Nanoscopic Assessment of Anti-SARS-CoV-2 Spike Neutralizing Antibody Using High-Speed AFM

Anti-spike neutralizing antibodies (S NAbs) have been developed for prevention and treatment against COVID-19. The nanoscopic characterization of the dynamic interaction between spike proteins and S NAbs remains difficult. By using high-speed atomic force microscopy (HS-AFM), we elucidate the molecular property of an S NAb and its interaction with spike proteins. The S NAb appeared as monomers with a Y conformation at low density and formed hexameric oligomers at high density. The dynamic S NAb-spike protein interaction at RBD induces neither RBD opening nor S1 subunit shedding. Furthermore, the interaction was stable at endosomal pH. These findings indicated that the S NAb could have a negligible risk of antibody-dependent enhancement. Dynamic movement of spike proteins on small extracellular vesicles (S sEV) resembled that on SARS-CoV-2. The sensitivity of variant S sEVs to S NAb could be evaluated using HS-AFM. Altogether, we demonstrate a nanoscopic assessment platform for evaluating the binding property of S NAbs.

Automated summary

In this study, high-speed atomic force microscopy (HS-AFM) was used to investigate the molecular properties and interactions between spike proteins and S NAbs. The results showed that S NAbs existed as monomers in a Y conformation at low density and formed hexameric oligomers at high density. The dynamic interaction between S NAbs and spike proteins did not induce RBD opening or S1 subunit shedding, and the interaction remained stable at endosomal pH. Additionally, the movement of spike proteins on small extracellular vesicles (S sEV) resembled that on SARS-CoV-2, and the sensitivity of variant S sEVs to S NAbs could be evaluated using HS-AFM. Overall, this study provides a nanoscopic assessment platform for evaluating the binding properties of S NAbs.