Research groups from the European Molecular Biology Laboratory (EMBL) identify synthetic nanobodies that could inhibit SARS-CoV-2 from infecting human cells.
The ability of SARS-CoV-2 to infect cells depends on interactions between the viral spike protein and the human cell surface protein, angiotensin-converting enzyme 2 (ACE2). For the virus to attach to the cell surface, the spike protein binds ACE2 using three finger-like protrusions, called the receptor binding domains (RBDs). Blocking the RBDs could potential stop the virus from entering human cells.
Nanobodies, small antibodies found in camels and llamas, are promising as tools against viruses due to their high stability and small size. Although obtaining them from animals is time consuming, technological advances now allow for rapid selection of synthetic nanobodies, called sybodies. A technology platform to select sybodies from large synthetic libraries was recently developed in the lab of Markus Seeger at the University of Zurich, and made available for this study.
EMBL Hamburg’s Christian Löw group searched through the existing libraries to find sybodies that could block SARS-CoV-2 from infecting human cells. First, they used the viral spike protein’s RBDs as the marker to select sybodies that bind to them. Next, they tested the selected sybodies according to their stability, effectiveness, and the precision of binding. Out of the sybodies that could bind sybody 23 turned out to be particularly effective in blocking RBDs.
Researchers of the Dmitri Svergun group at EMBL Hamburg analysed the binding of sybody 23 to the RBDs by small-angle X-ray scattering, to understand the mechanism behind sybody 23 and the viral RBDs, In addition, Martin Hällberg at CSSB and Karolinska Institutet used cryo-electron microscopy to determine the structure of the full SARS-CoV-2 spike bound to sybody 23.
The RBDs switch between two positions; one to bind to ACE2 and another to hide from the immune system. The molecular structures revealed that sybody 23 binds RBDs in both positions, and blocks the areas where ACE2 would normally bind. This ability to block RBDs regardless of their position might explain why sybody 23 is so effective.
Finally, to test if sybody 23 can neutralise a virus, Ben Murrell research group at Karolinska Institutet used a different virus, called a lentivirus, and was modified such that it carried SARS-CoV-2 spike proteins on its surface. They observed that sybody 23 successfully disabled the modified virus in vitro. Additional tests will be necessary to confirm whether this sybody could stop SARS-CoV-2 infection in the human body.
The researchers started the project as soon as they received approval from EMBL leadership to reopen their laboratories during the COVID-19 lockdown. They managed to select the candidate sybodies and perform the analyses in just a few weeks.
“Getting the results so quickly was only possible because the methodologies we used had already been established for other research projects unrelated to SARS-CoV-2. Developing these tools would have taken significantly more time and resources,” said Christian Löw, one of the lead scientists in the study.
The results of this project provide a potential way to treat COVID-19 using synthetic nanobodies. In addition to this study, the scientists will perform further analyses to confirm whether sybody 23 could be an effective COVID-19 treatment. [APBN]