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Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2.
Nat Struct Mol Biol. 2020 09; 27(9):846-854.NS

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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Publisher Full Text (DOI)

Authors+Show Affiliations

Huo J
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.
Le Bas A
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.
Ruza RR
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
Duyvesteyn HME
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
Mikolajek H
Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
Malinauskas T
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
Tan TK
MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
Rijal P
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.
Dumoux M
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK.
Ward PN
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.
Ren J
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
Zhou D
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
Harrison PJ
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.
Weckener M
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK.
Clare DK
Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
Vogirala VK
Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
Radecke J
Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
Moynié L
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK.
Zhao Y
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
Gilbert-Jaramillo J
Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
Knight ML
Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
Tree JA
National Infection Service, Public Health England, Porton Down, Salisbury, UK.
Buttigieg KR
National Infection Service, Public Health England, Porton Down, Salisbury, UK.
Coombes N
National Infection Service, Public Health England, Porton Down, Salisbury, UK.
Elmore MJ
National Infection Service, Public Health England, Porton Down, Salisbury, UK.
Carroll MW
National Infection Service, Public Health England, Porton Down, Salisbury, UK.
Carrique L
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
Shah PNM
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
James W
Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
Townsend AR
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.
Stuart DI
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.
Owens RJ
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK. raymond.owens@rc-harwell.ac.uk. Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK. raymond.owens@rc-harwell.ac.uk. 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.
Naismith JH
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK. naismith@strubi.ox.ac.uk. Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK. naismith@strubi.ox.ac.uk. 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.

MeSH

Amino Acid SequenceAngiotensin-Converting Enzyme 2Antibodies, NeutralizingAntibodies, ViralAntibody AffinityAntigen-Antibody ReactionsBetacoronavirusBinding, CompetitiveCOVID-19Coronavirus InfectionsCryoelectron MicroscopyCrystallography, X-RayEpitopesHumansImmunoglobulin Fc FragmentsModels, MolecularPandemicsPeptide LibraryPeptidyl-Dipeptidase APneumonia, ViralProtein BindingProtein ConformationReceptors, VirusRecombinant Fusion ProteinsSARS-CoV-2Sequence Homology, Amino AcidSingle-Domain AntibodiesSpike Glycoprotein, Coronavirus

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32661423

Citation

Huo, Jiandong, et al. "Neutralizing Nanobodies Bind SARS-CoV-2 Spike RBD and Block Interaction With ACE2." Nature Structural & Molecular Biology, vol. 27, no. 9, 2020, pp. 846-854.
Huo J, Le Bas A, Ruza RR, et al. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2. Nat Struct Mol Biol. 2020;27(9):846-854.
Huo, J., Le Bas, A., Ruza, R. R., Duyvesteyn, H. M. E., Mikolajek, H., Malinauskas, T., Tan, T. K., Rijal, P., Dumoux, M., Ward, P. N., Ren, J., Zhou, D., Harrison, P. J., Weckener, M., Clare, D. K., Vogirala, V. K., Radecke, J., Moynié, L., Zhao, Y., ... Naismith, J. H. (2020). Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2. Nature Structural & Molecular Biology, 27(9), 846-854. https://doi.org/10.1038/s41594-020-0469-6
Huo J, et al. Neutralizing Nanobodies Bind SARS-CoV-2 Spike RBD and Block Interaction With ACE2. Nat Struct Mol Biol. 2020;27(9):846-854. PubMed PMID: 32661423.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2. AU - Huo,Jiandong, AU - Le Bas,Audrey, AU - Ruza,Reinis R, AU - Duyvesteyn,Helen M E, AU - Mikolajek,Halina, AU - Malinauskas,Tomas, AU - Tan,Tiong Kit, AU - Rijal,Pramila, AU - Dumoux,Maud, AU - Ward,Philip N, AU - Ren,Jingshan, AU - Zhou,Daming, AU - Harrison,Peter J, AU - Weckener,Miriam, AU - Clare,Daniel K, AU - Vogirala,Vinod K, AU - Radecke,Julika, AU - Moynié,Lucile, AU - Zhao,Yuguang, AU - Gilbert-Jaramillo,Javier, AU - Knight,Michael L, AU - Tree,Julia A, AU - Buttigieg,Karen R, AU - Coombes,Naomi, AU - Elmore,Michael J, AU - Carroll,Miles W, AU - Carrique,Loic, AU - Shah,Pranav N M, AU - James,William, AU - Townsend,Alain R, AU - Stuart,David I, AU - Owens,Raymond J, AU - Naismith,James H, Y1 - 2020/07/13/ PY - 2020/05/21/received PY - 2020/06/26/accepted PY - 2020/7/15/pubmed PY - 2020/9/20/medline PY - 2020/7/15/entrez SP - 846 EP - 854 JF - Nature structural & molecular biology JO - Nat Struct Mol Biol VL - 27 IS - 9 N2 - 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. SN - 1545-9985 UR - https://www.unboundmedicine.com/medline/citation/32661423/Neutralizing_nanobodies_bind_SARS_CoV_2_spike_RBD_and_block_interaction_with_ACE2_ DB - PRIME DP - Unbound Medicine ER -