Biparatopic nanobodies targeting the receptor binding domain efficiently neutralize SARS-CoV-2

Phillip Pymm; Samuel J Redmond; Olan Dolezal; Francesca Mordant; Ester Lopez; James P Cooney; Kathryn C Davidson; Ebene R Haycroft; Chee Wah Tan; Rebecca Seneviratna; Samantha L Grimley; Damian F J Purcell; Stephen J Kent; Adam K Wheatley; Lin-Fa Wang; Andrew Leis; Alisa Glukhova; Marc Pellegrini; Amy W Chung; Kanta Subbarao; Adam P Uldrich; Wai-Hong Tham; Dale I Godfrey; Nicholas A Gherardin

doi:10.1016/j.isci.2022.105259

Biparatopic nanobodies targeting the receptor binding domain efficiently neutralize SARS-CoV-2

iScience. 2022 Nov 18;25(11):105259. doi: 10.1016/j.isci.2022.105259. Epub 2022 Oct 4.

Authors

Phillip Pymm^{1

2}, Samuel J Redmond³, Olan Dolezal⁴, Francesca Mordant³, Ester Lopez³, James P Cooney^{1

2}, Kathryn C Davidson^{1

2}, Ebene R Haycroft³, Chee Wah Tan⁵, Rebecca Seneviratna³, Samantha L Grimley³, Damian F J Purcell³, Stephen J Kent^{3

6}, Adam K Wheatley^{3

5}, Lin-Fa Wang⁵, Andrew Leis¹, Alisa Glukhova^{1

2

7

8}, Marc Pellegrini^{1

2}, Amy W Chung³, Kanta Subbarao³, Adam P Uldrich³, Wai-Hong Tham^{1

2}, Dale I Godfrey³, Nicholas A Gherardin³

Affiliations

¹ 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 & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, VIC 3000, Australia.
⁴ Commonwealth Scientific and Industrial Research Organisation (CSIRO) Biomedical Program, Clayton, VIC 3168, Australia.
⁵ Programme in Emerging Infectious Diseases, Duke NUS Medical School, Singapore 169857, Singapore.
⁶ Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne VIC 3010, Australia.
⁷ Drug Discovery Biology, Monash Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville 3052 VIC, Australia.
⁸ WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.

Abstract

The development of therapeutics to prevent or treat COVID-19 remains an area of intense focus. Protein biologics, including monoclonal antibodies and nanobodies that neutralize virus, have potential for the treatment of active disease. Here, we have used yeast display of a synthetic nanobody library to isolate nanobodies that bind the receptor-binding domain (RBD) of SARS-CoV-2 and neutralize the virus. We show that combining two clones with distinct binding epitopes within the RBD into a single protein construct to generate biparatopic reagents dramatically enhances their neutralizing capacity. Furthermore, the biparatopic nanobodies exhibit enhanced control over clinically relevant RBD variants that escaped recognition by the individual nanobodies. Structural analysis of biparatopic binding to spike (S) protein revealed a unique binding mode whereby the two nanobody paratopes bridge RBDs encoded by distinct S trimers. Accordingly, biparatopic nanobodies offer a way to rapidly generate powerful viral neutralizers with enhanced ability to control viral escape mutants.

Keywords: Immunology; microbiology; structural biology.