Dissecting binding and immune evasion mechanisms for ultrapotent Class I and Class 4/1 neutralizing antibodies of SARS-CoV-2 spike protein using a multi-pronged computational approach: neutral frustration architecture of binding interfaces and immune escape hotspots drives adaptive evolution

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Authors: Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker
Cited by: 4
References: 130

Abstract

, F456, L455) that are more permissive to variation. MM-GBSA energy decomposition confirms that van der Waals-driven hydrophobic packing dominates binding, with primary hotspots contributing disproportionately to affinity, while electrostatic networks provide auxiliary stabilization. Conformational and mutational frustration analyses demonstrate that immune escape hotspots reside in neutral-frustration "playgrounds" that permit mutational exploration without destabilizing the RBD, explaining the repeated emergence of convergent mutations across lineages. Our results establish that broad neutralization arises not from ultra-high-affinity anchors, but rather from strategic energy distribution across rigid, evolutionary interfaces. By linking distributed binding, neutral frustration landscapes, and viral fitness constraints, this framework provides a predictive blueprint for designing next-generation therapeutics and vaccines capable of withstanding viral evolution.

Fields of Study & Subjects

vaccines and immunoinformatics approaches SARS-CoV-2 and COVID-19 Research Monoclonal and Polyclonal Antibodies Research

Publication details

Journal / source
Physical Chemistry Chemical Physics
Publisher
Royal Society of Chemistry (RSC)
Volume
28
Issue
7
Pages
4518–4543
Publication date
1 January 2026
Language
EN