Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2

• Published in: Nature chemical biology Vol. 17; no. 1; pp. 113 - 121
• Main Authors: Bracken, Colton J., Lim, Shion A., Solomon, Paige, Rettko, Nicholas J., Nguyen, Duy P., Zha, Beth Shoshana, Schaefer, Kaitlin, Byrnes, James R., Zhou, Jie, Lui, Irene, Liu, Jia, Pance, Katarina, Zhou, Xin X., Leung, Kevin K., Wells, James A.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.01.2021; Nature Publishing Group
• Subjects: 631/154/51; 631/250/255; 631/326/596/4130; 631/45/535; 631/92/469; ACE2; Affinity; Angiotensin; Angiotensin-converting enzyme 2; Angiotensin-Converting Enzyme 2 - antagonists & inhibitors; Angiotensin-Converting Enzyme 2 - chemistry; Angiotensin-Converting Enzyme 2 - genetics; Angiotensin-Converting Enzyme 2 - immunology; Animals; Antibodies; Antibodies, Neutralizing - chemistry; Antibodies, Neutralizing - genetics; Antibodies, Neutralizing - immunology; Antibodies, Viral - chemistry; Antibodies, Viral - genetics; Antibodies, Viral - immunology; Binders; Binding sites; Binding Sites, Antibody - genetics; Binding Sites, Antibody - immunology; Biochemical Engineering; Biochemistry; Bioorganic Chemistry; Cell Biology; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Chlorocebus aethiops; COVID-19; Cryoelectron Microscopy; Epitopes; HEK293 Cells; Humans; Models, Molecular; Neutralization; Neutralizing; Peptide Library; Peptidyl-dipeptidase A; Phages; Prophylaxis; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Receptors; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Single-Chain Antibodies - chemistry; Single-Chain Antibodies - genetics; Single-Chain Antibodies - immunology; Spike Glycoprotein, Coronavirus - antagonists & inhibitors; Spike Glycoprotein, Coronavirus - chemistry; Spike Glycoprotein, Coronavirus - genetics; Spike Glycoprotein, Coronavirus - immunology; Spike protein; Vero Cells
• ISSN: 1552-4450; 1552-4469; 1552-4469
• DOI: 10.1038/s41589-020-00679-1

Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC 50 ) of 4.0 nM (180 ng ml −1 ). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy. A screening approach finds VH-domain antibodies that bind the SARS-CoV-2 Spike protein receptor-binding domain at its interface with host ACE2. Bi-paratopic and multivalent binders have high affinity and potency.