A slightly crazy idea to deactivate the coronavirus

When the COVID-19 pandemic was first recognized for the threat it poses, researchers scrambled to find anything that could block the spread of the virus. While vaccines have gained much of the attention lately, there was also hope that we could develop a therapy that would block the worst effects of the virus. Most of them have been extremely handy: identifying enzymes essential for virus replication and testing drugs that block similar enzymes from other viruses. These drugs are designed to be relatively easy to store and administer, and in some cases have already been tested for safety in humans, making them reasonable choices for quickly preparing something for use.

But the tools we have developed in biotechnology allow us to do much less practical things and an article published today describes how they can be used to inactivate SARS-CoV-2. This is by no means a route to practical therapy, but it does provide a fantastic window into what we can accomplish by manipulating biology.

Throw it in the trash

The whole effort described in the new article focuses on one simple idea: If you figure out how to destroy one of the virus’s key proteins, it won’t be able to infect anything. And, conveniently, our cells have a system for destroying proteins, because that is often a useful thing to do. In some cases, the destroyed proteins are damaged; in others, proteins are made and destroyed at high rates to allow the cell to respond quickly to changing conditions. In a few cases, changes in the environment or the activation of signaling pathways can trigger widespread protein destruction, allowing the cell to rapidly change its behavior.

This system is based on a small protein called “ubiquitin”. When a protein must be targeted for destruction, enzymes called ubiquitin ligases chemically bind a chain of ubiquitins to it. These serve as a label recognized by the enzymes that digest all the proteins to which ubiquitin is attached.

So, the idea behind the new work is to identify a key viral protein and figure out how to attach ubiquitin to it. The cell would then take care of the rest, digesting the viral protein and thus blocking the production of any useful virus in that cell. In this case, the researchers decided to target the spike protein that is found on the surface of coronaviruses and allows them to attach and infect new cells.

Unfortunately, there are no proteins that bind ubiquitin to the viral spike protein. Or rather, no protein matched this description.

But a Harvard team has now produced one.

Bioengineering

The team’s method of doing this began with the fact that we know something that sticks to the viral spike protein: the cellular protein that it locks onto to enter the cell. It’s called angiotensin-converting enzyme 2, or ACE2, but we’ll call it green protein because that’s the color we’re using in this diagram. The idea was to find a part of this protein that sticks to the peak (aka the red protein) and bind it to a protein adding ubiquitin (in blue). It sounds pretty straightforward.

But there is a complication: the green protein also adheres to other proteins found on healthy, uninfected cells. So if you’re not careful, your virus-destroying enzyme will also end up destroying proteins essential for the health of uninfected cells. Which would be a pretty big “oopsy”.

To solve this problem, the researchers uploaded data that showed the atomic-level details of the structure of red and green proteins, as well as how these proteins interact. (Yes, it’s available.) Then they transferred that data into a software package that found the most energetically favored interactions between proteins. (Yes, those do exist.) They asked the program to virtually slice up the green protein and find smaller pieces that met two conditions: the pieces stuck to the red protein of the virus but not the one found on the surface of the virus. healthy human cells. .

With a red-specific piece of the green protein identified, the researchers fused it to something that stuck to the blue protein, which would bind ubiquitin to the red protein. This hybrid would act as a bridge, connecting the red viral protein to a blue protein which would attach ubiquitin to it.

It worked, but not particularly well. The authors linked the peak (the red one) to a fluorescent protein and found that the production of their hybrid protein reduced fluorescence by about 30%. Better than nothing, but not great.

Optimization

So how do you improve it? The researchers used the software package to make mutations at each location of their green protein fragment, and they verified what each did for its affinity for the viral spike protein. Anything that looked promising, they put it into the actual protein. One of them significantly improved performance; now, instead of reducing the fluorescence by 30%, it has dropped by 50%.

But that was not the end of their efforts. The green fragment / linker hybrid they constructed served as a bridge by sticking to both the red protein and the blue ubiquitin-binding protein. To further increase efficiency, the researchers simplified things a bit by directly connecting the blue enzyme to the green fragment. With this in place, there is a direct link between the protein that the red protein adheres to and the blue protein that ensures its destruction. This reduced the amount of fluorescent spike protein in cells by 60%.

So, an amazing application of biotechnology, right? Sadly, it’s also likely that this is absolutely unnecessary, and not just because we don’t know if a 60% reduction is significant. For this to be effective, cells would have to make it because they have active infections. Which means we have to insert the gene that encodes the protein they have built into the cells, at least temporarily. We can certainly do it – it’s a technology behind some of the leading vaccine candidates. But for a vaccine to work, we don’t need a gene that is active in so many cells. To protect an entire organ, we could do it.

Bottom line: It will likely be a non-starter, especially as promising vaccines and many other potential therapies are in the works for safety testing. Yet the things that make this type of technology extremely impractical for treating humans against a virus may not apply to other use cases such as bacteria, crops, animals, or even less urgent medical needs. . So while the details of this work aren’t really meaningful, the fact that we’ve developed all of the underlying technology needed for it is worth keeping in mind.

Communications Biology, 2020. DOI: 10.1038 / s42003-020-01470-7 (About DOIs).