Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that bind a conserved membrane proximal epitope of the spike

De Cae, S.; Van Molle, I.; van Schie, L.; Shoemaker, S. R.; Deckers, J.; Debeuf, N.; Lameire, S.; Nerinckx, W.; Roose, K.; Fijalkowska, D.; Devos, S.; Desmet, A.-S.; Zavala Marchan, J. C.; Venneman, T.; Ghassabeh, G. H.; Sedeyn, K.; Ballegeer, M.; Vanheerswynghels, M.; De Wolf, C.; Demol, H.; Vanhaverbeke, P.; Lonigro, C.; Bockstal, V.; Rinaldi, M.; Abdelnabi, R.; Neyts, J.; Marqusee, S.; Lambrecht, B. N.; Callewaert, N.; Remaut, H.; Saelens, X.; Schepens, B.

doi:10.1101/2023.03.10.531533

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bioRxiv · 10.1101/2023.03.10.531533

Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that bind a conserved membrane proximal epitope of the spike

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Abstract

Currently circulating SARS-CoV-2 variants have gained complete or significant resistance to all SARS-CoV-2-neutralizing antibodies that have been used in the clinic. Such antibodies can prevent severe disease in SARS-CoV-2 exposed patients for whom vaccines may not provide optimal protection. Here, we describe single-domain antibodies (VHHs), also known as nanobodies, that can broadly neutralize SARS-CoV-2 with unusually high potency. Structural analysis revealed their binding to a unique, highly conserved, membrane proximal, quaternary epitope in the S2 subunit of the spike. Furthermore, a VHH-human IgG1 Fc fusion, efficiently expressed in Chinese hamster ovary cells as a stable antibody construct, protected hamsters against SARS-CoV-2 replication in a therapeutic setting when administered systemically at low dose. This VHH-based antibody represents a new candidate anti-COVID-19 biologic that targets the Achilles heel of the viral spike.

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De Cae, S., Van Molle, I., van Schie, L., Shoemaker, S. R., Deckers, J., Debeuf, N., Lameire, S., Nerinckx, W., Roose, K., Fijalkowska, D., Devos, S., Desmet, A.-S., Zavala Marchan, J. C., Venneman, T., Ghassabeh, G. H., Sedeyn, K., Ballegeer, M., Vanheerswynghels, M., De Wolf, C., Demol, H., Vanhaverbeke, P., Lonigro, C., Bockstal, V., Rinaldi, M., Abdelnabi, R., Neyts, J., Marqusee, S., Lambrecht, B. N., Callewaert, N., Remaut, H., Saelens, X., Schepens, B.. 2023-03-10. Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that bind a conserved membrane proximal epitope of the spike. https://doi.org/10.1101/2023.03.10.531533

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