An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction

Leo Hanke; Laura Vidakovics Perez; Daniel J Sheward; Hrishikesh Das; Tim Schulte; Ainhoa Moliner-Morro; Martin Corcoran; Adnane Achour; Gunilla B Karlsson Hedestam; B Martin Hällberg; Ben Murrell; Gerald M McInerney

doi:10.1038/s41467-020-18174-5

An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction

Nat Commun. 2020 Sep 4;11(1):4420. doi: 10.1038/s41467-020-18174-5.

Authors

Affiliations

¹ Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
² Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
³ Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
⁴ Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden.
⁵ Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden. [email protected].
⁶ Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany. [email protected].
⁷ Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden. [email protected].
⁸ Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden. [email protected].

^# Contributed equally.

Abstract

SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the 'up' and 'down' conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.

Publication types

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

MeSH terms

Amino Acid Sequence
Angiotensin-Converting Enzyme 2
Angiotensin-Converting Enzyme Inhibitors / pharmacology*
Animals
Antibodies, Neutralizing / immunology
Antibodies, Neutralizing / pharmacology
Antibodies, Viral / chemistry
Antibodies, Viral / immunology
Betacoronavirus / drug effects*
Betacoronavirus / immunology
Betacoronavirus / metabolism
Binding Sites
COVID-19
Camelids, New World / immunology*
Chlorocebus aethiops
Coronavirus Infections / drug therapy*
Coronavirus Infections / virology
Cryoelectron Microscopy
Epitopes / immunology
Epitopes / metabolism
HEK293 Cells
Humans
Male
Models, Molecular
Pandemics
Peptidyl-Dipeptidase A / chemistry
Peptidyl-Dipeptidase A / metabolism*
Pneumonia, Viral / drug therapy*
Pneumonia, Viral / virology
Protein Binding
SARS-CoV-2
Single-Domain Antibodies / immunology
Single-Domain Antibodies / isolation & purification
Single-Domain Antibodies / pharmacology*
Spike Glycoprotein, Coronavirus / antagonists & inhibitors*
Spike Glycoprotein, Coronavirus / chemistry
Spike Glycoprotein, Coronavirus / immunology
Spike Glycoprotein, Coronavirus / metabolism
Vero Cells

Substances

Angiotensin-Converting Enzyme Inhibitors
Antibodies, Neutralizing
Antibodies, Viral
Epitopes
Single-Domain Antibodies
Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2
Peptidyl-Dipeptidase A
ACE2 protein, human
Angiotensin-Converting Enzyme 2