SARS-CoV-2 Neutralization by “Sybodies,” (Synthetic Nanobodies)

The key objective of COVID-19 therapeutics has been to interrupt the interaction between the SARS-CoV-2 virus spike protein and its receptor on host cells, ACE2. This is achieved by therapeutic neutralising antibodies and constitutes a potential treatment. Traditionally, however, antibody production is a somewhat slow and costly process. Now, the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies, targeting the SARS-CoV-2 spike protein receptor-binding domain (RBD), has been reported by a German group of researchers.

                             

The spike protein binds ACE2 using three finger-like protrusions, called the receptor-binding domains (RBDs), to allow the virus to hook onto the cell surface. Therefore, blocking the RBDs has the potential to stop the entry of the virus into human cells. Using antibodies, this can be done.

Due to their high stability and small size, nanobodies, tiny antibodies found in camels and llamas, are promising as tools against viruses. Although it is time-consuming to obtain them from animals, technological advances now allow synthetic nanobodies, called sybodies, to be selected quickly. Recently, in the laboratory of Markus Seeger, PhD, assistant professor at the University of Zurich, a technology platform for selecting sybodies from large synthetic libraries was developed and made available for this study.

Through the existing libraries, the laboratory of Christian Löw, PhD, group leader of EMBL Hamburg, searched for sybodies that could block SARS-CoV-2 from infecting human cells. First, to pick those sybodies that bind to them, they used the RBDs of the viral spike protein as bait. Next, the selected sybodies were tested according to their stability, efficacy, and binding precision. One of the best binders, called sybody 23, proved to be particularly effective in blocking RBDs.

The authors wrote, "Several binders with low nanomolar affinities and successful neutralisation activity have been identified, of which Sb23 showed high affinity and neutralised pseudoviruses with an IC50 of 0.6 μg / mL."

Researchers in the group of Dmitri Svergun, PhD, senior scientist at EMBL Hamburg, studied the binding of sybody 23 to the RBDs by small-angle X-ray scattering to learn exactly how sybody 23 interacts with the viral RBDs. In addition, at the Karolinska Institutet, Martin Hällberg, PhD, used cryo-EM to determine the structure of the complete SARS-CoV-2 spike bound to the sys-bound 23.

"The authors clarified that "sybody 23 binds competitively at the ACE2 binding site" was shown by the cryo-EM structure of the spike bound to sybody 23. In addition, they noted, "the cryo-EM reconstruction showed an odd conformation of the spike where two RBDs are in the 'up' ACE2-binding conformation.

The RBDs switch between two positions: the RBDs poke out in the "up" position, prepared to bind ACE2; they are furled in the "down" position to hide from the human immune system. The molecular structures showed that in both 'up' and 'down' positions, sybody 23 binds RBDs and blocks the areas where ACE2 would usually bind. This ability to block RBDs irrespective of their location may explain why Sybody 23 is so effective.

Finally, the group of Ben Murrell at Karolinska Institutet used a different virus, called a lentivirus, to test whether sybody 23 would neutralise a virus, adjusted so that it carried the spike protein of SARS-CoV-2 on its surface. They observed that the modified virus was successfully disabled in vitro by Sybody 23. Additional testing will be needed to confirm whether the SARS-CoV-2 infection in the human body can be prevented.

"In these days, the collaborative spirit was immense, and everyone was inspired to participate," said Löw. As soon as they obtained permission from EMBL management to reopen their laboratories after the COVID-19 lockdown, the researchers began the project. In just a few weeks, they managed to pick candidate sybodies and conduct the analyses.

It was only possible to get the results so quickly because the methodologies we used were already developed for other research projects unrelated to SARS-CoV-2. It would have taken considerably more time and money to build these instruments, ”said Löw.

The outcomes of this project highlight the possibility of a possible way to treat COVID-19. In future research , scientists will carry out further studies to confirm whether syringe 23 may be an effective treatment for COVID-19.