentially became prevalent, with mutations spread around the viral genome, including on the spike (S) protein; in order to understand the resultant in gains in infectivity, we interrogated in silico both the equilibrium binding and the binding pathway of the virus’ receptor-binding domain (RBD) to the angiotensin-converting enzyme 2 (ACE2) receptor. We interrogated the molecular recognition between the RBD of different variants and ACE2 through supervised molecular dynamics (SuMD) and classic molecular dynamics (MD) simulations to address the effect of mutations on the possible S protein binding pathways. Our results indicate that compensation between binding pathway efficiency and stability of the complex exists for the Omicron BA.1 receptor binding domain, while Omicron BA.2′s mutations putatively improved the dynamic recognition of the ACE2 receptor, suggesting an evolutionary advantage over the previous strains.
    Original languageEnglish
    Article number1607
    Number of pages12
    JournalBiomolecules
    Volume12
    Issue number11
    DOIs
    Publication statusPublished - 31 Oct 2022

    Bibliographical note

    This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

    Keywords

    • Sars-Cov-2
    • spike protein ACE-2
    • molecular dynamics
    • supervised molecular dynamics
    • binding pathway

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