Director's Blog - 31 March 2020 - Bio21 'doing our bit' for SARS-CoV-2 research

Dear Bio21 Community Members,

As a scientific community that includes academic and industry members, as well as platform technology facilities run by expert teams, we are in unique position to make a valuable contribution to our society and world during the coronavirus Covid-19 pandemic. As problems solvers our work can provide hope and purpose.

Therefore, I’d like to share with you some of the projects, proposals and collaborations that are taking place within the Bio21 community to support the scientific effort towards combatting the SARS-CoV-2 coronavirus.

As you may be aware, even though our Institute has for all intents and purposes moved to a ‘virtual institute’, our platforms remain on standby and are under routine maintenance. They are ready to spring to action for any COVID-19 research.

In our Advanced Microscopy Facility, Eric Hanssen and Andrew Leis, in collaboration with the Doherty Institute’s Julian Druce and Mike Catton, Director, Melbourne Health, used Bio21’s Transmission Electron Microscopes (L120 (120 kV) and TECMAI F30 (300 kV)) to obtain some of the first images of the isolated and cultured coronavirus. These microscopes make it possible to obtain 3D images of the virus, as the sample is rotated. What did they see?

“It looks like a coronavirus; it has the same phenotype as all viruses in the coronavirus family,” confirmed Eric Hanssen. “Basically, it’s a sphere with spikes on it. It is about 100 nm in size.” Images also reveal coronavirus particles inside the vacuoles of cultured cells. The work was published in the Medical Journal of Australia. These first images were valuable in identifying the type of virus. Higher resolution is needed to reveal the unique structural components of the spikes to help guide drug and vaccine design.

Once Eric and Andrew receive the whole (inactivated) virus samples from the Doherty Institute, it will be possible to use Bio21’s CryoEM microscopes to obtain images of the fine structure, potentially at atomic resolution. Our facility is ready to image these samples, once it is deemed safe to do so. It is incredible to have these powerful tools at our disposal to study the virus and globally Bio21 will part of the effort to obtain images of the virus. “Every cryoEM facility around the world is poised to look at coronavirus,” says Eric, with a hint of competitive spirit. Once the images are obtained, our scientists, such as the Rouiller group, would relish the opportunity to investigate the fine structures that make up the virus’ spike.

One exciting aspect of this work is that we are collaborating with the Walter and Eliza Hall Institute as part of a Bio21/Doherty/WEHI/Monash/Australian Animal Health Laboratories (AAHL) consortium and they are keen on developing ‘nanobodies’. The WEHI nanobodies will be obtained from llamas injected with antigens from the virus spike. So, down the track there might be a possibility of imaging whole virus particles interacting with potential therapeutic nanobodies and monoclonal antibodies (Mabs).

Determining the structure of the coronavirus is the first step for structure-based drug discovery. Our expertise in structural biology is key and already Bio21 teams, including my own, are focussed on the task. Craig Morton, together with Tracy Nero, has literally millions of structures of compounds in a vast library that he has collated from publicly available and commercial sources, as well as through collaborators, to start to virtual screen for a ‘good fit’ with the coronavirus protein structures. In particular, it is the proteins the virus needs to infect cells, replicate itself, or to complete its lifecycle, that could be targeted for drug design.

Craig explains: “The first two SARS-COV2 protein structures that became available, are the viral protease (PDB code 6LU7) and the spike protein (6VSB). The protease is an essential part of the viral life cycle – the virus genome gets translated into one enormous long protein that then gets chopped at specific sites by the protease, producing the individual proteins the virus needs. The spike protein is the cellular invasion tool; it recognises receptors on the surface of target cells (the human ACE2 protein) and binds to it, then fuses the viral membrane to the cellular membrane allowing the contents of the virus to enter the cell.”

“In other viral diseases targeting these activities – proteolytic processing of the polyprotein and receptor recognition / membrane fusion – have been proven to be effective as an antiviral therapy. I’m trying to identify small molecules that are able to bind to these SARS-COV2 proteins as potential starting points for a drug discovery campaign. There are also current protease inhibitors known to have an effect on the SARS-COV2 protease (at least in an in vitro assay) that I am looking at to see if they can be optimised to become more effective inhibitors.”

But, how to find the perfect fit? Craig uses the ‘FRED’ - Fast Exhaustive Docking Virtual Screening tool, to sift through his library. Craig selects the known target protein, e.g. the viral protease crystal structure, and then, like trying to find the connecting pieces in a 1000-piece puzzle, the program starts rapidly pairing compound structures to these proteins, one after another. It then ranks the top 1000 compounds for their binding affinity.

Craig is confident that we can solve this. How long will it take? If an existing, approved and commercially available drug is found that binds to the coronavirus covid-19 structures, a drug could become available straight away. However, developing a novel compound can take at least 18 months.

Two kinds of drugs that have been mentioned in the media are the anti-malarials Chloroquine and Hydroxychloroquine and the anti-viral drug used against Ebola, Remdesivir, produced by Gilead. Trials and testing are now needed to provide evidence of their efficacy against coronavirus.

Bio21’s Tilley lab has over 20 years expertise in studies of chloroquine as an antimalarial agent, including studies of the effect of chloroquine on cellular physiology. “This experience could underpin efforts to understand how chloroquine makes human cells inhospitable to infection by the coronavirus,” Leann says. We wish her well in her proposal.

These are just a few examples of how Bio21 is doing its bit to combat COVID-19. I am aware of many other ideas and projects including cell trafficking approaches from the McConville and Gleeson labs, computational biology approaches from the Ascher group, and an industry collaboration with the Rouiller lab. And our industry tenants are contributing with Circa, SYNthesis and CSL offering expertise and reagents. I would be delighted to hear of more examples and pass them by the Doherty expert panels.

With the academic and industry synthetic chemistry groups in our community, members of our community may also be involved in helping to synthesise novel antivirals.

Other contributions and approaches may include modulating the immune system’s response to the virus, developing rapid diagnostic kits and of course we are all holding out for a vaccine. The evidence that the coronavirus is relatively stable, is encouraging news for vaccine design.

So, in this time of the coronavirus crisis, our people in academia and industry, our powerful instruments and our expertise in structural biology are urgently called for. We are doing our bit and there is no time to waste! Bio21 may be virtual but its heart still beats with high priority research continuing.

Regards

Michael Parker