Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2

Nat Struct Mol Biol. 2020 Sep;27(9):846-854. doi: 10.1038/s41594-020-0469-6. Epub 2020 Jul 13.

Abstract

The SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than influenza. The SARS-CoV-2 receptor binding domain (RBD) of the spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) receptor as a prelude to viral entry into the cell. Using a naive llama single-domain antibody library and PCR-based maturation, we have produced two closely related nanobodies, H11-D4 and H11-H4, that bind RBD (KD of 39 and 12 nM, respectively) and block its interaction with ACE2. Single-particle cryo-EM revealed that both nanobodies bind to all three RBDs in the spike trimer. Crystal structures of each nanobody-RBD complex revealed how both nanobodies recognize the same epitope, which partly overlaps with the ACE2 binding surface, explaining the blocking of the RBD-ACE2 interaction. Nanobody-Fc fusions showed neutralizing activity against SARS-CoV-2 (4-6 nM for H11-H4, 18 nM for H11-D4) and additive neutralization with the SARS-CoV-1/2 antibody CR3022.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Antibodies, Neutralizing / immunology*
  • Antibodies, Neutralizing / metabolism
  • Antibodies, Neutralizing / ultrastructure
  • Antibodies, Viral / immunology*
  • Antibodies, Viral / metabolism
  • Antibodies, Viral / ultrastructure
  • Antibody Affinity
  • Antigen-Antibody Reactions / immunology
  • Betacoronavirus / immunology*
  • Betacoronavirus / metabolism
  • Binding, Competitive
  • Coronavirus Infections*
  • Cryoelectron Microscopy
  • Crystallography, X-Ray
  • Epitopes / immunology
  • Humans
  • Immunoglobulin Fc Fragments / genetics
  • Immunoglobulin Fc Fragments / immunology
  • Models, Molecular
  • Pandemics*
  • Peptide Library
  • Peptidyl-Dipeptidase A / metabolism*
  • Peptidyl-Dipeptidase A / ultrastructure
  • Pneumonia, Viral*
  • Protein Binding
  • Protein Conformation
  • Receptors, Virus / metabolism*
  • Receptors, Virus / ultrastructure
  • Recombinant Fusion Proteins / immunology
  • Recombinant Fusion Proteins / metabolism
  • Sequence Homology, Amino Acid
  • Single-Domain Antibodies / immunology*
  • Single-Domain Antibodies / metabolism
  • Single-Domain Antibodies / ultrastructure
  • Spike Glycoprotein, Coronavirus / immunology*
  • Spike Glycoprotein, Coronavirus / metabolism
  • Spike Glycoprotein, Coronavirus / ultrastructure

Substances

  • Antibodies, Neutralizing
  • Antibodies, Viral
  • Epitopes
  • Immunoglobulin Fc Fragments
  • Peptide Library
  • Receptors, Virus
  • Recombinant Fusion Proteins
  • Single-Domain Antibodies
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2
  • Peptidyl-Dipeptidase A
  • angiotensin converting enzyme 2

Supplementary concepts

  • COVID-19
  • severe acute respiratory syndrome coronavirus 2