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Exploring the diverse binding ability of SARS-CoV-2 variant RBDs to different antibody classes: a computational

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Area of Science:

  • Virology
  • Immunology
  • Structural Biology

Background:

  • The SARS-CoV-2 spike protein's receptor-binding domain (RBD) is a key target for neutralizing antibodies.
  • Viral evolution and mutations continuously alter the RBD's antigenic landscape, impacting antibody efficacy.

Purpose of the Study:

  • To investigate the binding profiles of six neutralizing antibodies (VIR-7229, S2E12, OMI-42, ZCB11, S309, SA55) against SARS-CoV-2 RBD variants.
  • To understand the role of mutations and glycosylation in antibody evasion and viral adaptation.

Main Methods:

  • Computational approaches including molecular dynamics simulations.
  • Binding free energy estimation using the MM-PBSA method.

Main Results:

  • Antibodies ZCB11 and S2E12 showed reduced binding to Omicron subvariants (XBB.1.5, BA.2.86, KP.3, MV.1).
  • OMI-42 was evaded by BA.2.86, KP.3, and MV.1; S309 showed reduced affinity to multiple variants.
  • Glycans significantly contribute to antibody-RBD interactions, with dual glycans increasing stability.
  • SA55 and VIR-7229 maintained robust binding across all studied variants.
  • Viral mutations employ charge-increasing and neutral strategies to evade antibodies while enhancing ACE2 binding.

Conclusions:

  • Antibody efficacy varies significantly against evolving SARS-CoV-2 variants.
  • Glycosylation patterns play a critical role in antibody-RBD complex stability.
  • Viral evolution utilizes distinct mutation strategies to overcome antibody responses.
  • The charge-centric hypothesis explains binding affinity variations driven by electrical interactions.