CICR General Resources
A chemical probe refers to a chemical tool, generally a small molecule, which has utility in interrogating and advancing the understanding of biological systems. The use of these probes can strongly benefit cancer research. However, it is critical that researchers use probes wisely, meaning that the right probe should be applied in the right setting.
The following is a brief guide for the research community to improve the use, discovery, and development of chemical probes in cancer research. Since these probes can have a direct impact on our understanding of biological systems, we hope that this information will improve the quality and integrity of chemistry in all aspects of cancer research. In addition to providing guidance to researchers themselves, we believe that the information provided here may serve as a useful reference to reviewers of literature to ensure that the highest standards are met when small molecules are used as tools in cancer research. Use the links below for more information.
There are a number of resources that describe specific chemical probes and the criteria for their quality as probes. Not only is the activity and selectivity profile of these compounds given, but also negative controls and in vivo activities. A number of these organizations will even provide these probes to researchers. Examples are given below:
- Chemical Probes.org.This site recommends appropriate chemical probes for biological targets, using a wiki-like community of experts.
- The Cancer Therapeutics Response Portal links genetic, lineage, and other cellular features of cancer cell lines to small-molecule probe response.
- Structural Genomics Consortium (SGC). The SGC has developed more than 30 probes, all targeting epigenetic targets. The probe criteria are published and these probes are provided to the research community.
- Boehringer Ingelheim has made a number of their internally-developed chemical probes available to the public. Access it here.
Relevant Review Articles
- Wu Q, et. al. (2019). A chemical toolbox for the study of bromodomains and epigenetic signaling. Nat Commun. 2019 Apr 23;10(1):1915.
- Scheer, S. et. al. (2018). A Chemical Biology Toolbox for the Study of Protein Methyltransferases and Epigenetic Signaling. BioRxiv (Cold Spring Harbor Laboratory), 1-27.
- Workman, P., & Collins, I. (2010).
Probing the probes: Fitness factors for small molecule tools.
Chemistry and Biology, 17(6), 561-577.
- Schreiber, S. L. et. al. (2015).
Advancing biological understanding and therapeutics discovery with small-molecule probes.
Cell, 161, 1252-1265.
- Arrowsmith, C. H.; et. al. (2015). The promise and peril of chemical probes.
Nature Chemical Biology, 11, 536-541.
- Blagg, Julian and Workman, Paul (2017). Choose and Use Your Chemical Probe Wisely to Explore Cancer Biology. Cancer Cell, 32, 9-25.
- Scheer, S. et. al. (2019). A chemical biology toolbox to study proteinmethyl transferases and epigenetic signaling. Nature Comm, 10: 19, 14.
Some Recent Probe Publications
- Xie, X.C. et. al. (2019) A chemical probe of CARM1 alters epigenetic plasticity against breast cancer cell invasion. Elife. 2019 Oct 28;8.
- Böttcher J. et. al. (2019). Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3. Nat Chem Biol. 2019 Aug;15(8):822-829.
- Bonday ZQ. et. al. (2019). LLY-283, a Potent and Selective Inhibitor of Arginine Methyltransferase 5, PRMT5, with Antitumor Activity. ACS Med Chem Lett. 2018 Apr 23;9(7):612-617
Chemical Probe Profiling Resources
Researchers often face challenges in determining how a compound’s cellular activity is related to a biochemical target. Below is a list of vendors and services to help investigators determine whether a particular compound will exhibit target engagement in cells or is selective against a target of interest. It should be noted that these resources are representative and not intended to be comprehensive of the types of services available to the cancer research community. It should also be stressed that the CICR does not endorse using these over alternative services.
- DiscoverRx. A commercial company that runs panel screening across large target families, particularly kinases.
- Eurofins. A commercial vendor that also has large panels of target family assays available, such as kinases or GPCRs.
- KiNativ. Fee-for-service platform that allows the profiling of all native protein and lipid kinases in cell/tissue lysates.
- NCI-60 Panel. The National Cancer Institute’s screen uses 60 different human tumor cell lines and represents leukemia, melanoma and cancers of the lung, colon, brain, ovary, breast, prostate, and kidney cancers. The service is offered at no cost to submitters, although the requests are reviewed prior to screening.
- Pelago Bioscience. Cellular thermal shift assay (CETSA) based services, e.g. target engagement potency determinations or target agnostic proteome-wide mass spectrometric CETSA drug profiling.
- Reaction Biology Corporation. A commercial vendor that has large assay panels available, particularly kinase and epigenetic targets.
- Axelsson, H. et. al. (2018) In Situ Target Engagement in Cells. ACS Chem. Biol. 13 (4),
- S. Klaeger (2017) The target landscape of clinical kinase drugs. Science 358, eaan4368
(2017). DOI: 10.1126/science.aan4368
- Knapp, S., et al. (2013).
A public-private partnership to unlock the untargeted kinome.
Nature Chemical Biology, 9(1), 3-6.
- Jensen, A. J., et al. (2015).
CETSA: A target engagement assay with potential to transform drug discovery.
Future Medicinal Chemistry, 7(8), 975-978.
Ill-suited Probes and Identifying False Positives
These are online resources that provide filters to flag potential “bad actor” compounds:
- FAF Drugs. This is a free online filter for screening large compound libraries in silico. The tool is described in detail here (open access).
- Aggregator Advisor. An aggregator advisor database that may help distinguishing between bona fide and artifactual screening hits. This resource is available online and free-of-charge.
- Promiscuous compounds and other ill-suited probes within Chemical Probes.org is a link to a set of compounds that is commonly misused and should be avoided if at all possible
- Baell, J. B., & Walters, M. A. (2014). Chemical con artists foil drug discovery.
- Irwin, J. J., et al. (2015).
An aggregator advisor for ligand discovery.
J. Med. Chem. 58(17), 7076-7087.
- Goode, D. R. et al. (2008). Identification of promiscuous small molecule activators in high-throughput enzyme activation screens.
J. Med. Chem. 51(8), 2346-2349.
- Baell, J. B. (2011). Redox-active nuisance screening compounds and their classification.
Drug Discovery Today 16(17-18), 840-841.
- Baell, J. B. & Holloway, G. A. (2010). New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays.
J. Med. Chem. 53(7), 2719-2740.
- Thorne, N. et al. (2010).
Apparent activity in high-throughput screening: origins of compound-dependent assay interference.
Curr. Opin. Chem. Biol. 3, 315-324.
Volunteer CICR-AACR Probes Expert Members
The following is a running list of CICR-AACR members who have volunteered to serve as a resource to research in need of discussing aspects of chemical probes. If you have questions regarding the use of probes or any of the above material, please contact any of the individuals below:
Ivan Cornella-Taracido, PhD
(Probe design and evaluation of target engagement and mechanism of action; lipid kinases and epigenetic regulators; chemo-genomics and chemo-proteomics)
Angela N. Koehler, PhD
(transcriptional regulators; protein-protein interactions)
Massachusetts Institute of Technology (MIT)
Michael R. Michaelides, PhD
(kinases, protein-protein interaction targets, epigenetic targets (HDACs, HMTs, HATs))
Vinod F. Patel, PhD
Henry Pauls, PhD
University Health Network, Canada
Alex G. Waterson, PhD
(kinase inhibitors; protein-protein interaction inhibitors; fragment-based drug discovery; structure-guided drug design)
Vanderbilt University School of Medicine
Iain D.G. Watson, PhD
(protein-protein interactions and the ubiquitin proteosome pathway)
Ontario Institute for Cancer Research, Canada