Enlarge /. Diagram of the structure of the spike protein of the virus.
When the COVID-19 pandemic was first recognized as a threat, researchers looked for information that could block the virus from spreading. While vaccines have received a lot of attention lately, there was also hope that we could develop a therapy that would block the virus' worst effects. Most of these came in extremely handy: identify enzymes that are essential for the virus to replicate, and test drugs that block similar enzymes from other viruses. These drugs are relatively easy to store and administer, and in some cases have been tested for safety in humans. This makes them a sensible choice for getting something up and running quickly.
However, with the tools we have developed in biotechnology, we can do some far less practical things. An article published today describes how they can be used to inactivate SARS-CoV-2. This is in no way a route to practical therapy, but it does offer a fantastic window into what we can achieve by manipulating biology.
Throw it in the trash
All of the effort described in the new article centers on one simple idea: if you figure out how to destroy any of the virus's key proteins, nothing can infect it. And conveniently, our cells have a protein destruction system, as this is often useful. In some cases the destroyed proteins are damaged; In other cases, the proteins are made and destroyed in increased increments so that the cell can respond quickly to changing conditions. In some cases, changes in the environment or activation of signaling pathways can trigger widespread protein destruction, allowing the cell to change its behavior quickly.
This system is based on a small protein called "ubiquitin". When a protein is to be specifically destroyed, enzymes called ubiquitin ligases chemically link a chain of ubiquitins to it. These act as a label that is recognized by enzymes that digest proteins with ubiquitin attached.
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So the idea behind the new work is to identify a central viral protein and find out how ubiquitin can be bound to it. The cell would then take care of the rest, digesting the viral protein, thus blocking the production of useful viruses in that cell. In this case, the researchers decided to target the spike protein found on the surface of coronaviruses, allowing them to attach to and infect new cells.
Unfortunately, there are no proteins that bind ubiquitin to the viral spike protein. Or rather, there were no proteins that matched this description.
But a team at Harvard has now produced one.
Biotechnology
The team's method began by knowing something stuck to the viral spike protein: the cellular protein it attaches to in order to get into the cell. This is known as Angiotensin Converting Enzyme 2, or ACE2, but we call it the green protein as this is the color we are using in this diagram. The idea was to find a part of this protein that sticks to the tip (also known as the red protein) and attach it to a ubiquitin-adding protein (blue). Seems simple enough.
Enlarge /. On the left the normal interactions between virus peak (red) and ACE2 (green) during the infection. Right: Use these interactions to destroy the spike protein.
John Timmer
But there is a complication: the green protein also clings to other proteins found on healthy, uninfected cells. So if you're not careful, your virus-killing enzyme will also destroy proteins that are essential to the health of uninfected cells. Which would be a pretty big oopsie.
To solve this problem, the researchers downloaded the data that showed the details of the structure of the red and green proteins at the atomic level, as well as the interaction of these proteins. (Yes, it is available.) Then they put that data into a software package that finds the most energetically preferred interactions between proteins. (Yes, they exist.) They asked the program to virtually slice the green protein and find smaller pieces that met two conditions: The pieces stuck to the red protein of the virus, but not to the one that was on the surface more healthy human cells was found.
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After identifying a specific red piece of the green protein, the researchers fused it with something attached to the blue protein that would link ubiquitin to the red protein. This hybrid would act as a bridge, connecting the viral red protein to a blue one that would attach ubiquitin to it.
Enlarge /. The plan: bring in the blue enzyme to bind ubiquitin to the spike protein, which leads to its destruction and thus blocks the production of viruses.
John Timmer
That worked, but not particularly well. The authors linked the tip (the red one) to a fluorescent protein and found that the production of their hybrid protein reduced fluorescence by about 30 percent. Better than nothing – but not great.
optimization
So how can you do better? The researchers used the software package to make mutations at every single location in their green protein fragment, and they checked what each did for their affinity for the viral spike protein. Anything that looked promising became the actual protein. One of them increased the performance significantly; Instead of reducing fluorescence by 30 percent, it has now decreased by 50 percent.
But that was not the end of their efforts. The green fragment / linker hybrid they built served as a bridge by adhering to both the red and the ubiquitin-binding blue protein. To further increase efficiency, the researchers simplified things a little by linking the blue enzyme directly to the green fragment. There is thus a direct connection between the protein to which the red clings and the blue that ensures its destruction. This reduced the amount of fluorescent spike protein present in cells by 60 percent.
An amazing application of biotechnology, isn't it? Unfortunately, it's probably also absolutely useless, and not just because we don't know if a 60 percent reduction makes sense. For this to be effective, it would have to be done by cells as they have active infections. That said, we need to insert, at least temporarily, the gene that encodes the protein they built into cells. We definitely can – it's a technology that some of the leading vaccine candidates rely on. But for a vaccine to work, no gene has to become active in so many cells. To protect an entire organ, we could.
The Conclusion: This is likely a non-starter, especially given the promising vaccines and many other potential therapies for safety testing are in the pipeline. Still, the things that make this type of technology extremely impractical for treating humans against a virus may not apply to other use cases like bacteria, plants, animals, or even less urgent medical needs. While the details of this work don't really matter, it should be borne in mind that we have developed all of the underlying technologies that are required to do this.
Communication Biology, 2020. DOI: 10.1038 / s42003-020-01470-7 (About DOIs).
