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The promise and peril of chemical probes

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Arrowsmith, Cheryl H, Audia, James E, Austin, Christopher, Baell, Jonathan, Bennett, Jonathan, Blagg, Julian, Bountra, Chas, Brennan, Paul E, Brown, Peter J, Bunnage, Mark E, Buser-Doepner, Carolyn, Campbell, Robert M, Carter, Adrian J, Cohen, Philip, Copeland, Robert A, Cravatt, Ben, Dahlin, Jayme L, Dhanak, Dashyant, Edwards, Aled M, Frederiksen, Mathias, Frye, Stephen V, Gray, Nathanael, Grimshaw, Charles E, Hepworth, David, Howe, Trevor, Huber, Kilian V M, Jin, Jian, Knapp, Stefan, Kotz, Joanne D, Kruger, Ryan G, Lowe, Derek, Mader, Mary M, Marsden, Brian, Mueller-Fahrnow, Anke, Müller, Susanne, O'Hagan, Ronan C, Overington, John P, Owen, Dafydd R, Rosenberg, Saul H, Ross, Ruth, Roth, Bryan, Schapira, Matthieu, Schreiber, Stuart L, Shoichet, Brian, Sundström, Michael, Superti-Furga, Giulio, Taunton, Jack, Toledo-Sherman, Leticia, Walpole, Chris, Walters, Michael A, Willson, Timothy M, Workman, Paul, Young, Robert N, Zuercher, William J·2015·Nature Chemical Biology

DOI 10.1038/nchembio.1867PMC PMC4706458

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Abstract

Chemical probes are powerful reagents with increasing impacts on biomedical research. However, probes of poor quality or that are used incorrectly generate misleading results. To help address these shortcomings, we will create a community-driven wiki resource to improve quality and convey current best practice.

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BindingDB Entry 50016483: Design and synthesis of efficient fluororethylene-peptidomimetic inhibitors of dipeptidyl peptidase III (DPP3).
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BindingDB Entry 50007035: A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function.
BindingDB (2021) · UC San Diego · doi:10.7270/q27s7s2s
FAIRsharing record for: Drug Target Commons
FAIRsharing Team, & Tang, J. (2023) · FAIRsharing.org · doi:10.25504/fairsharing.2e2bb2
BindingDB Entry 50018672: Discovery and Characterization of the Potent and Highly Selective 1,7-Naphthyridine-Based Inhibitors BAY-091 and BAY-297 of the Kinase PIP4K2A.
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BindingDB Entry 50047691: Non-Substrate Based, Small Molecule Inhibitors of the Human Isoprenylcysteine Carboxyl Methyltransferase.
BindingDB (2017) · UC San Diego · doi:10.7270/q2c82c8p
BindingDB Entry 50012799: The transcriptional repressor REV-ERB as a novel target for disease.
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BindingDB Entry 50022489: Covalent-Allosteric Inhibitors to Achieve Akt Isoform-Selectivity.
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BindingDB Entry 7927: Characterisation of Photoaffinity-Based Chemical Probes by Fluorescence Imaging and Native-State Mass Spectrometry.
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BindingDB Entry 50016002: Comparative Analysis of Small-Molecule LIMK1/2 Inhibitors: Chemical Synthesis, Biochemistry, and Cellular Activity.
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BindingDB Entry 50019872: Expanding Chemical Probe Space: Quality Criteria for Covalent and Degrader Probes.
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BindingDB Entry 50019631: Chemical tools for the Gid4 subunit of the human E3 ligase C-terminal to LisH (CTLH) degradation complex.
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BindingDB Entry 50017542: High-Throughput Screening Platform in Postnatal Heart Cells and Chemical Probe Toolbox to Assess Cardiomyocyte Proliferation.
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BindingDB Entry 50047583: Feeling Nature's PAINS: Natural Products, Natural Product Drugs, and Pan Assay Interference Compounds (PAINS).
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BindingDB Entry 50006564: Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300.
BindingDB (2020) · UC San Diego · doi:10.7270/q2ht2sb9
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BindingDB (2025) · UC San Diego · doi:10.7270/q2wh2vkk
BindingDB Entry 50010334: Early identification of promiscuous attributes of aldose reductase inhibitors using a DMSO-perturbation assay.
BindingDB (2021) · UC San Diego · doi:10.7270/q2s46whw
BindingDB Entry 50000957: Benzoisoquinolinediones as Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains.
BindingDB (2020) · UC San Diego · doi:10.7270/q2xg9tks
BindingDB Entry 50008549: Developing Inhibitors of the p47phox-p22phox Protein-Protein Interaction by Fragment-Based Drug Discovery.
BindingDB (2021) · UC San Diego · doi:10.7270/q2tq64xb
BindingDB Entry 7582: Inhibition of Mcl-1 through covalent modification of a noncatalytic lysine side chain.
BindingDB (2016) · UC San Diego · doi:10.7270/q2fn1513
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BindingDB (2021) · UC San Diego · doi:10.7270/q2fb5665
BindingDB Entry 7602: Design and characterization of bivalent BET inhibitors.
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BindingDB Entry 50023601: Discovery and Evaluation of Active Site-Directed, Potent, and Selective Sulfophenyl Acetic Amide-Based Inhibitors for the Laforin Phosphatase.
BindingDB (2026) · UC San Diego · doi:10.7270/q2m04bd7
BindingDB Entry 50017626: Probing Embryonic Development Enables the Discovery of Unique Small-Molecule Bone Morphogenetic Protein Potentiators.
BindingDB (2023) · UC San Diego · doi:10.7270/q20c50vh
BindingDB Entry 50002035: Exploiting a water network to achieve enthalpy-driven, bromodomain-selective BET inhibitors.
BindingDB (2020) · UC San Diego · doi:10.7270/q2b56nb2
BindingDB Entry 50020533: Structure-Guided Design of a Domain-Selective Bromodomain and Extra Terminal N-Terminal Bromodomain Chemical Probe.
BindingDB (2024) · UC San Diego · doi:10.7270/q2qc0807
BindingDB Entry 50000619: Creation of a Novel Class of Potent and Selective MutT Homologue 1 (MTH1) Inhibitors Using Fragment-Based Screening and Structure-Based Drug Design.
BindingDB (2019) · UC San Diego · doi:10.7270/q25d8v9q
BindingDB Entry 50012775: GSK789: A Selective Inhibitor of the First Bromodomains (BD1) of the Bromo and Extra Terminal Domain (BET) Proteins.
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BindingDB Entry 50002436: Reviewing Hit Discovery Literature for Difficult Targets: Glutathione Transferase Omega-1 as an Example.
BindingDB (2020) · UC San Diego · doi:10.7270/q23t9kvg
BindingDB Entry 50018918: It's ok to be outnumbered - sub-stoichiometric modulation of homomeric protein complexes.
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BindingDB Entry 50048978: Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors.
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BindingDB Entry 7443: Discovery of a Selective Covalent Inhibitor of Lysophospholipase-like 1 (LYPLAL1) as a Tool to Evaluate the Role of this Serine Hydrolase in Metabolism.
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BindingDB Entry 50011600: Pan-SMARCA/PB1 Bromodomain Inhibitors and Their Role in Regulating Adipogenesis.
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BindingDB Entry 50018060: BAY-069, a Novel (Trifluoromethyl)pyrimidinedione-Based BCAT1/2 Inhibitor and Chemical Probe.
BindingDB (2023) · UC San Diego · doi:10.7270/q2sn0f31
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BindingDB Entry 50012666: A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation.
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BindingDB Entry 50021885: Discovery of Two Highly Selective Structurally Orthogonal Chemical Probes for Activin Receptor-like Kinases 1 and 2.
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BindingDB Entry 50047692: Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor.
BindingDB (2017) · UC San Diego · doi:10.7270/q27h1mjz
BindingDB Entry 50047257: Disrupting Acetyl-Lysine Recognition: Progress in the Development of Bromodomain Inhibitors.
BindingDB (2017) · UC San Diego · doi:10.7270/q2x92d6h
BindingDB Entry 50011511: Potent and Selective Inhibitors of MTH1 Probe Its Role in Cancer Cell Survival.
BindingDB (2022) · UC San Diego · doi:10.7270/q2tb1bhr
BindingDB Entry 50000989: Design of a Biased Potent Small Molecule Inhibitor of the Bromodomain and PHD Finger-Containing (BRPF) Proteins Suitable for Cellular and in Vivo Studies.
BindingDB (2020) · UC San Diego · doi:10.7270/q29k4dq5
BindingDB Entry 50008430: Selective, Small-Molecule Co-Factor Binding Site Inhibition of a Su(var)3-9, Enhancer of Zeste, Trithorax Domain Containing Lysine Methyltransferase.
BindingDB (2021) · UC San Diego · doi:10.7270/q2r78jk4
BindingDB Entry 50007088: Discovery and Characterization of the Potent and Selective P2X4 Inhibitor
BindingDB (2021) · UC San Diego · doi:10.7270/q2m048rw
BindingDB Entry 50021202: Development of Novel Phosphonodifluoromethyl-Containing Phosphotyrosine Mimetics and a First-In-Class, Potent, Selective, and Bioavailable Inhibitor of Human CDC14 Phosphatases.
BindingDB (2025) · UC San Diego · doi:10.7270/q2zc87hr
BindingDB Entry 50011123: Development of 2-(4-pyridyl)-benzimidazoles as PKN2 chemical tools to probe cancer.
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BindingDB Entry 50019163: Rational Design of a New RXR Agonist Scaffold Enabling Single-Subtype Preference for RXRα, RXRβ, and RXRγ.
BindingDB (2024) · UC San Diego · doi:10.7270/q232016b
BindingDB Entry 50049076: Discovery of a Chemical Probe Bisamide (CCT251236): An Orally Bioavailable Efficacious Pirin Ligand from a Heat Shock Transcription Factor 1 (HSF1) Phenotypic Screen.
BindingDB (2019) · UC San Diego · doi:10.7270/q2kw5j9d
BindingDB Entry 50022622: Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition.
BindingDB (2025) · UC San Diego · doi:10.7270/q2pr81rq
BindingDB Entry 50002550: Group-Based Optimization of Potent and Cell-Active Inhibitors of the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrroli
BindingDB (2020) · UC San Diego · doi:10.7270/q2736tj6
BindingDB Entry 50022559: Discovery of the SMYD3 Inhibitor BAY-6035 Using Thermal Shift Assay (TSA)-Based High-Throughput Screening.
BindingDB (2025) · UC San Diego · doi:10.7270/q2q2451v
BindingDB Entry 50021711: Discovery of a Potent, Selective, and Cell-Active SPIN1 Inhibitor.
BindingDB (2025) · UC San Diego · doi:10.7270/q2zc87kn
BindingDB Entry 50012727: Positional Analogue Scanning: An Effective Strategy for Multiparameter Optimization in Drug Design.
BindingDB (2022) · UC San Diego · doi:10.7270/q2h135q7
BindingDB Entry 50019265: MSC-1186, a Highly Selective Pan-SRPK Inhibitor Based on an Exceptionally Decorated Benzimidazole-Pyrimidine Core.
BindingDB (2024) · UC San Diego · doi:10.7270/q2w09b8t
BindingDB Entry 50018828: Discovery and Characterization of BAY-805, a Potent and Selective Inhibitor of Ubiquitin-Specific Protease USP21.
BindingDB (2024) · UC San Diego · doi:10.7270/q2k078hk
BindingDB Entry 50007060: Discovery of BAY-298 and BAY-899: Tetrahydro-1,6-naphthyridine-Based, Potent, and Selective Antagonists of the Luteinizing Hormone Receptor Which Reduce Sex Hormone Levels in Vivo.
BindingDB (2021) · UC San Diego · doi:10.7270/q29p34x6
BindingDB Entry 50048252: Non-kinase targets of protein kinase inhibitors.
BindingDB (2018) · UC San Diego · doi:10.7270/q2125vnc
BindingDB Entry 50008322: Polypharmacology by Design: A Medicinal Chemist's Perspective on Multitargeting Compounds.
BindingDB (2021) · UC San Diego · doi:10.7270/q25t3pv2
BindingDB Entry 50002721: Modulators of 14-3-3 Protein-Protein Interactions.
BindingDB (2020) · UC San Diego · doi:10.7270/q2rb7781
BindingDB Entry 50011493: Online informatics resources to facilitate cancer target and chemical probe discovery.
BindingDB (2022) · UC San Diego · doi:10.7270/q27h1p69
BindingDB Entry 50008462: Discovery of a Potent and Selective Fragment-like Inhibitor of Methyllysine Reader Protein Spindlin 1 (SPIN1).
BindingDB (2021) · UC San Diego · doi:10.7270/q2jm2f0x
BindingDB Entry 50015357: Targeting Small GTPases and Their Prenylation in Diabetes Mellitus.
BindingDB (2024) · UC San Diego · doi:10.7270/q2t43z8r

Authors: Arrowsmith, C. H., Audia, J. E., Austin, C., Baell, J., Bennett, J., Blagg, J., Bountra, C., Brennan, P. E., Brown, P. J., Bunnage, M. E., Buser-Doepner, C., Campbell, R. M., Carter, A. J., Cohen, P., Copeland, R. A., Cravatt, B., Dahlin, J. L., Dhanak, D., Edwards, A. M., Frederiksen, M., Frye, S. V., Gray, N., Grimshaw, C. E., Hepworth, D., Howe, T., Huber, K. V. M., Jin, J., Knapp, S., Kotz, J. D., Kruger, R. G., Lowe, D., Mader, M. M., Marsden, B., Mueller-Fahrnow, A., Müller, S., O'Hagan, R. C., Overington, J. P., Owen, D. R., Rosenberg, S. H., Ross, R., Roth, B., Schapira, M., Schreiber, S. L., Shoichet, B., Sundström, M., Superti-Furga, G., Taunton, J., Toledo-Sherman, L., Walpole, C., Walters, M. A., Willson, T. M., Workman, P., Young, R. N., & Zuercher, W. J.
Affiliations: University of Toronto (CA)
Constellation Pharmaceuticals (United States) (US)
National Institutes of Health (US)
Monash University (AU)
Merck & Co., Inc., Rahway, NJ, USA (United States) (US)
Institute of Cancer Research (GB)
University of Oxford (GB)
Structural Genomics Consortium (CA)
Pfizer (United States) (US)
Eli Lilly (United States) (US)
Boehringer Ingelheim (Germany) (DE)
University of Dundee (GB)
Epizyme (United States) (US)
Scripps Research Institute (US)
Mayo Clinic (US)
Novartis (Switzerland) (CH)
University of North Carolina at Chapel Hill (US)
Harvard University (US)
Janssen (United Kingdom) (GB)
Austrian Academy of Sciences (AT)
Icahn School of Medicine at Mount Sinai (US)
Broad Institute (US)
GlaxoSmithKline (United States) (US)
Vertex Pharmaceuticals (United States) (US)
European Bioinformatics Institute (GB)
AbbVie (United States) (US)
University of California, San Francisco (US)
Karolinska University Hospital (SE)
Howard Hughes Medical Institute (US)
University of Minnesota (US)
Simon Fraser University (CA)
Corresponding author: Edwards, Aled M
ORCID: Arrowsmith, Cheryl H
Audia, James E
Austin, Christopher
Baell, Jonathan
Blagg, Julian
Bountra, Chas
Brennan, Paul E
Brown, Peter J
Bunnage, Mark E
Campbell, Robert M
Carter, Adrian J
Cohen, Philip
Copeland, Robert A
Dahlin, Jayme L
Edwards, Aled M
Frederiksen, Mathias
Frye, Stephen V
Gray, Nathanael
Grimshaw, Charles E
Hepworth, David
Huber, Kilian V M
Jin, Jian
Knapp, Stefan
Kotz, Joanne D
Mader, Mary M
Marsden, Brian
Müller, Susanne
Overington, John P
Owen, Dafydd R
Ross, Ruth
Roth, Bryan
Schapira, Matthieu
Schreiber, Stuart L
Shoichet, Brian
Sundström, Michael
Taunton, Jack
Walters, Michael A
Willson, Timothy M
Workman, Paul
Young, Robert N
Zuercher, William J
Venue: Nature Chemical Biology
Publisher: Springer Science and Business Media LLC
Published: 2015-07-21
Volume: 11
Issue: 8
Pages: 536-541
ISSN: 1552-4450 (ISSN-L)
1552-4469
DOI: 10.1038/nchembio.1867
PMC: PMC4706458
OpenAlex: W1516646538
Cited by: 839
References: 41
Citations by year: 2026: 37 · 2025: 57 · 2024: 62 · 2023: 67 · 2022: 67 · 2021: 81 · 2020: 86 · 2019: 75 · 2018: 79 · 2017: 98 · 2016: 103 · 2015: 25
FWCI: 48.56
Type: journal article
Language: en
Update notices: erratum (2015-10-20)
Open access: hybrid
doi.org
Licence: other-oa
www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature Chemical Biology (publishedVersion, other-oa)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
Discovery Research Portal (University of Dundee) (submittedVersion, other-oa)
Deakin Research Online (Deakin University) (submittedVersion)
eScholarship (California Digital Library) (submittedVersion)
Figshare (submittedVersion, cc-by)
UNC Libraries
Funders: Eli Lilly and Company
Pfizer
GlaxoSmithKline
Harvard University
University of Dundee
Wellcome Trust (106169/Z/14/Z, 104104, 106169, 104104/A/14/Z, 100294)
Constellation Pharmaceuticals
Cancer Research UK (11566)
University of Oxford
Monash University
Österreichischen Akademie der Wissenschaften
University of Toronto
National Institutes of Health
University of North Carolina at Chapel Hill
Novartis Institutes for BioMedical Research
Medical Research Council (MR/K000985/1)
National Institute of General Medical Sciences (R01GM103893)
Janssen Research and Development
National Center for Advancing Translational Sciences
UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill
Topics: Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
Keywords: chemical probes, best practices, wikis, research reproducibility, chemical biology
MeSH terms: Humans, Molecular Weight, Sensitivity and Specificity, Molecular Probes, Intellectual Property, Internet, Information Dissemination, Biomedical Research, Small Molecule Libraries

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