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TitleSelection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 5588, Year 2020
Publish dateNov 4, 2020
AuthorsTânia F Custódio / Hrishikesh Das / Daniel J Sheward / Leo Hanke / Samuel Pazicky / Joanna Pieprzyk / Michèle Sorgenfrei / Martin A Schroer / Andrey Yu Gruzinov / Cy M Jeffries / Melissa A Graewert / Dmitri I Svergun / Nikolay Dobrev / Kim Remans / Markus A Seeger / Gerald M McInerney / Ben Murrell / B Martin Hällberg / Christian Löw /
PubMed AbstractThe 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 ...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 IC 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.
External linksNat Commun / PubMed:33149112 / PubMed Central
MethodsEM (single particle)
Resolution2.94 - 3.06 Å
Structure data

EMDB-11616, PDB-7a25:
Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23)
Method: EM (single particle) / Resolution: 3.06 Å

EMDB-11617, PDB-7a29:
Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation
Method: EM (single particle) / Resolution: 2.94 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • severe acute respiratory syndrome coronavirus 2
  • synthetic construct (others)
KeywordsACE2 protein, human / Angiotensin-Converting Enzyme 2 / Antibodies, Monoclonal / Antibodies, Neutralizing / Antibodies, Viral / Betacoronavirus / COVID-19 / Coronavirus Infections / Cryoelectron Microscopy / Humans / Neutralization Tests / Pandemics / Peptidyl-Dipeptidase A / Pneumonia, Viral / Protein Binding / Protein Conformation / Protein Domains / Receptors, Virus / SARS-CoV-2 / Single-Domain Antibodies / Spike Glycoprotein, Coronavirus / spike protein, SARS-CoV-2 / VIRAL PROTEIN / complex / nanobody / spike

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