Small-molecule inhibitors guide

by Professor Stephen Taylor

A great deal of effort has been made to develop small molecule inhibitors and to make them available to the scientific community as research tools. However, with so many becoming commercially available, identifying the right tool for a particular application can be a challenge. To help researchers make an informed choice, we've pointed out a number of considerations to help you select the most appropriate inhibitors:

  • What can you learn from the scientific literature? Publications providing insight into selectivity and potency will be particularly helpful. It may be that some inhibitors are already well established as useful tools in your field. Conversely, there may be literature showing that a particular inhibitor suffers from serious disadvantages. 
  • Has the inhibitor been shown to inhibit the target in vitro? Ideally there should be a rational correlation between biochemical inhibition in vitro and effective inhibition in cells. For established inhibitors this may be known from the literature. For new and/or relatively uncharacterized inhibitors, you may need to consider running in vitro experiments alongside your cell based assays.
  • How potent is the inhibitor? Ideally you should use an inhibitor at the lowest concentration in order to minimize off-target effects. As a general rule, compounds that are effective in cells only at concentrations >10 μM should be used with caution, as these are likely to target proteins non-specifically. Ideally, cellular phenotypes should be dose-dependent, so performing experiments with a range of drug concentrations is recommended.
  • How selective is the inhibitor? While an inhibitor may be relatively selective for the protein you are trying to target, it will likely bind other “off-target” proteins. If they are known, then you may be able to design control experiments to show that they are not inhibited at the concentration used to inhibit the target. 
  • Do different inhibitors yield similar results? If you are fortunate to be in a position to test multiple inhibitors, then demonstrating that multiple molecules of a similar structure, e.g. the same scaffold but with different substituents, give similar results is very helpful. Moreover, potency in cells should correlate with in vitro potency. Even better, if a truly independent inhibitor (e.g. from a chemically distinct chemical series) gives a similar phenotype that is extremely encouraging as it is likely to have a different spectrum of off-target effects. 
  • Do you have a good negative control? Often, cells or proteins exposed only to the solvent (e.g. DMSO) act as a negative control. For well established inhibitors this may be satisfactory. For new and/or relatively uncharacterized inhibitors a closely related analog that is inactive in in vitro assays would serve as a good negative control. 
  • Do you have a good positive control? If you are reporting that a small molecule inhibitor is not having a particular effect, then you need to include a positive control to demonstrate that the drug is behaving as expected.
  • Can you rescue the phenotype? A powerful way to rule out off-target effects is to rescue the small molecule–induced phenotype by ectopic expression of a drug-resistant transgene. Though identification of drug-resistant mutants is extremely difficult, they provide ideal opportunities for delineating on and off-target effects.

Our aim is to offer the highest quality information for all our small molecule inhibitors and activators. We use published literature to deliver biological information to help you choose the right product for your system.

As with all our products, results will vary from cell type to cell type and different in vivo systems. We always recommend testing each product thoroughly for your particular system as well as consulting the literature for previous publications in your research area.


  • Weiss WA et al. Recognizing and exploiting differences between RNAi and small-molecule inhibitors. Nat Chem Biol, 3(12):739-44, 2007.
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