An international team of researchers has identified two sugar-binding proteins that act as the “Achilles’ heel” of SARS-CoV-2 variants – point to in a promising direction towards treatment for COVID-19 in all its variations.
In a study spearheaded by LSI Director Dr. Josef Penninger and researchers at IMBA–the Institute of Molecular Biotechnology of the Austrian Academy of Sciences–the team found the sugars have therapeutic potential across COVID-19 variants. Their findings were published today in EMBO.
As the pandemic continues to surge, finding new ways to contain the spread of SARS-COV-2 remains urgent. The virus’s Spike (S) protein has been an object of intense interest among researchers working to combat the virus, as it is the primary mechanism SARS-CoV-2 uses to enter cells. The Spike targets ACE2 receptors (angiotensin converting enzyme 2) – proteins found on surface of many types of cells, and binds to this gateway to gain entry and transmit infection.
The S protein’s key role in the survival and spread of the virus indicates SARS-CoV-2 is using camouflage in order to hide from the host’s immune system–in this case, the mechanism is glycosylation–a sugar coat formed at specific sites of the Spike protein.
Spotting the wolf in sheep’s clothing
Lectins, the sugar-binding proteins came to mind as the researchers considered ways to hobble the virus. “We intuitively thought that the lectins could help us find new interaction partners of the sugar-coated Spike protein,” says co-first author David Hoffmann, a former PhD student in the Penninger lab at IMBA. Their musings proved to be spot on: the glycosylation sites of the SARS-CoV-2 Spike protein remain highly conserved among circulating variants. If they could identify the lectins that bind these glycosylation sites, the researchers would be well on their way to developing robust therapeutic interventions.
The team developed and tested a library of over 140 mammalian lectins. Among these, two were found to strongly bind to the SARS-CoV-2 S protein: Clec4g and CD209c. “We now have tools at hand that can bind the virus’ protective layer and thereby block the virus from entering cells,” summarizes Stefan Mereiter, co-first author and postdoctoral researcher in the Penninger lab. Mereiter then exclaims: “This mechanism could indeed be the Achilles’ heel scientists have been longing to find!”
The road from SARS-CoV-2’s “immunity shield” or “sheep’s clothing” to its Achilles’ heel involved several state-of-the-art research techniques. In collaboration with Peter Hinterdorfer of the Institute of Biophysics at the University of Linz, Austria, the team used high-tech biophysical methods to analyze how the lectin binding takes place in detail. For example, the researchers measured which binding forces and how many bonds occur between the lectins and the Spike protein. This also made it clear to which sugar structures Clec4g and CD209c attach.
Therapeutic interventions on the horizon
The team also found that the two lectins bind to the N-glycan site N343 of the Spike protein. This specific site is so crucial to the Spike that it will persist in any infectious variant. Deletion of this glycosylation site actually renders the Spike protein unstable. Other groups have also shown that viruses with mutated N343 were non-infectious. “This means, that our lectins bind to a glycan site that is essential for Spike function – it is therefore very unlikely that a mutant could ever arise that lacks this glycan,” explains Mereiter.
The two lectins also decreased SARS-CoV-2 infectivity of human lung cells, an exciting discovery for the team, as these findings hold promise for pan-variant therapeutic interventions against SARS-CoV-2. “The approach compares to the mechanism of the drug candidate ‘APN01’ (Apeiron Biologics), which is undergoing advanced clinical trials,” says Dr. Penninger. “This is a bioengineered human ACE2 that also binds to the Spike protein. When the Spike protein is occupied by the drug, the gateway into the cell is blocked. Now, we identified naturally occurring, mammalian lectins that are capable of doing just that!”
The production of the recombinant SARS-CoV-2 Spike protein under controlled conditions was carried out at the Institute of Biochemistry of the University of Natural Resources and Life Sciences (BOKU), Vienna and coordinated by Prof. Lukas Mach as part of the BOKU Covid initiative. This production respected the precise localization of the conserved sugar chain that allow endogenous lectins to attach the virus. This highly specialized form of glycoprotein analysis has been the research focus of Friedrich Altmann’s group at BOKU for decades.
“Although the analysis of the spike glycoprotein is already quite a considerable challenge under normal conditions, it was only possible to perform the necessary measurements in these special times of home-office, distance-learning and hard lock-downs due to the great teamwork of everyone. I would like to express my sincere thanks to all the people involved,” says BOKU group leader Johannes Stadlmann.
This work involved an international team of researchers including: Ali Mirazimi at Karolinska Institutet in Stockholm, Sweden, and Austrian researchers Johannes Stadlmann, Chris Oostenbrink, Lukas Mach and Friedrich Altmann at BOKU, and Peter Hinterdorfer at the Johannes Kepler University Linz, as well as Gerald Wirnsberger at Apeiron Biologics, Vienna.
Read the paper
Hoffmann D., Mereiter, S. et al., “Identification of lectin receptors for conserved SARS-CoV-2 glycosylation sites”, EMBO J, 2021. DOI: 10.15252/embj.2021108375
©IMP/IMBA Graphics 2021. The protein and glycan structures were provided by Chris Oostenbrink (BOKU).