Accelerating PERx reaction enables covalent nanobodies for potent neutralization of SARS-CoV-2 and variants

Chem. 2022 Oct 13;8(10):2766-2783. doi: 10.1016/j.chempr.2022.07.012. Epub 2022 Jul 18.


The long-lasting COVID-19 pandemic and increasing SARS-CoV-2 variants demand effective drugs for prophylactics and treatment. Protein-based biologics offer high specificity, yet their noncovalent interactions often lead to drug dissociation and incomplete inhibition. Here, we have developed covalent nanobodies capable of binding with SARS-CoV-2 irreversibly via a proximity-enabled reactive therapeutic (PERx) mechanism. A latent bioreactive amino acid (FFY) was designed and genetically encoded into nanobodies to accelerate the PERx reaction rate. Compared with the noncovalent wild-type nanobody, the FFY-incorporated covalent nanobodies neutralized both wild-type SARS-CoV-2 and its Alpha, Delta, Epsilon, Lambda, and Omicron variants with drastically higher potency. This PERx-enabled covalent-nanobody strategy and the related insights into increased potency can be valuable to developing effective therapeutics for various viral infections.

Keywords: COVID-19; SARS-CoV-2; covalent protein drug; genetic code expansion; infectious disease; latent bioreactive unnatural amino acid; nanobody; proximity-enabled reactivity; spike-ACE2 interaction; sulfur fluoride exchange (SuFEx) click chemistry.