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

Nat Commun. 2020 Nov 4;11(1):5588. doi: 10.1038/s41467-020-19204-y.

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 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Angiotensin-Converting Enzyme 2
  • Antibodies, Monoclonal / immunology
  • Antibodies, Neutralizing / immunology
  • Antibodies, Viral / immunology
  • Betacoronavirus / immunology*
  • COVID-19
  • Coronavirus Infections / prevention & control*
  • Cryoelectron Microscopy
  • Humans
  • Neutralization Tests
  • Pandemics / prevention & control*
  • Peptidyl-Dipeptidase A / metabolism*
  • Pneumonia, Viral / prevention & control*
  • Protein Binding
  • Protein Conformation
  • Protein Domains / immunology
  • Receptors, Virus / metabolism
  • SARS-CoV-2
  • Single-Domain Antibodies / immunology*
  • Spike Glycoprotein, Coronavirus / immunology*
  • Spike Glycoprotein, Coronavirus / metabolism*

Substances

  • Antibodies, Monoclonal
  • Antibodies, Neutralizing
  • Antibodies, Viral
  • Receptors, Virus
  • Single-Domain Antibodies
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2
  • Peptidyl-Dipeptidase A
  • ACE2 protein, human
  • Angiotensin-Converting Enzyme 2