Allostery Links hACE2 Binding, Pan-variant Neutralization and Helical Extension in the SARS-CoV-2 Spike Protein

Area of Science:

• Virology
• Immunology
• Structural Biology

Background:

• The SARS-CoV-2 spike protein has known neutralizing epitopes within the receptor binding domain (RBD).
• A previously predicted fourth RBD epitope targeted by antibody ICO-hu104 had an unclear neutralization mechanism due to its distance from the hACE2 binding site.

Purpose of the Study:

• To investigate the neutralization mechanism of the pan-neutralizing antibody ICO-hu104 against full-length SARS-CoV-2 spike proteins from different variants.
• To elucidate the allosteric effects of ICO-hu104 binding on spike protein conformation and function.

Main Methods:

• Hydrogen-deuterium exchange mass spectrometry (HDX-MS) was used to analyze ICO-hu104 binding to Wuhan, Delta, and Omicron spike proteins.
• Computational modeling was employed to assess the propagation of allosteric effects.

Main Results:

• ICO-hu104 binding induced increased deuterium uptake in the HR1 domain of later variants, suggesting potential destabilization.
• Allosteric effects were observed to propagate to the S2 coiled-coil region, impacting viral fusion mechanisms.
• This demonstrates a distinct neutralization mechanism compared to previous antibodies targeting the RBD.

Conclusions:

• ICO-hu104 employs an alternative neutralization strategy by inducing allosteric changes in the spike protein, distinct from direct RBD epitope targeting.
• This finding opens new therapeutic avenues targeting non-RBD epitopes through allosteric modulation of the spike protein.