The coronavirus genome consists of a single stranded mRNA with a special sequence called s2m. S2m folds into a complex and highly conserved structure which suggests it is vital to the virus’s function. S2m’s exact role is still a mystery, but its supposed functional importance makes it a promising target for antiviral drugs that can work as treatments against coronavirus! Many groups are working on a structural analysis of coronavirus since it will help provide the foundation for developing COVID-19 antiviral drugs. The Scott Lab at UCSC has resolved a crystal structure of the s2m component of COVID-19, which turns out to be almost identical to the s2m component found on the SARS virus.

Crystal Structure of the S2M component of the Coronavirus genome. (pdb: 1xjr)

The first thing that struck me about this structure is its complexity. At first glance, I see some disruptions in the helix, such as in the lower left corner and near the core of the RNA, which is suggestive of a potential binding site. That is, a binding site for a killer antiviral drug! A straightforward way of testing whether a structure is capable of binding drugs is by scanning it for deep cavities or pockets. You can find pockets on structures such as DNA, protein and RNA by running it through pocket finding software. In my quick and scrappy exploratory analysis of COVID-19’s RNA component, I am choosing to run it through fpocket. Fpocket is an open source geometric pocket finding approach that simply fills deep cavities on a structure with spheres, indicating that it found a potentially targetable pocket.

Structural analysis with pocket finding software!

The pocket finding software was able to detect three separate pockets (represented by the white, blue and green spheres) on the coronavirus genome

The image above shows the same coronavirus s2m structure with its surface component visualized. Showing the surface gives us a better idea of where these pockets are located. I ran this structure through the pocket finding software and it returned three separate pockets on the structure. The pockets are represented as little spheres. They are color-coded depending on how “pocket-like” they are. For instance, the software ranked the white pocket as the most pocket-like, and worth most of our attention. The blue pocket is ranked the second most pocket-like, and the green pocket is considered the least pocket like.

So what is a “good” pocket anyway?

A pocket is not just any ole hole that you find in a structure. There are some rules associated with picking a good pocket, and pocket finding software does not always follow them. Here are some basic guidelines for discerning ideal pockets:

The pocket should be of large size. Not necessarily huge, but it needs to have enough space to be able to hold a drug-like molecule. Cup your hands together. Now imagine roughly that space and size but on an RNA such as the section of the COVID-19 genome we are looking at now. That’s about the size of an ideal pocket. The pocket should be deep so that it forms a cave, but not too buried where a drug couldn’t find its way into it. This is kind of like a Goldilocks situation. It can’t be too exposed, but it needs to be slightly exposed to allow entry. The pocket should be found on a structurally secure area of the RNA. So one thing that is important to know about RNA is that they are pretty floppy. In the images I have shown you here they seem stiff, but they actually are constantly moving. Imagine I took a picture of someone’s long hair flowing in the wind. In the picture, it might look sturdy, even to the point where it can support small objects. However, we know this is just a snapshot and hair is actually really flexible. This same principle applies to RNA. There are some parts of it that are extremely floppy, and won’t reliably keep its pocket-like shape despite what our snapshot tells us.

Let’s see how much we agree with the software’s ranking of these pockets.

Close-up of pocket 1

Here is a close-up of pocket 1. I can immediately see why the software ranked this pocket as the best on the structure. Geometric pocket finding software tend to prioritize larger pockets, and this pocket is the largest of the three. However, the actual cavity is too solvent accessible, or too exposed! Ideal pockets tend to be deep and buried so that small molecules or drugs can bind inside them and not worry about flying out. In addition, I don’t trust the structural integrity of this pocket. When I look at this pocket in the context of the entire of the RNA, I can tell this helical region is probably very flexible. My opinion is that this is not a feasible binding site for an antiviral drug.

Close-up of pocket 2

Above is a close-up of pocket 2. Now this is much better! This pocket is located in a deep cavity, it is not too exposed, and it has a decently large size. The pocket also appears to be in a structurally secure region of the RNA. I don’t think it’s very mobile. We got ourselves a winner!

Close-up of pocket 3

Finally, here is a close-up of pocket 3. Now I agree with the pocket finding software that this pocket is not the best. Even though it seems to be in an inflexible region of the RNA, it is small and really exposed. I don’t think an antiviral drug will feel very cozy in this pocket.

We just looked at three potential binding sites for an antiviral drug via a structural analysis of coronavirus!

To us, this virus is an invisible menace that has disrupted our everyday life. After looking at the structure of the s2m segment of the coronavirus genome, I dare say that coronavirus’s potential weak spot, pocket 2, is worth some consideration.

There are teams around the world analyzing the coronavirus structure, and finding innovative ways to treat and prevent the spread of this virus. For those not involved in research or healthcare, remember that we all play a role in fighting this together! Make sure to wash your hands, practice social distancing, avoid touching your face, be kind to others, and please stop buying all the toilet paper!

For a follow up analysis on binding a drug to pocket two, here’s a link to part 2 of this post!

For more information about targeting viral genomes with small molecules, check out this paper.