Structural characterisation of a nanobody derived from a naïve library that neutralises SARS-CoV-2

doi:10.21203/rs.3.rs-32948/v1

This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.

Research Article

Jiangdong 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, Julika Radeke, Yuguang Zhao, Javier Gilbert-Jaramillo, Michael Knight, Loic Carrique, Pranav N.M. Shah, William James, Alain Townsend, David I. Stuart, Raymond J. Owens, James H. Naismith

Jiangdong Huo

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK.

Audrey Le Bas

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Reinis R. Ruza

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Helen M.E. Duyvesteyn

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Halina Mikolajek

Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK.

Tomas Malinauskas

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Tiong Kit Tan

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.

Pramila Rijal

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.

Maud Dumoux

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK

Philip N. Ward

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Jingshan Ren

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Daming Zhou

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Peter J. Harrison

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Julika Radeke

Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK

Yuguang Zhao

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Javier Gilbert-Jaramillo

Sir William Dunn School of Pathology, University of Oxford OX1 3RE, UK

Michael Knight

Sir William Dunn School of Pathology, University of Oxford OX1 3RE, UK

Loic Carrique

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Pranav N.M. Shah

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

William James

Sir William Dunn School of Pathology, University of Oxford OX1 3RE, UK

Alain Townsend

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK

David I. Stuart

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Raymond J. Owens

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK

Corresponding Author

James H. Naismith

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK

Corresponding Author

DOI:

License:

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The SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than seasonal flu. 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 naïve llama single chain nanobody library and PCR maturation we have produced a nanobody, H11-D4, with a KD 9 nM for RBD that blocks the binding of RBD to the ACE2. Single particle cryo-electron microscopy revealed that H11-D4 binds to each of the three RBDs in the Spike trimer. The 1.8 Å crystal structure of the H11-D4 – RBD complex has illuminated the molecular interactions that drive the high affinity. H11-D4 binds to an epitope on RBD that overlaps with the ACE2 binding, explaining the blocking of ACE2 binding. The nanobody showed potent neutralising activity against live SARS-CoV-2 virus.

Keywords

SARS-CoV-2, nanobody, H11-D4, spike protein receptor binding domain, human angiotensin-converting enzyme 2

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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.

Research Article

Jiangdong 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, Julika Radeke, Yuguang Zhao, Javier Gilbert-Jaramillo, Michael Knight, Loic Carrique, Pranav N.M. Shah, William James, Alain Townsend, David I. Stuart, Raymond J. Owens, James H. Naismith

Jiangdong Huo

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK.

Audrey Le Bas

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Reinis R. Ruza

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Helen M.E. Duyvesteyn

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Halina Mikolajek

Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK.

Tomas Malinauskas

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Tiong Kit Tan

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.

Pramila Rijal

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.

Maud Dumoux

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK

Philip N. Ward

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Jingshan Ren

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Daming Zhou

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Peter J. Harrison

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Julika Radeke

Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK

Yuguang Zhao

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Javier Gilbert-Jaramillo

Sir William Dunn School of Pathology, University of Oxford OX1 3RE, UK

Michael Knight

Sir William Dunn School of Pathology, University of Oxford OX1 3RE, UK

Loic Carrique

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Pranav N.M. Shah

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

William James

Sir William Dunn School of Pathology, University of Oxford OX1 3RE, UK

Alain Townsend

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK

David I. Stuart

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Raymond J. Owens

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK

Corresponding Author

James H. Naismith

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK

Corresponding Author

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History

CURRENT STATUS: Published

View the published article at Nature Structural & Molecular Biology.

Version 1

Posted 01 Jun, 2020

MetricsComments: 0PDF Downloads: ...HTML Views: ...

Subject Areas

Molecular Biology

DOI:

10.21203/rs.3.rs-32948/v1

Download PDF

License:

This work is licensed under a CC BY 4.0 License. Read Full License

View the published article at Nature Structural & Molecular Biology.

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

This is a list of supplementary files associated with this preprint. Click to download.

Supplementarytablesandfigures.pdf

Research Article

Jiangdong Huo

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK.

Audrey Le Bas

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Reinis R. Ruza

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Helen M.E. Duyvesteyn

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Halina Mikolajek

Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK.

Tomas Malinauskas

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

Tiong Kit Tan

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.

Pramila Rijal

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.

Maud Dumoux

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK

Philip N. Ward

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Jingshan Ren

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Daming Zhou

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Peter J. Harrison

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Julika Radeke

Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK

Yuguang Zhao

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Javier Gilbert-Jaramillo

Sir William Dunn School of Pathology, University of Oxford OX1 3RE, UK

Michael Knight

Sir William Dunn School of Pathology, University of Oxford OX1 3RE, UK

Loic Carrique

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Pranav N.M. Shah

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.

William James

Sir William Dunn School of Pathology, University of Oxford OX1 3RE, UK

Alain Townsend

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK

David I. Stuart

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK

Raymond J. Owens

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK

Corresponding Author

James H. Naismith

Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK

Corresponding Author

DOI:

10.21203/rs.3.rs-32948/v1

Download PDF

License:

This work is licensed under a CC BY 4.0 License. Read Full License

Abstract

Keywords

SARS-CoV-2, nanobody, H11-D4, spike protein receptor binding domain, human angiotensin-converting enzyme 2

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