Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

Jiandong Huo; Yuguang Zhao; Jingshan Ren; Daming Zhou; Helen M E Duyvesteyn; Helen M Ginn; Loic Carrique; Tomas Malinauskas; Reinis R Ruza; Pranav N M Shah; Tiong Kit Tan; Pramila Rijal; Naomi Coombes; Kevin R Bewley; Julia A Tree; Julika Radecke; Neil G Paterson; Piyada Supasa; Juthathip Mongkolsapaya; Gavin R Screaton; Miles Carroll; Alain Townsend; Elizabeth E Fry; Raymond J Owens; David I Stuart

doi:10.1016/j.chom.2020.06.010

Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

Cell Host Microbe. 2020 Sep 9;28(3):445-454.e6. doi: 10.1016/j.chom.2020.06.010. Epub 2020 Jun 19.

Authors

Jiandong Huo¹, Yuguang Zhao², Jingshan Ren³, Daming Zhou², Helen M E Duyvesteyn², Helen M Ginn⁴, Loic Carrique², Tomas Malinauskas², Reinis R Ruza², Pranav N M Shah², Tiong Kit Tan⁵, Pramila Rijal⁶, Naomi Coombes⁷, Kevin R Bewley⁷, Julia A Tree⁷, Julika Radecke⁴, Neil G Paterson⁴, Piyada Supasa⁸, Juthathip Mongkolsapaya⁹, Gavin R Screaton⁸, Miles Carroll¹⁰, Alain Townsend⁶, Elizabeth E Fry², Raymond J Owens¹, David I Stuart¹¹

Affiliations

¹ Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK; The Rosalind Franklin Institute, Harwell Campus, OX11 0FA, UK; Protein Production UK, Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, OX11 0FA, UK.
² Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK.
³ Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK. Electronic address: ren@strubi.ox.ac.uk.
⁴ Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK.
⁵ MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.
⁶ MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK; Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7FZ, UK.
⁷ National Infection Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK.
⁸ Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
⁹ Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 73170, Thailand.
¹⁰ National Infection Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK; Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
¹¹ Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, OX4 2JY, UK. Electronic address: dave@strubi.ox.ac.uk.

Abstract

There are as yet no licensed therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2, initiating conformational changes that drive membrane fusion. We find that the monoclonal antibody CR3022 binds the RBD tightly, neutralizing SARS-CoV-2, and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilizing CR3022 epitope is inaccessible in the prefusion spike, suggesting that CR3022 binding facilitates conversion to the fusion-incompetent post-fusion state. Cryogenic electron microscopy (cryo-EM) analysis confirms that incubation of spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope could be useful therapeutically, possibly in synergy with an antibody that blocks receptor attachment.

Keywords: CR3022; SARS-CoV-2; X-ray crystallography; antibody; cryo-electron microscopy; epitope; neutralization; receptor binding domain; spike; therapeutic.

Publication types

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

MeSH terms

Allosteric Site
Amino Acid Sequence
Angiotensin-Converting Enzyme 2
Antibodies, Monoclonal / immunology
Antibodies, Neutralizing / immunology*
Antibodies, Neutralizing / therapeutic use
Antibodies, Viral / immunology*
Antibodies, Viral / therapeutic use
Antigen-Antibody Complex / chemistry
Betacoronavirus / chemistry*
Betacoronavirus / genetics
Betacoronavirus / immunology*
COVID-19
COVID-19 Drug Treatment
COVID-19 Vaccines
Coronavirus Infections / drug therapy
Coronavirus Infections / immunology
Coronavirus Infections / prevention & control
Coronavirus Infections / therapy*
Coronavirus Infections / virology
Cryoelectron Microscopy
Crystallography, X-Ray
Host Microbial Interactions / immunology
Humans
Models, Molecular
Neutralization Tests
Pandemics
Peptidyl-Dipeptidase A / chemistry
Pneumonia, Viral / immunology
Pneumonia, Viral / therapy*
Pneumonia, Viral / virology
Receptors, Virus / chemistry
SARS-CoV-2
Spike Glycoprotein, Coronavirus / chemistry*
Spike Glycoprotein, Coronavirus / genetics
Spike Glycoprotein, Coronavirus / immunology*
Viral Vaccines / immunology
Viral Vaccines / therapeutic use
Virus Internalization

Substances

Antibodies, Monoclonal
Antibodies, Neutralizing
Antibodies, Viral
Antigen-Antibody Complex
COVID-19 Vaccines
Receptors, Virus
Spike Glycoprotein, Coronavirus
Viral Vaccines
spike protein, SARS-CoV-2
Peptidyl-Dipeptidase A
ACE2 protein, human
Angiotensin-Converting Enzyme 2

Abstract

Publication types

MeSH terms

Substances

Grants and funding