The growing number of protein structures solved by this microscopic technique will have a major impact on drug discovery

It’s not every week that a protein structure makes the cover and editorial of prestigious weekly science journal Nature. But the issue of 5th July 2018 is an exception. Pride of place for this week is given to the structure of the human α1β2γ2 GABAA receptor.

Image of the GABAA receptor (created from PDB entry 6D6U)

 

Image of the GABAA receptor (created from PDB entry 6D6U)

There are at least two reasons why this is of significant interest. First, the protein is the target for a variety of famous (or perhaps, infamous) drugs: the closely-related benzodiazepines Valium (diazepam) and Xanax (alprazolam) to name just two.

The chemical structures of Valium (left) and Xanax (right)

It is hoped therefore that the publication of this structure will aid drug design efforts targeting this receptor to treat a variety of neurological disorders.

But, second, and for the purposes of this blog, the point of interest is that the structure of this protein was solved not by X-ray crystallography, which has been the workhorse of structural biology for decades, but by a rapidly emerging technique known as cryo-electron microscopy, or cryo-EM for short. (The “cryo” refers to the fact that the technique requires the freezing of the sample being studied – hence the title of this blog). Its importance to science can be gauged by the fact that, just last year, the Nobel Prize in Chemistry was awarded to three researchers who had devoted their research careers to advancing the technique.

Historically, the potential of cryo-EM for application in drug discovery has been severely restricted by two limitations: the minimum size of the structures it could be used to study and the resolution of the images generated.1 However, some significant technological advances in recent years have largely overcome these problems resulting in a burgeoning number of protein structures being resolved to the kind of resolution that makes them useful for drug design projects.

Cryo-EM is thus becoming a powerful complement to the more familiar X-ray crystallography2 as it can be used to determine atomic-level structures of proteins that have proven either refractory to crystallization (such as g–secretase,3 historically a target for Alzheimer’s disease therapeutics) or difficult to crystallize in specific functional states (e.g., ion channels like TRPV14, a target for potential pain treatments).

The number of cryo-EM structures deposited per year in the Protein Data Bank has grown ten-fold in the last decade – over 500 were submitted in 2017. While this is only about 5% of the number of X-ray structures submitted in the same time period, the value of cryo-EM is already becoming apparent and will surely increase in the future as more researchers become familiar with the technique and its output.

The conclusion from the recent review by Renaud and colleagues1 seems very apt: “It seems … likely that [X-ray crystallography and cryo-EM] will remain as complementary approaches for drug discovery for some time, although the boundaries that determine the method of choice have begun shifting in favour of cryo‑EM and will continue to do so.”

Further Reading:

[1] Cryo‑EM in drug discovery: achievements, limitations and prospects. Jean-Paul Renaud, Ashwin Chari, Claudio Ciferri, Wen‑ti Liu, Hervé-William Rémigy, Holger Stark and Christian Wiesmann. Nature Reviews Drug Discovery 2018, 17, 471-492. doi:10.1038/nrd.2018.77

[2] Single-Particle Cryo-EM at Crystallographic Resolution. Yifan Cheng. Cell 2015, 161, 450-457. doi: 10.1016/j.cell.2015.03.049

[3] Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity. Eva Nogales and Sjors H.W. Scheres. Molecular Cell 2015, 58, 677-689. doi: 10.1016/j.molcel.2015.02.019

[4] Cryo electron microscopy to determine the structure of macromolecular complexes. Marta Carroni and Helen R. Saibil. Methods 2016, 95, 78-85. doi: 10.1016/j.ymeth.2015.11.023

[5] Pushing the limits of computational structure-based drug design with a cryo-EM structure: The Ca²+ Channel α2δ-1 Subunit as a Test Case. Journal of Chemical Information and Modeling July 27, 2018doi: 10.1021/acs.jcim.8boo347