Binding of Glycans to the SARS CoV‐2 Spike Protein, an Open Question: NMR Data on Binding Site Localization, Affinity, and Selectivity

Abstract

We have used NMR experiments to explore binding of selected glycans and glycomimetics to the SARS CoV‑2 spike glycoprotein (S‑protein) and to its receptor binding domain (RBD). STD NMR experiments confirm binding of sialoglycans to the S‑protein of the prototypic Wuhan strain virus and yield dissociation constants in the mM range. The absence of STD effects for sialoglycans in the presence of the Omicron/BA.1 S‑protein reflects a loss of binding as a result of S‐protein evolution. Likewise, no STD effects are observed for the deletion mutant Δ 143‐145 of the Wuhan S‐protein, supporting localization of the binding site in the N‐terminal domain (NTD). The glycomimetics Oseltamivir and Zanamivir bind weakly to the S‑protein of both virus strains. Binding of blood group antigens to the Wuhan S‑protein cannot be confirmed by STD NMR. Using 1 H, 15 N TROSY HSQC based chemical shift perturbation (CSP) experiments we exclude binding of any of the ligands studied to the RBD of the Wuhan S‑protein. Our results put reported data on glycan binding into perspective and shed new light on the potential role of glycan‐binding to the S‐protein.