Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape

Paul-Albert Koenig; Hrishikesh Das; Hejun Liu; Beate M Kümmerer; Florian N Gohr; Lea-Marie Jenster; Lisa D J Schiffelers; Yonas M Tesfamariam; Miki Uchima; Jennifer D Wuerth; Karl Gatterdam; Natalia Ruetalo; Maria H Christensen; Caroline I Fandrey; Sabine Normann; Jan M P Tödtmann; Steffen Pritzl; Leo Hanke; Jannik Boos; Meng Yuan; Xueyong Zhu; Jonathan L Schmid-Burgk; Hiroki Kato; Michael Schindler; Ian A Wilson; Matthias Geyer; Kerstin U Ludwig; B Martin Hällberg; Nicholas C Wu; Florian I Schmidt

doi:10.1126/science.abe6230

Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape

Science. 2021 Feb 12;371(6530):eabe6230. doi: 10.1126/science.abe6230. Epub 2021 Jan 12.

Authors

Paul-Albert Koenig^{1

2}, Hrishikesh Das^#³, Hejun Liu^#⁴, Beate M Kümmerer^{5

6}, Florian N Gohr^#², Lea-Marie Jenster^#², Lisa D J Schiffelers^#², Yonas M Tesfamariam^#², Miki Uchima^#², Jennifer D Wuerth^#², Karl Gatterdam⁷, Natalia Ruetalo⁸, Maria H Christensen², Caroline I Fandrey², Sabine Normann², Jan M P Tödtmann⁹, Steffen Pritzl⁹, Leo Hanke¹⁰, Jannik Boos¹¹, Meng Yuan⁴, Xueyong Zhu⁴, Jonathan L Schmid-Burgk¹², Hiroki Kato¹³, Michael Schindler⁸, Ian A Wilson^{4

14}, Matthias Geyer⁷, Kerstin U Ludwig¹¹, B Martin Hällberg^{15

16}, Nicholas C Wu^{17

18

19}, Florian I Schmidt^{1

2}

Affiliations

¹ Core Facility Nanobodies, Medical Faculty, University of Bonn, 53127 Bonn, Germany. [email protected] [email protected] [email protected] [email protected].
² Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
³ Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
⁴ Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
⁵ Institute of Virology, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
⁶ German Centre for Infection Research (DZIF), partner site Bonn-Cologne, 53127 Bonn, Germany.
⁷ Institute of Structural Biology, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
⁸ Institute for Medical Virology and Epidemiology, Section Molecular Virology, University Hospital Tübingen, 72076 Tübingen, Germany.
⁹ Core Facility Nanobodies, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
¹⁰ Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
¹¹ Institute of Human Genetics, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
¹² Institute for Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
¹³ Institute of Cardiovascular Immunology, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
¹⁴ The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
¹⁵ Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden. [email protected] [email protected] [email protected] [email protected].
¹⁶ Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestrasse 85, 22607 Hamburg, Germany.
¹⁷ Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. [email protected] [email protected] [email protected] [email protected].
¹⁸ Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
¹⁹ Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

^# Contributed equally.

Abstract

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread, with devastating consequences. For passive immunization efforts, nanobodies have size and cost advantages over conventional antibodies. In this study, we generated four neutralizing nanobodies that target the receptor binding domain of the SARS-CoV-2 spike protein. We used x-ray crystallography and cryo-electron microscopy to define two distinct binding epitopes. On the basis of these structures, we engineered multivalent nanobodies with more than 100 times the neutralizing activity of monovalent nanobodies. Biparatopic nanobody fusions suppressed the emergence of escape mutants. Several nanobody constructs neutralized through receptor binding competition, whereas other monovalent and biparatopic nanobodies triggered aberrant activation of the spike fusion machinery. These premature conformational changes in the spike protein forestalled productive fusion and rendered the virions noninfectious.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Substitution
Angiotensin-Converting Enzyme 2 / metabolism
Animals
Antibodies, Neutralizing / chemistry
Antibodies, Neutralizing / immunology*
Antibodies, Neutralizing / metabolism
Antibodies, Viral / chemistry
Antibodies, Viral / immunology*
Antibodies, Viral / metabolism
Antibody Affinity
Antigens, Viral / immunology
Binding Sites, Antibody
COVID-19 / immunology*
COVID-19 / virology
Cell Line
Cryoelectron Microscopy
Epitopes
Humans
Membrane Fusion
Mutation
Protein Binding
Protein Conformation
Protein Domains
Receptors, Coronavirus / metabolism
SARS-CoV-2 / genetics
SARS-CoV-2 / immunology*
SARS-CoV-2 / physiology
Single-Domain Antibodies / chemistry
Single-Domain Antibodies / immunology*
Single-Domain Antibodies / metabolism
Spike Glycoprotein, Coronavirus / chemistry
Spike Glycoprotein, Coronavirus / genetics
Spike Glycoprotein, Coronavirus / immunology*
Spike Glycoprotein, Coronavirus / metabolism
Virus Replication

Substances

Antibodies, Neutralizing
Antibodies, Viral
Antigens, Viral
Epitopes
Receptors, Coronavirus
Single-Domain Antibodies
Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2
Angiotensin-Converting Enzyme 2

Abstract

Publication types

MeSH terms

Substances

Grants and funding