(841) Structural characterization of antibodies binding the conserved central helix and membrane-proximal lower stalk of coronavirus spike glycoprotein

Introduction/Rationale: The ongoing threat of zoonotic coronavirus spillover into humans, exemplified by severe acute respiratory syndrome virus 2 (SARS-CoV-2), underscores the urgent need for pan-coronavirus therapeutics that can be deployed to mitigate future pandemics.

Methods: Here, we identified monoclonal antibodies from COVID-19 convalescent donors that target two conserved epitopes in the S2 domain of the coronavirus Spike glycoprotein: the central helix (CH) and a membrane-proximal epitope in the heptad repeat 2 (HR2), which we designate the lower stalk (LS).

Results: CH-directed antibodies exhibited broad cross-reactivity across betacoronaviruses, whereas LS-directed antibodies demonstrated reactivity primarily within sarbecoviruses. Using cryogenic electron microscopy (cryo-EM), we determined sub-4 Å structures of three cross-reactive CH antibodies—ch.005, ch.007, and ch.010—bound to the prefusion-stabilized SARS-CoV-2 S2 protein, revealing distinct binding poses and contact residues relative to previously described CH antibodies. In parallel, X-ray crystallography studies yielded a sub-2 Å structure of the ls.019 Fab in complex with the LS peptide, providing, to our knowledge, the first structural visualization of a human monoclonal antibody engaging this epitope.

Conclusion: Together, these findings advance our knowledge of two conserved and structurally vulnerable sites within the coronavirus S2 subunit–the central helix and the lower stalk–that can guide the development of broad-spectrum antibody therapeutics and vaccines against current and emerging coronaviruses.