Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2

Custodio, T. F.; Das, H.; Sheward, D. J.; Hanke, L.; Pazicky, S.; Pieprzyk, J.; Sorgenfrei, M.; Schroer, M.; Gruzinov, A.; Jeffries, C.; Graewert, M.; Svergun, D. I.; Dobrev, N.; Remans, K.; Seeger, M.; McInerney, G. M.; Murrell, B.; Hällberg, B. M.; Löw, C.

doi:10.1101/2020.06.23.165415

bioRxiv · 10.1101/2020.06.23.165415

Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2

Custodio, T. F.·Das, H.·Sheward, D. J.·Hanke, L.·Pazicky, S.·Pieprzyk, J.·Sorgenfrei, M.·Schroer, M.·Gruzinov, A.·Jeffries, C.·Graewert, M.·Svergun, D. I.·Dobrev, N.·Remans, K.·Seeger, M.·McInerney, G. M.·Murrell, B.·Hällberg, B. M.·Löw, C.

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Abstract

The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development times and costly production. Here, we report the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies (Sb), that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Several binders with low nanomolar affinities and efficient neutralization activity were identified of which Sb23 displayed high affinity and neutralized pseudovirus with an IC50 of 0.6 {micro}g/ml. A cryo-EM structure of the spike bound to Sb23 showed that Sb23 binds competitively in the ACE2 binding site. Furthermore, the cryo-EM reconstruction revealed a novel conformation of the spike where two RBDs are in the up ACE2-binding conformation. The combined approach represents an alternative, fast workflow to select binders with neutralizing activity against newly emerging viruses.

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Custodio, T. F., Das, H., Sheward, D. J., Hanke, L., Pazicky, S., Pieprzyk, J., Sorgenfrei, M., Schroer, M., Gruzinov, A., Jeffries, C., Graewert, M., Svergun, D. I., Dobrev, N., Remans, K., Seeger, M., McInerney, G. M., Murrell, B., Hällberg, B. M., Löw, C.. 2020-06-23. Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2. https://doi.org/10.1101/2020.06.23.165415

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