OK, all this cryo-electron microscopy stuff is great, new protein structures, things that are huge, that can’t be crystallized, fine, fine: but when, the medicinal chemists in the audience ask, will we be able to use it for structure-based drug discovery? This new review tries to answer just that question.
The first thing that you think about is resolution. The closer you can pin down the location of every single atom around the binding site, the better the shape you’re in for SBDD. As it stands right now, according to the authors, there are 672 structures in the EMDB archives at 4Å resolution or better. But only 75 of those are better than 3Å, and only 12 are at 2.5Å or better. And there are only five structures below 3Å with small molecule ligands in them, so there’s the state of the art. Here they are: paromomycin with the Leishmania ribosome, GSK2837808A with lactate dehydrogenase B, resiniferatoxin with TRPV1, UPCDC30245 with p97, and PETG with beta-galactosidase. And there’s only one paper (mefloquine with the Plasmodium 80S ribosome, from last year) that shows use of cryo-EM structural data to propose and test new compounds, although you’d have to think that this is happening industrially, outside the current range of open publication. But by any standards, it’s early. Very early.
The paper identifies some bottlenecks that are going to have to be widened for this technique to become a regular part of the process. Sample preparation and data collection are the first. As it is now, cryo-EM is largely a handcrafted art form, especially at the high-resolution end of things. In particular, my impression is that collecting data to get down to below 3Å resolution can really send you out on the long tail as you fill in gaps in the data set. Significant automation needs to be brought in for higher throughput (people are actively working on this), and there need to be improvements in both the processes and the hardware in order to increase the success rates at the same time.
Once you get past that, the next barrier is working up all those data points. As it stands, say the authors, the best software (while semi-automated) is far from being able to generate structures without significant human oversight and intervention. It’s another art form at this point, and it needs experienced people with good judgment at the controls. The progress of instrumentation, though, has always been to make such people less valuable and necessary for any given machine, which seems a bit perverse until you consider what short supply they’re in. Work is underway in this area as well, to try to make things as robust as X-ray data processing has become, but it’s not there yet.
The authors also emphasize a key point: making the whole process faster is not only useful, it’s essential if cryo-EM is to have the maximum impact in a drug discovery organization. There are many, many techniques out there that started out being able to provide interesting and useful information, but too slowly to have any effect on actual drug projects. Some of them picked up speed and are now able to catch the bus (as it takes off in a cloud of dust), and others haven’t, or not yet. But projects move right along (or should), and if you’re always running behind the crowd, yelling “Hold on, guys! I think I found something else!” you’re not going to be as effective as you could be.
Overall, though, rapid progress is expected. The experience of X-ray crystallography helps a great deal: we know what high-thoughput systems look like in that (related) field, so we know what to aim for and what the differences and weak points probably are. And the demand for this technique is huge: a really robust cryo-EM setup would be a huge help in drug discovery and would illuminate binding events for targets that are almost complete black boxes as things stand now. Structure-based methods are not the instant answer to all your problems, of course, but they’re still pretty damned useful, especially for the kinds of proteins that cryo-EM can target. So speed the day. Revisiting this topic in a couple of years should show some real advances.