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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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Pasqua AE, Sharp SY, Chessum NEA, Hayes A, Pellegrino L, Tucker MJ, Miah A, Wilding B, Evans LE, Rye CS, Mok NY, Liu M, Henley AT, Gowan S, De Billy E, te Poele R, Powers M, Eccles SA, Clarke PA, Raynaud FI, Workman P, Jones K, Cheeseman MD. HSF1 Pathway Inhibitor Clinical Candidate (CCT361814/NXP800) Developed from a Phenotypic Screen as a Potential Treatment for Refractory Ovarian Cancer and Other Malignancies. J Med Chem 2023; 66:5907-5936. [PMID: 37017629 PMCID: PMC10150365 DOI: 10.1021/acs.jmedchem.3c00156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Indexed: 04/06/2023]
Abstract
CCT251236 1, a potent chemical probe, was previously developed from a cell-based phenotypic high-throughput screen (HTS) to discover inhibitors of transcription mediated by HSF1, a transcription factor that supports malignancy. Owing to its activity against models of refractory human ovarian cancer, 1 was progressed into lead optimization. The reduction of P-glycoprotein efflux became a focus of early compound optimization; central ring halogen substitution was demonstrated by matched molecular pair analysis to be an effective strategy to mitigate this liability. Further multiparameter optimization led to the design of the clinical candidate, CCT361814/NXP800 22, a potent and orally bioavailable fluorobisamide, which caused tumor regression in a human ovarian adenocarcinoma xenograft model with on-pathway biomarker modulation and a clean in vitro safety profile. Following its favorable dose prediction to human, 22 has now progressed to phase 1 clinical trial as a potential future treatment for refractory ovarian cancer and other malignancies.
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Affiliation(s)
- A. Elisa Pasqua
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Swee Y. Sharp
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Nicola E. A. Chessum
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Angela Hayes
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Loredana Pellegrino
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Michael J. Tucker
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Asadh Miah
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Birgit Wilding
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Lindsay E. Evans
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Carl S. Rye
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - N. Yi Mok
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Manjuan Liu
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Alan T. Henley
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Sharon Gowan
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Emmanuel De Billy
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Robert te Poele
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Marissa Powers
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Suzanne A. Eccles
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul A. Clarke
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Florence I. Raynaud
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul Workman
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Keith Jones
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Matthew D. Cheeseman
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
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Antolin AA, Workman P, Al-Lazikani B. Public resources for chemical probes: the journey so far and the road ahead. Future Med Chem 2021; 13:731-747. [PMID: 31778323 DOI: 10.4155/fmc-2019-0231] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
High-quality small molecule chemical probes are extremely valuable for biological research and target validation. However, frequent use of flawed small-molecule inhibitors produces misleading results and diminishes the robustness of biomedical research. Several public resources are available to facilitate assessment and selection of better chemical probes for specific protein targets. Here, we review chemical probe resources, discuss their current strengths and limitations, and make recommendations for further improvements. Expert review resources provide in-depth analysis but currently cover only a limited portion of the liganded proteome. Computational resources encompass more proteins and are regularly updated, but have limitations in data availability and curation. We show how biomedical scientists may use these resources to choose the best available chemical probes for their research.
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Affiliation(s)
- Albert A Antolin
- The Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
- CRUK ICR/Imperial Convergence Science Centre, London, SM2 5NG, UK
| | - Paul Workman
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
- CRUK ICR/Imperial Convergence Science Centre, London, SM2 5NG, UK
| | - Bissan Al-Lazikani
- The Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
- CRUK ICR/Imperial Convergence Science Centre, London, SM2 5NG, UK
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Applications of liquid biopsy in the Pharmacological Audit Trail for anticancer drug development. Nat Rev Clin Oncol 2021; 18:454-467. [PMID: 33762744 DOI: 10.1038/s41571-021-00489-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 02/06/2023]
Abstract
Anticancer drug development is a costly and protracted activity, and failure at late phases of clinical testing is common. We have previously proposed the Pharmacological Audit Trail (PhAT) intended to improve the efficiency of drug development, with a focus on the use of tumour tissue-based biomarkers. Blood-based 'liquid biopsy' approaches, such as targeted or whole-genome sequencing studies of plasma circulating cell-free tumour DNA (ctDNA) and circulating tumour cells (CTCs), are of increasing relevance to this drug development paradigm. Liquid biopsy assays can provide quantitative and qualitative data on prognostic, predictive, pharmacodynamic and clinical response biomarkers, and can also enable the characterization of disease evolution and resistance mechanisms. In this Perspective, we examine the promise of integrating liquid biopsy analyses into the PhAT, focusing on the current evidence, advances, limitations and challenges. We emphasize the continued importance of analytical validation and clinical qualification of circulating tumour biomarkers through prospective clinical trials.
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