What is a chemical probe? A chemical probe is simply a reagent—a selective small-molecule modulator of a protein’s function—that allows the user to ask mechanistic and phenotypic questions about its molecular target in cell-based or animal studies. Importantly, a chemical probe is not a key that interacts with only one lock (the protein target) in a cell no matter what concentration it is applied. It is a molecule that is governed by the same rules of chemistry as any other; therefore, experiments using chemical probes must be designed and interpreted with care.

Potency and selectivity are two key properties to consider when designing an experiment with a chemical probe. Potency refers to the amount of chemical probe a researcher needs to add to a system (e.g., cultured cells) to see an impact on the protein of interest. The more potent the chemical probe, the less of it a researcher needs to use. Using less is desirable in any system. Remember Avagadro’s number? Every mol of probe a scientist adds to an experimental system contains 6.02 x 1023 molecules of that probe. With that many molecules running around, some of them are bound to interact with proteins in addition to the one of interest; thus, using the smallest amount possible will minimize the number of molecules available to interact with unexpected proteins. Selectivity, which refers to the amount of chemical probe a researcher can use to perturb the protein of interest without also perturbing related proteins, is also important. Together, data about the potency and selectivity of a probe helps a researcher define the upper and lower concentration limits where a probe can be applied with confidence that it will impact the intended protein target and a limited number of off-target proteins.

When applying chemical probes in experiments, context always matters. Chemical probes are typically validated for use as specific modulators of a protein target in a small number of cell lines. To apply a chemical probe – even a well validated one – in a new system for the first time, it is important to remember that the protein of interest may be expressed at different concentrations in the new system compared with the original: indeed, it may not be expressed at all. Likewise, other off-target proteins may also be expressed at different levels in the new system. Thus, it is critical to establish that the recommended concentration range for a probe is applicable to the new system.

We have created the portal to help scientists sift through the massive amount of data available about chemical probes. We hope to help scientists who are not experts in chemistry determine which probe is best for them to use and how to apply that probe in a manner that yields robust and reproducible data. To help us achieve these goals, we have enlisted a panel of chemical probe experts to make recommendations about chemical probes and how to use them.

Importantly, our probe evaluations will focus only on this goal. There are many examples of pan-active or nonspecific probes that we will not be recommending scientists use in this context. This does not mean we do not recognize that these molecules may still have value. Indeed, there are many examples in the literature where scientists have used nonspecific chemical tools to reveal new biology, and even where scientists have used probes at much higher concentrations than the ones we will recommend because it allows them to discover new biology. We applaud these efforts and enjoy seeing scientists pursue creative ways of applying chemical tools to discover new biology.

The literature, however, is rife with publications where a chemical probe is applied to interrogate a specific target protein, and the chemical probe of choice is either not specific for that protein or is applied at excessive concentrations, rendering it a nonspecific agent. The portal is here to help address this problem. We aim to make the portal a helpful community resource that helps us remember that while chemical probes can be powerful tools, they are not magic bullets. We hope you will join our community. Please come back and visit the portal after our relaunch on Jun 30, 2016. We look forward to learning more about chemical probes with you!

No magic bullets