Allostery links hACE2 binding, pan-variant neutralisation and helical extension in the SARS-CoV-2 Spike protein

Abstract

The SARS-CoV-2 spike protein is highly antigenic, with epitopes in three distinct regions of the receptor binding domain (RBD) alone that have known mechanisms of neutralization. In previous work, we predicted a fourth RBD epitope based on allosteric conformational perturbations measured by hydrogen-deuterium exchange mass spectrometry (HDX-MS) upon complexation with the canonical spike protein target, human angiotensin-converting enzyme 2 (hACE2). We subsequently identified a pan-neutralizing antibody (ICO-hu104) with the predicted epitope, however, as the epitope was somewhat distant from the hACE2 binding interface, and our previous work limited to the spike RBD, the neutralization mechanism was unclear. Using HDX-MS, we investigated the binding of ICO-hu104 to the full-length SARS-CoV-2 spike protein from Wuhan, Delta and Omicron variants. We demonstrate that binding of ICO-hu104 at its epitope results in an increase in deuterium uptake in the distant HR1 domain for variants of concern, which in a biological context could be indicative of destabilisation of the helices within this region, promoting S1 shedding or failure of helical extension during S2-mediated fusion. This is supported by our computational modelling, highlighting propagation of allosteric effects to the S2 coiled-coil region. Collectively, this work demonstrates an alternative neutralization mechanism for ICO-hu104 which is distinct from its first-generation predecessors and thus opens alternative avenues targeting non-RBD epitopes through assessment of allosteric perturbations. HighlightsO_LIHDX-MS reveals decreased deuterium uptake within the HR1 region of S2 for SARS-CoV-2 spike protein for variants of concern when bound to ICO-hu104. C_LIO_LIComputational modelling validates high allosteric coupling between ICO-hu104 epitope and HR1 region. C_LIO_LISuggests an alternative neutralization mechanism from its predecessor ICO-hu23, whereby destabilisation of helices within the HR1 region promotes S1 shedding and/or failure of helical extension during S2-mediated fusion. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/635280v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1175bdborg.highwire.dtl.DTLVardef@8fb17borg.highwire.dtl.DTLVardef@1cd13f7org.highwire.dtl.DTLVardef@d9c121_HPS_FORMAT_FIGEXP M_FIG C_FIG