Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant.

Gennady Verkhivker

doi:10.3390/ijms23042172

Abstract

Structural and biochemical studies have recently revealed a range of rationally engineered nanobodies with efficient neutralizing capacity against the SARS-CoV-2 virus and resilience against mutational escape. In this study, we performed a comprehensive computational analysis of the SARS-CoV-2 spike trimer complexes with single nanobodies Nb6, VHH E, and complex with VHH E/VHH V nanobody combination. We combined coarse-grained and all-atom molecular simulations and collective dynamics analysis with binding free energy scanning, perturbation-response scanning, and network centrality analysis to examine mechanisms of nanobody-induced allosteric modulation and cooperativity in the SARS-CoV-2 spike trimer complexes with these nanobodies. By quantifying energetic and allosteric determinants of the SARS-CoV-2 spike protein binding with nanobodies, we also examined nanobody-induced modulation of escaping mutations and the effect of the Omicron variant on nanobody binding. The mutational scanning analysis supported the notion that E484A mutation can have a significant detrimental effect on nanobody binding and result in Omicron-induced escape from nanobody neutralization. Our findings showed that SARS-CoV-2 spike protein might exploit the plasticity of specific allosteric hotspots to generate escape mutants that alter response to binding without compromising activity. The network analysis supported these findings showing that VHH E/VHH V nanobody binding can induce long-range couplings between the cryptic binding epitope and ACE2-binding site through a broader ensemble of communication paths that is less dependent on specific mediating centers and therefore may be less sensitive to mutational perturbations of functional residues. The results suggest that binding affinity and long-range communications of the SARS-CoV-2 complexes with nanobodies can be determined by structurally stable regulatory centers and conformationally adaptable hotspots that are allosterically coupled and collectively control resilience to mutational escape.

Highlights

IntroductionThe body of structural and biochemical studies of the SARS-CoV-2 S complexes with different classes of potent antibodies targeting distinct binding epitopes of the S-receptor-binding domain (RBD) as well as various antibody cocktails and combinations have revealed multiple conformation-dependent epitopes, highlighting the link between conformational plasticity and adaptability of S proteins and capacity for eliciting specific binding and broad neutralization responses [16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]
By quantifying energetic and allosteric determinants of the SARS-CoV-2 S binding with nanobodies, we analyze the effects of escaping mutations and the effect of the Omicron variant mutations on nanobody binding
All-atom molecular dynamics (MD) simulations with the explicit inexamine how structural plasticity of the receptor-binding domain (RBD) regions can be modulated by binding and clusion of the glycosylation shield could provide a rigorous assessment of the conformadetermine specific dynamic signatures induced by different classes of nanobodies targeting tional landscape the SARS-CoV-2 proteins; such with directthe simulations remainoftechnically distinct bindingof epitopes

Summary

Introduction

The body of structural and biochemical studies of the SARS-CoV-2 S complexes with different classes of potent antibodies targeting distinct binding epitopes of the S-RBD as well as various antibody cocktails and combinations have revealed multiple conformation-dependent epitopes, highlighting the link between conformational plasticity and adaptability of S proteins and capacity for eliciting specific binding and broad neutralization responses [16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]. Designed antibody cocktails simultaneously targeting different binding epitopes on the SARS-CoV-2 RBD demonstrated improved resilience against mutational escape [33,34,35]

Methods

Results

Conclusion