A Crystal Clear Approach for Designing Better Painkillers
David Clark, PhD

A Crystal Clear Approach for Designing Better Painkillers

Since its discovery by the father and son team of Henry and Lawrence Bragg early in the 20th century, X-ray diffraction has made a huge impact on numerous fields in science. So much so, that UNESCO denoted 2014 the International Year of Crystallography to mark the centenary of the discovery of the technique.

The first protein structure to be solved by X-ray crystallography was myoglobin back in 1958. Since the early 1980s, the rate at which protein structures have been deposited in the publicly accessible Protein Data Bank has increased exponentially, passing the 100,000 mark in 2014. However, some families of proteins have proved more resistant than others to solution by X-ray crystallography. This is particularly true of membrane-bound proteins such as G-protein-coupled receptors (GPCRs), a group of proteins with a vital role in transmitting signals across cell membranes. This was a source of frustration to drug designers, since GPCRs constitute a substantial fraction (30-50%) of the drug targets of interest to the pharmaceutical industry.

It wasn’t until 2007 that the first X-ray crystal structure of a therapeutically-relevant GPCR (the beta-2 adrenergic receptor, which plays a key role in asthma) was published but since then, a growing number of GPCR drug targets have been characterised crystallographically. The impact of the availability of detailed 3-D information on a particular GPCR target – the mu-opioid receptor  (MOR, shown below) – was clearly illustrated by a recent paper in Nature.

The MOR is a member of the GPCR family and is an important drug target in the development of new pain medications.  It is also the target through which well-known analgesics such as morphine and codeine exert their effects. These opiate-based drugs, although effective pain relievers, are well-known for their adverse side-effects, including constipation and potentially fatal respiratory depression.

A transatlantic team of academic researchers employed the crystal structure of the MOR (reported in 2012) in a virtual screening campaign during which more than three million commercially available chemical compounds were assessed by a computational “docking” program that measured how well they fit into the receptor’s binding site. The best 2,500 were visually assessed in the context of the binding site and just 23 of them were purchased for experimental testing.  Of those 23, seven showed binding affinities in the range of 2.3 to 14 micromolar and thus constituted a promising start.

A few of these active compounds were predicted to bind in a novel way to the MOR binding site and so these were followed up with further docking experiments and the purchase of an additional 15 analogues. The best of these had a much improved binding affinity of 42 nanomolar and this was further optimised by a small chemical change to yield a compound denoted PZM21 (chemical structure shown below), with an affinity for the MOR of 1 nanomolar.

Detailed studies of PZM21 proved it to be a novel and selective MOR ligand capable of providing long-lasting pain relief with an apparent elimination of respiratory depression. The fact that this compound was discovered by the experimental testing of fewer than 50 compounds is remarkable and clearly shows the powerful influence of the X-ray structure on the project. It is amazing to think that, just 10 years ago, such an achievement would have seemed an impossibility to most drug designers and it makes me optimistic that other challenging families of proteins, such as ion channels, will ultimately yield up their secrets to X-ray crystallography.

With new GPCR X-ray structures still being reported regularly, it seems clear that a new era of structure-enabled drug discovery for this target family is upon us bringing with it the hope of new and improved therapeutics in the foreseeable future.

How to cite:

Clark, David. A Crystal Clear Approach for Designing Better Painkillers. Eureka blog. September 7, 2016. Available: https://eureka.criver.com/a-crystal-clear-approach-for-designing-painkillers/