A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo

Leo Hanke,Ainhoa Moliner-Morro,Laura Perez Vidakovics,Vivien Karl,Gerald M Mcinerney,B Martin Hällberg,Ben Murrell,Changil Kim,Hrishikesh Das,Bartlomiej Porebski,Jonathan M Coquet,Egon Urgard,Natalie L Smith,Daniel J Sheward,Alec Pankow,Gabriel K Pedersen,Erdinc Sezgin,Oscar Fernandez-Capetillo

doi:10.1038/s41467-021-27610-z

Abstract

Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer–dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.

Highlights

Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape
The emergence of new virus variants that evade antibody-mediated neutralization mandates the identification of molecules with a more diverse set of binding epitopes and neutralization mechanisms allowing for neutralization of a variety of virus variants
Using a pseudotyped lentivirus (PSV) neutralization assay (Fig. 1b), we found that Fu2 was ~10 times more potent than Ty1, with an IC50 in the range of 106 ng/ml (7 nM)

Summary

Introduction

Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. We describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer–dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. This resulted in earlier elution, and besides a possible spike dimer, this construct gave rise to an even earlier elution peak suggesting the induction of higher-order spike multimers

Methods

Results

Conclusion