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

Custódio TF, Das H, Sheward DJ, Hanke L, Pazicky S, Pieprzyk J, Sorgenfrei M, Schroer MA, Gruzinov AY, Jeffries CM, Graewert MA, Svergun DI, Dobrev N, Remans K, Seeger MA, McInerney GM, Murrell B, Hällberg BM, Löw C

Nat Commun 11 (1) - [2020-11-04; online 2020-11-04]

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 µg/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 an unusual 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.

Category: Biochemistry

Category: Other

Category: Proteins

Funder: H2020

Funder: KAW/SciLifeLab

Funder: VR

Research Area: Host cell systems biology and targets

Type: Journal article

PubMed 33149112

DOI 10.1038/s41467-020-19204-y

Crossref 10.1038/s41467-020-19204-y

Github: MST and BLI data
SASBDB SASDJF4: Synthetic nanobody Sybody 23 (Sy23)
SASBDB SASDJG4: SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD)
SASBDB SASDJH4: SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) bound to the synthetic nanobody Sybody 23 (Sy23)
PDB: 7A25 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) (1-up)
PDB: 7A29 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) (2-up)
EMDB EMD-11617: Cryo-EM density maps of SARS-CoV-2 spike glycoprotein with Sb23 bound (2-up)
Sequences of all the selected sybodies from the study

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