22 July 2015

Introducing the Chemical Probes Portal

Chemical probes can be incredibly powerful reagents for understanding biology. A potent, selective, and cell-active modulator of a specific protein can be invaluable for figuring out what that protein actually does. Fragment-based methods can be effective at identifying these tool compounds, as we've described here and here.

Unfortunately, good chemical probes are difficult to discover, and scientists are left struggling with suboptimal reagents that hit multiple targets, often through pathological mechanisms. This leads to "pollution of the scientific literature," in Jonathan Baell's memorable phrasing. Despite our occasional PAINS Shaming, high-profile articles in C&EN and Nature, and even a dedicated blog, the problem continues. What is to be done?

Yesterday, a team of 53 authors from 46 academic and industrial organizations published a Commentary in Nature Chemical Biology entitled "The promise and peril of chemical probes" (see here for excellent coverage in Nature, here for Science's take, and here for In the Pipeline). This provides a good working definition for a chemical probe. According to the Structural Genomics Consortium, a chemical probe for epigenetics targets must have:

  • Potency < 100 nM against the desired target
  • >30-fold selectivity vs related targets
  • On-target cell activity < 1 ┬ÁM

It should also be profiled against a larger panel of potential off-targets, and a related inactive compound (such as a stereoisomer) should be available as a control.

After discussing examples of high-quality probes, the researchers turn their attention to what they term – rather charitably – "probes of lesser value:"
The continued use of these probes poses a major problem: tens of thousands of publications each year use them to generate research of suspect conclusions, at great cost to the taxpayer and other funders, to scientific careers and to the reliability of the scientific literature.
The authors then go on to describe best-practices. For example, even high-quality probes can give spurious results when used at high concentrations. As Paracelsus recognized five centuries ago, the dose makes the poison.

All of this is important, but as the authors acknowledge, it's been said before. What really differentiates the Commentary is the simultaneous launch of a companion web site, the Chemical Probes Portal. Its creators hope that this will lead to vigorous community discussion around questions such as:

Is there a probe for my target protein?
Which ones should I use?
How should I use this probe properly?
Is this probe suitable for use in animal models?

Currently the Portal lists just seven probes with links to references and descriptions of selectivity, solubility, and the like. All of these are “good probes,” but hopefully this will expand: the paper itself discusses the shortcomings of molecules such as staurosporine, chaetocin, obatoclax, and gossypol, and including them in the portal with detailed warnings would be valuable for the scientific community.

I hope this takes off. Understanding the natural world is hard enough even with well-behaved reagents and carefully controlled experiments. Practical Fragments will check back in a year or so to see how the site is doing. In the meantime, probe cautiously!

1 comment:

Peter Kenny said...

Given the enthusiasm of the drug discovery community for metrics is tempting to define probe efficiency (PE) by scaling number of probes by number of authors. PE for this study is 0.13 and I’ve avoided the temptation to multiply it by RT to make the metric appear more physical.

Probe selectivity is indeed important and it’s important to remember that selectivity in physiological situations is dependent not only on Kd but also concentration (both of probe and species with which the probe has to compete). I would question why the selectivity criterion is restricted to ‘related targets’ and how ‘related’ is defined. When assessing selectivity it may be worth taking account of the number of assays in which the probe has been characterized because one is more likely to observe comparable activity in two or more assays if you run many assays. One needs to be a bit careful assessing kinase selectivity because different assays may have been run at different ATP concentrations but all see the same intracellular ATP concentration.

I think we need to be careful how we think about PAINS in the context of probe evaluation because the term seems to have a number of meanings. We have PAINS that show frequent-hitter behavior in a small panel of AlphaScreen assays (which may be taking out singlet oxygen) and we have PAINS for which cysteine reactivity has been experimentally characterized (which do not necessarily show frequent-hitter behavior). As I’ve said before, we need to make a clear distinction between what we know and what we believe.