Vol 9. Issue 13 / April 20, 2009

The Right Direction

By Eric Sauter

It happens sometimes. When you find what you set out to find, it turns out to be the thing you can't use. But that doesn't mean you aren't making progress. As the saying goes, you can't always get what you want, but sometimes you get what you need.

A new study, published in an advance online edition of the Journal of Biological Chemistry on March 3, 2009, illustrates the point.

Phil LoGrasso, associate professor in the Department of Molecular Therapeutics and senior director of drug discovery in the Translational Research Institute at Scripps Florida, and his colleagues have been investigating a number of compounds as potential therapeutics for Parkinson's disease, a primary interest for his drug discovery research program, as well as other diseases.

In the new study, the team set out to develop inhibitors for the enzyme JNK3 that would be selective over p38, a close relative. Both kinases are part of the mitogen-activated protein (MAP) family, which plays multiple roles in mediating signals from cytokines, growth factors, and environmental stress (such as ultra-violet radiation and oxygen deficiency).

Both JNK3 and p38 have been implicated in the inflammatory process and have generated great interest as drug targets. p38 has garnered considerable scrutiny, particularly for the treatment of rheumatoid arthritis and Crohn's disease. However, there have been fewer reports of selective JNK inhibitors, and the clinical development of JNK inhibitors lags that of p38 – an imbalance that the LoGrasso team hopes to correct.

"The essence of the study was to see if we could produce JNK3 inhibitors with greater than 1,000-fold selectivity over p38," LoGrasso said. "To do this we employed traditional medicinal chemistry principles coupled with structure-based drug design. We wanted to make sure that any inhibitors we synthesized had no significant p38 inhibition activity, as p38 inhibitors tend to be toxic."

LoGrasso and his colleagues first looked at a potent class of compounds, the indazoles – which are widely used to produce everything from perfumes to medicines – but were unable to establish significant selectivity for JNK3 over p38. In other words, the indazole-based inhibitors were potent inhibitors of both JNK3 and p38. "That's valuable information to have," said LoGrasso.

This roadblock led the scientists to the amino-pyrazole class of inhibitors, known to be active as anticancer agents; these did indeed produce compounds with greater than 2,800-fold selectivity over p38. Oddly enough, the selectivity differences between the indazole class and the amino-pyrazole class arose despite the nearly identical binding of these two compound classes to JNK3.

"It was an interesting discovery," LoGrasso said, "although we're still unclear why that might be. X-ray crystallography didn't reveal an answer, but some structure-activity relationships [a medicinal chemistry method of inserting new chemical groups into biochemical compounds to modify their activity] did give us some clues. As it turns out, the amino-pyrazole class that was selective for JNK3 has an essentially flat molecular structure. This allowed the molecules to bind to the smaller active site of JNK3 compared to the large site of p38."

But while the amino-pyrazole class showed good selectivity for JNK over p38, it turns out that they aren't very good development candidates because of the poor cell potency of this class of compounds. As a result, LoGrasso is not going to pursue the amino-pyrazoles as inhibitors in his pursuit of new drugs to treat Parkinson's disease.

"In the final analysis, they weren't what we were after," said LoGrasso.
But at least now they know where not to look.

The first author of the study, Structure Activity Relationships and X-Ray Structures Describing the Selectivity of Amino- Pyrazole Inhibitors for c-jun-N-terminal Kinase 3 (JNK3) over p38, is Ted Kamenecka of The Scripps Research Institute. Other authors include Jeff Habel, Derek Duckett, Weimin Chen, Yuan Yuan Ling, Bozena Frackowiak, Rong Jiang, Youseung Shin, and Xinyi Song of The Scripps Research Institute. The study can be viewed at http://www.jbc.org/cgi/content/abstract/M809430200v1.

This work was supported by the National Institutes of Health. Portions of the research were carried out at the Stanford Synchrotron Radiation Laboratory (SSRL), a facility operated by Stanford University and supported by the Department of Energy and the National Institutes of Health.


Send comments to: mikaono[at]scripps.edu


Associate Professor Phil LoGrasso and his team are investigating compounds as potential therapeutics for Parkinson's disease.