An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction

Nat Commun. 2020 Sep 4;11(1):4420. doi: 10.1038/s41467-020-18174-5.

Abstract

SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the 'up' and 'down' conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Angiotensin-Converting Enzyme 2
  • Angiotensin-Converting Enzyme Inhibitors / pharmacology*
  • Animals
  • Antibodies, Neutralizing / immunology
  • Antibodies, Neutralizing / pharmacology
  • Antibodies, Viral / chemistry
  • Antibodies, Viral / immunology
  • Betacoronavirus / drug effects*
  • Betacoronavirus / immunology
  • Betacoronavirus / metabolism
  • Binding Sites
  • COVID-19
  • Camelids, New World / immunology*
  • Chlorocebus aethiops
  • Coronavirus Infections / drug therapy*
  • Coronavirus Infections / virology
  • Cryoelectron Microscopy
  • Epitopes / immunology
  • Epitopes / metabolism
  • HEK293 Cells
  • Humans
  • Male
  • Models, Molecular
  • Pandemics
  • Peptidyl-Dipeptidase A / chemistry
  • Peptidyl-Dipeptidase A / metabolism*
  • Pneumonia, Viral / drug therapy*
  • Pneumonia, Viral / virology
  • Protein Binding
  • SARS-CoV-2
  • Single-Domain Antibodies / immunology
  • Single-Domain Antibodies / isolation & purification
  • Single-Domain Antibodies / pharmacology*
  • Spike Glycoprotein, Coronavirus / antagonists & inhibitors*
  • Spike Glycoprotein, Coronavirus / chemistry
  • Spike Glycoprotein, Coronavirus / immunology
  • Spike Glycoprotein, Coronavirus / metabolism
  • Vero Cells

Substances

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