Single-domain antibody for binding the conserved epitope in the SARS-CoV-2 spike protein receptor-binding domain

Vorobyev PO1, Tillib SV1,2
About authors

1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia

2 Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia

Correspondence should be addressed: Sergei V. Tillib
Vavilov str., 34/5, Moscow, 119334, Russia; ur.ygoloibeneg@billit moc.liamg@billit.iegres

About paper

Funding: the study was supported by the Ministry of Science and Higher Education of the Russian Federation (agreement № 075-15-2021-1086, contract № RF––193021X0015).

Acknowledgements: the authors thank M.V. Rutovskaya, Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, for assistance in immunization of the camel.

Author contribution: Vorobyev PO — molecular cloning and subsequent production of recombinant proteins (antigens for immunization); Tillib SV — developing general conception, carrying out immunization, developing the method for acquisition and primary analysis of the generated single-domain antibodies, manuscript writing.

Compliance with ethical standards: the study was approved by the Ethics Committee of the Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences (protocol № 17 of 11 February 2018); the animal was handled in strict compiance with the guidelines of the National Standard of the Russian Federation GOST R 53434–2009.

Received: 2022-12-19 Accepted: 2023-01-25 Published online: 2023-02-24

Several COVID-19 vaccines have been developed in the last three years using various tecnhiques. Multiple virus-neutralizing antibodies against SARS-CoV-2 have been also obtained to combat the pandemic. However, the use of these medications for prevention and potential treatment faces significant challenges due to the emergence of new mutant virus variants, both more contagious and escaping neutralization by the immune system, that is why it is necessary to continuously renew the vaccines and develop new therapeutic antibodies. The study was aimed to use the technology of generating single-domain antibodies (nanobodies) to target the surface spike (S) protein RBD conserved epitope of the broad spectrum of SARS-CoV-2 variants. Recombinant proteins that corresponded to RBDs of three important SARS-СoV-2 strains and the full-length S protein (Wuhan) were used as antigens for immunization of a camel in order to induce production of appropriate antibodies and/or as immobilized proteins for further cross selection of the nanobody clones with pre-set specificity by the phage display. A nanobody capable of effectively recognizing the conservative region in the S protein RBDs of the broad spectrum of pandemic SARS-CoV-2 variants, including Omicron, was selected from the generated immune library. Along with conventional use in immunoassays and diagnosis, the generated nanobody can be potentially used as a module for target-specific binding used to trap coronavirus in human upper airways during the development of novel combination antiviral drugs.

Keywords: SARS-CoV-2, nanobody, conserved epitope, single-domain antibody, virus retention


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