Chemical Probes / Classical Modulators

Chemical probes (classical modulators) are small molecule ligands targeting specific biomolecular target(s) (proteins). They allow scientists to ask mechanistic and phenotypic questions about a target in cell-based or animal studies.

Chemical probes play a major role linking a phenotype to a gene allowing the functional annotation of the human genome and validating new molecular targets. When a phenotype is observed upon treatment with the chemical probe, it is attributed to the protein targeted by the probe hence selectivity and potency, are essential attributes of chemical probes.

The Chemical Probes Team has put together a list of criteria to be used when selecting a probe for your experiment.

‘Classical’ Modulators


Evidence of target binding/activity modulation. (In-vitro IC50/Ki/Kd etc)

 Control Compounds

Similar structure with similar physicochemistry, non-binding against target)

Off-target activity

Evidence of wider in vitro profiling, especially within protein class

In-cell validation

Evidence and quantification of target engagement


• Need direct measure of target engagement (e.g. in cell binding or stabilisation) or proximal PD biomarker (e.g. specific phosphosite)

• Phenotype is target-engagement dependent (use inactive analogue as well as orthogonal probe with alternative chemotype, together with biomarker, to demonstrate target dependence)

Off-target activity in cells

• Assessment of effect on potent off-target(s) identified from in vitro profiling

• Orthogonal probe (active but different chemotype). Desirable

Evidence of cellular permeability

Demonstrable by steps above

Key References

•  Antolin AA, Workman P, Al-Lazikani B. Public resources for chemical probes: the journey so far and the road ahead. Future Med Chem. 201910.4155/fmc-2019-0231

•  Arrowsmith CH, et al. The promise and peril of chemical probes. Nat Chem Biol2015; 11, 536-541. 10.1038/nchembio.1867

•  Blagg J, Workman P. Choose and use your chemical probe wisely to explore cancer biology. Cancer Cell2017;  32, 9-25. 10.1016/j.ccell.2017.06.005

•  Bunnage ME, Chekler EL, Jones LH. Target validation using chemical probes. Nat Chem Biol. 2013; 9, 195-199. 10.1038/nchembio.1197

•  Frye SV. The art of the chemical probe. Nat Chem Biol. 2010; 6, 159-161. 10.1038/nchembio.296

•  Workman P, Collins I. Probing the probes: fitness factors for small molecule tools. Chem Biol. 2010; 17, 561-577. 10.1016/j.chembiol.2010.05.013