A group of more than 50 scientists has created a website to help biologists avoid poor-quality chemical reagents that undermine experiments in molecular biology and drug discovery.
The Chemical Probes Portal was recently created as a community-driven wiki site that recommends appropriate chemical probes for biological targets, provides guidance on their use, and documents their limitations. It also provides advice on the use of controls, such as chemically distinct probes for the same target and negative control compounds. The probes listed are reviewed by an international panel of researchers.
Although there have been many studies published reporting flaws in individual chemical tools, scientists continue to use them, biochemist Aled Edwards, head of the Structural Genomics Consortium and one of the creators of the site, told Nature News.
Edwards and dozens of co-authors describe their reasons for the creation of the portal in a commentary published in the 21 July issue of Nature Chemical Biology. They explain that although chemical probes are powerful reagents, probes of poor quality or that are used incorrectly generate misleading results.
Chemical probes are small molecules designed to bind to a specific protein and affect its function. They are valuable tools for biologists trying to find out where a protein localizes within a cell, what it interacts with, and what happens to it when cell processes are disrupted.
Nature News explains that probes, however, can often interfere with unintended proteins, and their reliability can vary by cell type or species. That can lead scientists who rely on such probes to make and publish unwarranted conclusions.
The commentary states that chemical reagents are only useful if they are potent, selective, and have a proven mechanism of action. “We now know that probes of this quality are difficult to produce and require substantial resources, commitment, and skill,” the article says. It also says that many of the chemical probes in use today were inadequately characterized and proven to be nonselective, or have activities that can interfere with features of common assays.
Edwards told Nature News that unreliable probes have led to thousands of papers with uninterpretable results as well as a failed clinical trial for breast cancer that involved more than 500 people in 2009. For example, one probe, initially described as an inhibitor of PI3 kinase, was reported more than a decade ago to have strong effects on many other proteins. Better probes for PI3 kinase exist, but nearly all chemical vendors advertise the original probe, and more than a thousand papers have been published on the outdated probe’s use since 2014.
How should the quality of a probe be verified? The commentary written by Edwards and colleagues states that, for example, probes against epigenetic targets should have in vitro potency at target protein concentrations <100 nM and have >30-fold selectivity than an industry standard selection of pharmacologically relevant off-targets. The article states that a good probe should have demonstrated on-target effects in cells at <1 μM, and have an inactive close analog of the compound to serve as a negative control.
Kip Guy, a chemical biologist at St. Jude Children’s Research Hospital, told Nature News that the database would be a helpful tool, because finding appropriate information in the scientific literature is onerous. He anticipates using the portal to design his own experiments, as well as in reviewing grants and scientific papers.
Although the portal currently only lists 7 probes, it has £50,000 (US $78,000) of seed funding from the London-based biomedical charity the Wellcome Trust, and a small group of researchers have pledged to curate and enter data on probes. The team hopes to hire someone to lead the project in the next few weeks, but will rely on community input.