Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice

Phillip Pymm; Amy Adair; Li-Jin Chan; James P Cooney; Francesca L Mordant; Cody C Allison; Ester Lopez; Ebene R Haycroft; Matthew T O'Neill; Li Lynn Tan; Melanie H Dietrich; Damien Drew; Marcel Doerflinger; Michael A Dengler; Nichollas E Scott; Adam K Wheatley; Nicholas A Gherardin; Hariprasad Venugopal; Deborah Cromer; Miles P Davenport; Raelene Pickering; Dale I Godfrey; Damian F J Purcell; Stephen J Kent; Amy W Chung; Kanta Subbarao; Marc Pellegrini; Alisa Glukhova; Wai-Hong Tham

doi:10.1073/pnas.2101918118

Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice

Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2101918118. doi: 10.1073/pnas.2101918118.

Authors

Phillip Pymm^{1

2}, Amy Adair¹, Li-Jin Chan^{1

2}, James P Cooney^{1

2}, Francesca L Mordant³, Cody C Allison^{1

2}, Ester Lopez³, Ebene R Haycroft³, Matthew T O'Neill¹, Li Lynn Tan¹, Melanie H Dietrich^{1

2}, Damien Drew¹, Marcel Doerflinger^{1

2}, Michael A Dengler^{1

2}, Nichollas E Scott³, Adam K Wheatley^{3

4}, Nicholas A Gherardin^{3

5}, Hariprasad Venugopal⁶, Deborah Cromer^{7

8}, Miles P Davenport⁷, Raelene Pickering⁹, Dale I Godfrey^{3

5}, Damian F J Purcell³, Stephen J Kent^{3

4}, Amy W Chung³, Kanta Subbarao^{3

10}, Marc Pellegrini^{1

2}, Alisa Glukhova^{1

11

12}, Wai-Hong Tham^{13

2}

Affiliations

¹ Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.
² Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia.
³ Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
⁴ Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia.
⁵ Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC 3010, Australia.
⁶ Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
⁷ Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia.
⁸ Department of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia.
⁹ Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia.
¹⁰ WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
¹¹ Drug Discovery Biology, Monash Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
¹² Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC 3010, Australia.
¹³ Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; [email protected].

Abstract

Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas immunized with coronavirus spike and receptor-binding domains (RBD) that disrupted RBD engagement with the human receptor angiotensin-converting enzyme 2 (ACE2) and potently neutralized SARS-CoV-2. Epitope mapping, X-ray crystallography, and cryo-electron microscopy revealed two distinct antigenic sites and showed two neutralizing nanobodies from different epitope classes bound simultaneously to the spike trimer. Nanobody-Fc fusions of the four most potent nanobodies blocked ACE2 engagement with RBD variants present in human populations and potently neutralized both wild-type SARS-CoV-2 and the N501Y D614G variant at concentrations as low as 0.1 nM. Prophylactic administration of either single nanobody-Fc or as mixtures reduced viral loads by up to 10⁴-fold in mice infected with the N501Y D614G SARS-CoV-2 virus. These results suggest a role for nanobody-Fc fusions as prophylactic agents against SARS-CoV-2.

Keywords: SARS-CoV-2; antiviral therapeutics; cryo-EM; crystallography; nanobodies.

Publication types

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

MeSH terms

Angiotensin-Converting Enzyme 2 / immunology
Animals
Antibodies, Neutralizing* / immunology
Antibodies, Neutralizing* / pharmacology
Antibodies, Viral* / immunology
Antibodies, Viral* / pharmacology
COVID-19 Drug Treatment*
COVID-19* / immunology
Camelids, New World
Humans
Mice
SARS-CoV-2 / immunology*
Single-Domain Antibodies* / immunology
Single-Domain Antibodies* / pharmacology

Substances

Antibodies, Neutralizing
Antibodies, Viral
Single-Domain Antibodies
ACE2 protein, human
Angiotensin-Converting Enzyme 2

Abstract

Publication types

MeSH terms

Substances

Grants and funding