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

doi:10.1016/j.chempr.2022.07.012

Chem

Volume 8, Issue 10, 13 October 2022, Pages 2766-2783

https://doi.org/10.1016/j.chempr.2022.07.012 Get rights and content

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Highlights

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Bioreactive Uaa FFY exhibits faster cross-linking kinetics than its predecessor, FSY
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FFY enables nanobodies to bind with SARS-CoV-2 spike covalently and irreversibly
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FFY incorporation drastically increases nanobodies’ potency in viral neutralization
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FSY-engineered human ACE2 receptor binds to SARS-CoV-2 spike covalently

The bigger picture

The long-lasting COVID-19 pandemic and increasing SARS-CoV-2 variants demand effective therapeutic strategies. Herein, we have engineered unique unnatural amino acids into proteins and developed covalent nanobodies capable of irreversibly binding with the viral spike protein. These covalent nanobodies are able to neutralize both SARS-CoV-2 and its different variants with drastic higher potency than traditional nanobodies, affording a potential prophylactic and medication for COVID-19. In addition, our strategy could provide an original general route to developing effective therapeutics for various other viral infections, such as influenza, hepatitis, AIDS, and anthrax.

Summary

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.

Graphical abstract

Keywords

covalent protein drug

SARS-CoV-2

genetic code expansion

latent bioreactive unnatural amino acid

proximity-enabled reactivity

sulfur fluoride exchange (SuFEx) click chemistry

spike-ACE2 interaction

COVID-19

nanobody

infectious disease

UN Sustainable Development Goals

SDG3: Good health and well-being

Data and code availability

All data supporting this study are available within the main article and supplemental information. This study did not generate any datasets or original code.

Cited by (0)

⁴: These authors contributed equally

⁵: Lead contact