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Huo J, Le Bas A, Ruza RR, Duyvesteyn HME, Mikolajek H, Malinauskas T, Tan TK, Rijal P, Dumoux M, Ward PN, Ren J, Zhou D, Harrison PJ, Weckener M, Clare DK, Vogirala VK, Radecke J, Moynié L, Zhao Y, Gilbert-Jaramillo J, Knight ML, Tree JA, Buttigieg KR, Coombes N, Elmore MJ, Carroll MW, Carrique L, Shah PNM, James W, Townsend AR, Stuart DI, Owens RJ, Naismith JH. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2. Nat Struct Mol Biol 2020; 27:846-854. [PMID: 32661423 DOI: 10.1038/s41594-020-0469-6] [Citation(s) in RCA: 353] [Impact Index Per Article: 88.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022]
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.
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MESH Headings
- 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
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Affiliation(s)
- Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Audrey Le Bas
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Reinis R Ruza
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Halina Mikolajek
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Tomas Malinauskas
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Pramila Rijal
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Centre for Translational Immunology, Chinse Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Maud Dumoux
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK
| | - Philip N Ward
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Jingshan Ren
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Peter J Harrison
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Miriam Weckener
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK
| | - Daniel K Clare
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Vinod K Vogirala
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Julika Radecke
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Lucile Moynié
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK
| | - Yuguang Zhao
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | | | - Michael L Knight
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Julia A Tree
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Karen R Buttigieg
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Naomi Coombes
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Michael J Elmore
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Loic Carrique
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Pranav N M Shah
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - William James
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Alain R Townsend
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Centre for Translational Immunology, Chinse Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK.
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK.
| | - James H Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK.
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK.
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