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Mader MM, Rudolph J, Hartung IV, Uehling D, Workman P, Zuercher W. Which Small Molecule? Selecting Chemical Probes for Use in Cancer Research and Target Validation. Cancer Discov 2023; 13:2150-2165. [PMID: 37712569 DOI: 10.1158/2159-8290.cd-23-0536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/17/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023]
Abstract
Small-molecule chemical "probes" complement the use of molecular biology techniques to explore, validate, and generate hypotheses on the function of proteins in diseases such as cancer. Unfortunately, the poor selection and use of small-molecule reagents can lead to incorrect conclusions. Here, we illustrate examples of poor chemical tools and suggest best practices for the selection, validation, and use of high-quality chemical probes in cancer research. We also note the complexity associated with tools for novel drug modalities, exemplified by protein degraders, and provide advice and resources to facilitate the independent identification of appropriate small-molecule probes by researchers. SIGNIFICANCE Validation of biological targets and pathways will be aided by a shared understanding of the criteria of potency, selectivity, and target engagement associated with small-molecule reagents ("chemical probes") that enable that work. Interdisciplinary collaboration between cancer biologists, medicinal chemists, and chemical biologists and the awareness of available resources will reduce misleading data generation and interpretation, strengthen data robustness, and improve productivity in academic and industrial research.
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Affiliation(s)
- Mary M Mader
- Indiana Biosciences Research Institute, Indianapolis, Indiana
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
| | - Joachim Rudolph
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
- Genentech, Inc., South San Francisco, California
| | - Ingo V Hartung
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
- Merck Healthcare KGaA, Darmstadt, Germany
| | - David Uehling
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Paul Workman
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
- Centre for Cancer Drug Discovery, The Institute of Cancer Research (London), Sutton, United Kingdom
- Chemical Probes Portal (www.chemicalprobes.org)
| | - William Zuercher
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
- F. Hoffmann-La Roche Ltd., Basel, Switzerland
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Sterling J, Baker JR, McCluskey A, Munoz L. Systematic literature review reveals suboptimal use of chemical probes in cell-based biomedical research. Nat Commun 2023; 14:3228. [PMID: 37270653 PMCID: PMC10239480 DOI: 10.1038/s41467-023-38952-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 05/23/2023] [Indexed: 06/05/2023] Open
Abstract
Chemical probes have reached a prominent role in biomedical research, but their impact is governed by experimental design. To gain insight into the use of chemical probes, we conducted a systematic review of 662 publications, understood here as primary research articles, employing eight different chemical probes in cell-based research. We summarised (i) concentration(s) at which chemical probes were used in cell-based assays, (ii) inclusion of structurally matched target-inactive control compounds and (iii) orthogonal chemical probes. Here, we show that only 4% of analysed eligible publications used chemical probes within the recommended concentration range and included inactive compounds as well as orthogonal chemical probes. These findings indicate that the best practice with chemical probes is yet to be implemented in biomedical research. To achieve this, we propose 'the rule of two': At least two chemical probes (either orthogonal target-engaging probes, and/or a pair of a chemical probe and matched target-inactive compound) to be employed at recommended concentrations in every study.
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Affiliation(s)
- Jayden Sterling
- Faculty of Medicine and Health, Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Jennifer R Baker
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Adam McCluskey
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Lenka Munoz
- Faculty of Medicine and Health, Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia.
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Licciardello MP, Workman P. The era of high-quality chemical probes. RSC Med Chem 2022; 13:1446-1459. [PMID: 36545432 PMCID: PMC9749956 DOI: 10.1039/d2md00291d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/11/2022] [Indexed: 11/29/2022] Open
Abstract
Small-molecule chemical probes are among the most important tools to study the function of proteins in cells and organisms. Regrettably, the use of weak and non-selective small molecules has generated an abundance of erroneous conclusions in the scientific literature. More recently, minimal criteria have been outlined for investigational compounds, encouraging the selection and use of high-quality chemical probes. Here, we briefly recall the milestones and key initiatives that have paved the way to this new era, illustrate examples of recent high-quality chemical probes and provide our perspective on future challenges and developments.
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Affiliation(s)
- Marco P. Licciardello
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer ResearchLondonUK
| | - Paul Workman
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer ResearchLondonUK,The Chemical Probes PortalUK
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Antolin AA, Sanfelice D, Crisp A, Villasclaras Fernandez E, Mica IL, Chen Y, Collins I, Edwards A, Müller S, Al-Lazikani B, Workman P. The Chemical Probes Portal: an expert review-based public resource to empower chemical probe assessment, selection and use. Nucleic Acids Res 2022; 51:D1492-D1502. [PMID: 36268860 PMCID: PMC9825478 DOI: 10.1093/nar/gkac909] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 01/30/2023] Open
Abstract
We describe the Chemical Probes Portal (https://www.chemicalprobes.org/), an expert review-based public resource to empower chemical probe assessment, selection and use. Chemical probes are high-quality small-molecule reagents, often inhibitors, that are important for exploring protein function and biological mechanisms, and for validating targets for drug discovery. The publication, dissemination and use of chemical probes provide an important means to accelerate the functional annotation of proteins, the study of proteins in cell biology, physiology, and disease pathology, and to inform and enable subsequent pioneering drug discovery and development efforts. However, the widespread use of small-molecule compounds that are claimed as chemical probes but are lacking sufficient quality, especially being inadequately selective for the desired target or even broadly promiscuous in behaviour, has resulted in many erroneous conclusions in the biomedical literature. The Chemical Probes Portal was established as a public resource to aid the selection and best-practice use of chemical probes in basic and translational biomedical research. We describe the background, principles and content of the Portal and its technical development, as well as examples of its applications and use. The Chemical Probes Portal is a community resource and we therefore describe how researchers can be involved in its content and development.
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Affiliation(s)
- Albert A Antolin
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Domenico Sanfelice
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Alisa Crisp
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Eloy Villasclaras Fernandez
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Ioan L Mica
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Yi Chen
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Ian Collins
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Aled Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, ONM5G 1L7, Canada,Chemical Probes Portal, www.chemicalprobes.org
| | | | | | - Paul Workman
- To whom correspondence should be addressed. Tel: +44 2087224580;
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