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

Jiandong Huo; Audrey Le Bas; Reinis R Ruza; Helen M E Duyvesteyn; Halina Mikolajek; Tomas Malinauskas; Tiong Kit Tan; Pramila Rijal; Maud Dumoux; Philip N Ward; Jingshan Ren; Daming Zhou; Peter J Harrison; Miriam Weckener; Daniel K Clare; Vinod K Vogirala; Julika Radecke; Lucile Moynié; Yuguang Zhao; Javier Gilbert-Jaramillo; Michael L Knight; Julia A Tree; Karen R Buttigieg; Naomi Coombes; Michael J Elmore; Miles W Carroll; Loic Carrique; Pranav N M Shah; William James; Alain R Townsend; David I Stuart; Raymond J Owens; James H Naismith

doi:10.1038/s41594-020-0469-6

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.

Authors

Jiandong Huo^{1

2

3}, Audrey Le Bas^{2

3}, Reinis R Ruza², Helen M E Duyvesteyn², Halina Mikolajek⁴, Tomas Malinauskas², Tiong Kit Tan⁵, Pramila Rijal^{5

6}, Maud Dumoux¹, Philip N Ward^{2

3}, Jingshan Ren², Daming Zhou², Peter J Harrison^{2

3}, Miriam Weckener¹, Daniel K Clare⁴, Vinod K Vogirala⁴, Julika Radecke⁴, Lucile Moynié¹, Yuguang Zhao², Javier Gilbert-Jaramillo⁷, Michael L Knight⁷, Julia A Tree⁸, Karen R Buttigieg⁸, Naomi Coombes⁸, Michael J Elmore⁸, Miles W Carroll⁸, Loic Carrique², Pranav N M Shah², William James⁷, Alain R Townsend^{5

6}, David I Stuart^{2

4}, Raymond J Owens^{9

10

11}, James H Naismith^{12

13

14}

Affiliations

¹ Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK.
² Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
³ Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK.
⁴ Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
⁵ MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
⁶ Centre for Translational Immunology, Chinse Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
⁷ Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
⁸ National Infection Service, Public Health England, Porton Down, Salisbury, UK.
⁹ Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK. raymond.owens@rc-harwell.ac.uk.
¹⁰ Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK. raymond.owens@rc-harwell.ac.uk.
¹¹ Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK. raymond.owens@rc-harwell.ac.uk.
¹² Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK. naismith@strubi.ox.ac.uk.
¹³ Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK. naismith@strubi.ox.ac.uk.
¹⁴ Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK. naismith@strubi.ox.ac.uk.

PMID: 32661423
DOI: 10.1038/s41594-020-0469-6

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 (K_D 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
Angiotensin-Converting Enzyme 2
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
COVID-19
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
SARS-CoV-2
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
ACE2 protein, human
Angiotensin-Converting Enzyme 2

Abstract

Publication types

MeSH terms

Substances

Grants and funding