1
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Kosar M, Sarott RC, Sykes DA, Viray AEG, Vitale RM, Tomašević N, Li X, Ganzoni RLZ, Kicin B, Reichert L, Patej KJ, Gómez-Bouzó U, Guba W, McCormick PJ, Hua T, Gruber CW, Veprintsev DB, Frank JA, Grether U, Carreira EM. Flipping the GPCR Switch: Structure-Based Development of Selective Cannabinoid Receptor 2 Inverse Agonists. ACS CENTRAL SCIENCE 2024; 10:956-968. [PMID: 38799662 PMCID: PMC11117691 DOI: 10.1021/acscentsci.3c01461] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 05/29/2024]
Abstract
We report a blueprint for the rational design of G protein coupled receptor (GPCR) ligands with a tailored functional response. The present study discloses the structure-based design of cannabinoid receptor type 2 (CB2R) selective inverse agonists (S)-1 and (R)-1, which were derived from privileged agonist HU-308 by introduction of a phenyl group at the gem-dimethylheptyl side chain. Epimer (R)-1 exhibits high affinity for CB2R with Kd = 39.1 nM and serves as a platform for the synthesis of a wide variety of probes. Notably, for the first time these fluorescent probes retain their inverse agonist functionality, high affinity, and selectivity for CB2R independent of linker and fluorophore substitution. Ligands (S)-1, (R)-1, and their derivatives act as inverse agonists in CB2R-mediated cAMP as well as G protein recruitment assays and do not trigger β-arrestin-receptor association. Furthermore, no receptor activation was detected in live cell ERK1/2 phosphorylation and Ca2+-release assays. Confocal fluorescence imaging experiments with (R)-7 (Alexa488) and (R)-9 (Alexa647) probes employing BV-2 microglial cells visualized CB2R expressed at endogenous levels. Finally, molecular dynamics simulations corroborate the initial docking data in which inverse agonists restrict movement of toggle switch Trp2586.48 and thereby stabilize CB2R in its inactive state.
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Affiliation(s)
- Miroslav Kosar
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Roman C. Sarott
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - David A. Sykes
- Faculty
of Medicine & Health Sciences, University
of Nottingham, Nottingham NG7 2UH, U.K.
- Centre
of Membrane Proteins and Receptors (COMPARE), University of Birmingham
and University of Nottingham, https://www.birmingham-nottingham.ac.uk/compare
| | - Alexander E. G. Viray
- Department
of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Rosa Maria Vitale
- Institute
of Biomolecular Chemistry, National Research
Council, Via Campi Flegrei
34, 80078 Pozzuoli, Italy
| | - Nataša Tomašević
- Center for
Physiology and Pharmacology, Medical University
of Vienna, Schwarzspanierstrasse
17, 1090 Vienna, Austria
| | - Xiaoting Li
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Rudolf L. Z. Ganzoni
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Bilal Kicin
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Lisa Reichert
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Kacper J. Patej
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Uxía Gómez-Bouzó
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Wolfgang Guba
- Roche
Pharma Research & Early Development, Roche Innovation Center Basel,
F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Peter J. McCormick
- Department
of Pharmacology and Therapeutics, University
of Liverpool, Ashton
Street, Liverpool L69 3GE, U.K.
| | - Tian Hua
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Christian W. Gruber
- Center for
Physiology and Pharmacology, Medical University
of Vienna, Schwarzspanierstrasse
17, 1090 Vienna, Austria
| | - Dmitry B. Veprintsev
- Faculty
of Medicine & Health Sciences, University
of Nottingham, Nottingham NG7 2UH, U.K.
- Centre
of Membrane Proteins and Receptors (COMPARE), University of Birmingham
and University of Nottingham, https://www.birmingham-nottingham.ac.uk/compare
| | - James A. Frank
- Department
of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
- Vollum
Institute, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Uwe Grether
- Roche
Pharma Research & Early Development, Roche Innovation Center Basel,
F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Erick M. Carreira
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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2
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Hoermann B, Dürr EM, Ludwig C, Ercan M, Köhn M. A strategy to disentangle direct and indirect effects on (de)phosphorylation by chemical modulators of the phosphatase PP1 in complex cellular contexts. Chem Sci 2024; 15:2792-2804. [PMID: 38404380 PMCID: PMC10882499 DOI: 10.1039/d3sc04746f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024] Open
Abstract
Chemical activators and inhibitors are useful probes to identify substrates and downstream effects of enzymes; however, due to the complex signaling environment within cells, it is challenging to distinguish between direct and indirect effects. This is particularly the case for phosphorylation, where a single (de)phosphorylation event can trigger rapid changes in many other phosphorylation sites. An additional complication arises when a single catalytic entity, which acts in the form of many different holoenzymes with different substrates, is activated or inhibited, as it is unclear which holoenzymes are affected, and in turn which of their substrates are (de)phosphorylated. Direct target engaging MS-based technologies to study targets of drugs do not address these challenges. Here, we tackle this by studying the modulation of protein phosphatase-1 (PP1) activity by PP1-disrupting peptides (PDPs), as well as their selectivity toward PP1, by using a combination of mass spectrometry-based experiments. By combining cellular treatment with the PDP with in vitro dephosphorylation by the enzyme, we identify high confidence substrate candidates and begin to separate direct and indirect effects. Together with experiments analyzing which holoenzymes are particularly susceptible to this treatment, we obtain insights into the effect of the modulator on the complex network of protein (de)phosphorylation. This strategy holds promise for enhancing our understanding of PP1 in particular and, due to the broad applicability of the workflow and the MS-based read-out, of chemical modulators with complex mode of action in general.
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Affiliation(s)
- Bernhard Hoermann
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
| | - Eva-Maria Dürr
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
| | - Christina Ludwig
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM) Freising Germany
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM) Freising Germany
| | - Melda Ercan
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
| | - Maja Köhn
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
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3
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Hu H, Tjaden A, Knapp S, Antolin AA, Müller S. A machine learning and live-cell imaging tool kit uncovers small molecules induced phospholipidosis. Cell Chem Biol 2023; 30:1634-1651.e6. [PMID: 37797617 DOI: 10.1016/j.chembiol.2023.09.003] [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: 05/20/2023] [Revised: 08/09/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
Drug-induced phospholipidosis (DIPL), characterized by excessive accumulation of phospholipids in lysosomes, can lead to clinical adverse effects. It may also alter phenotypic responses in functional studies using chemical probes. Therefore, robust methods are needed to predict and quantify phospholipidosis (PL) early in drug discovery and in chemical probe characterization. Here, we present a versatile high-content live-cell imaging approach, which was used to evaluate a chemogenomic and a lysosomal modulation library. We trained and evaluated several machine learning models using the most comprehensive set of publicly available compounds and interpreted the best model using SHapley Additive exPlanations (SHAP). Analysis of high-quality chemical probes extracted from the Chemical Probes Portal using our algorithm revealed that closely related molecules, such as chemical probes and their matched negative controls can differ in their ability to induce PL, highlighting the importance of identifying PL for robust target validation in chemical biology.
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Affiliation(s)
- Huabin Hu
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK; Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24 Uppsala, Sweden
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany
| | - Albert A Antolin
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK; ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Catalonia Barcelona, Spain.
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany.
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4
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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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5
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Schwickert M, Zimmermann RA, Habeck T, Hoba SN, Nidoieva Z, Fischer TR, Stark MM, Kersten C, Lermyte F, Helm M, Schirmeister T. Covalent S-Adenosylhomocysteine-Based DNA Methyltransferase 2 Inhibitors with a New Type of Aryl Warhead. ACS Med Chem Lett 2023; 14:777-787. [PMID: 37312859 PMCID: PMC10258905 DOI: 10.1021/acsmedchemlett.3c00062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/02/2023] [Indexed: 06/15/2023] Open
Abstract
The DNA methyltransferase 2 (DNMT2) is an RNA modifying enzyme associated with pathophysiological processes, such as mental and metabolic disorders or cancer. Although the development of methyltransferase inhibitors remains challenging, DNMT2 is not only a promising target for drug discovery, but also for the development of activity-based probes. Here, we present covalent SAH-based DNMT2 inhibitors decorated with a new type of aryl warhead. Based on a noncovalent DNMT2 inhibitor with N-benzyl substituent, the Topliss scheme was followed for optimization. The results showed that electron-deficient benzyl moieties highly increased affinity. By decorating the structures with strong electron-withdrawing moieties and leaving groups, we adjusted the electrophilicity to create covalent DNMT2 inhibitors. A 4-bromo-3-nitrophenylsulfonamide-decorated SAH derivative (80) turned out to be the most potent (IC50 = 1.2 ± 0.1 μM) and selective inhibitor. Protein mass spectrometry confirmed the covalent reaction with the catalytically active cysteine-79.
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Affiliation(s)
- Marvin Schwickert
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Robert A. Zimmermann
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Tanja Habeck
- Technical
University of Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Sabrina N. Hoba
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Zarina Nidoieva
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Tim R. Fischer
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Martin M. Stark
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Christian Kersten
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Frederik Lermyte
- Technical
University of Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Mark Helm
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Tanja Schirmeister
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
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6
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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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7
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Kim K, Ryu TY, Jung E, Han TS, Lee J, Kim SK, Roh YN, Lee MS, Jung CR, Lim JH, Hamamoto R, Lee HW, Hur K, Son MY, Kim DS, Cho HS. Epigenetic regulation of SMAD3 by histone methyltransferase SMYD2 promotes lung cancer metastasis. Exp Mol Med 2023:10.1038/s12276-023-00987-1. [PMID: 37121971 DOI: 10.1038/s12276-023-00987-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/20/2022] [Accepted: 02/07/2023] [Indexed: 05/02/2023] Open
Abstract
Epigenetic alterations, especially histone methylation, are key factors in cell migration and invasion in cancer metastasis. However, in lung cancer metastasis, the mechanism by which histone methylation regulates metastasis has not been fully elucidated. Here, we found that the histone methyltransferase SMYD2 is overexpressed in lung cancer and that knockdown of SMYD2 could reduce the rates of cell migration and invasion in lung cancer cell lines via direct downregulation of SMAD3 via SMYD2-mediated epigenetic regulation. Furthermore, using an in vitro epithelial-mesenchymal transition (EMT) system with a Transwell system, we generated highly invasive H1299 (In-H1299) cell lines and observed the suppression of metastatic features by SMYD2 knockdown. Finally, two types of in vivo studies revealed that the formation of metastatic tumors by shSMYD2 was significantly suppressed. Thus, we suggest that SMYD2 is a potential metastasis regulator and that the development of SMYD2-specific inhibitors may help to increase the efficacy of lung cancer treatment.
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Affiliation(s)
- Kwangho Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- College of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Tae Young Ryu
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Eunsun Jung
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Tae-Su Han
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
- Department of Biological Science, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jinkwon Lee
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Seon-Kyu Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yu Na Roh
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Moo-Seung Lee
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Cho-Rok Jung
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Jung Hwa Lim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ryuji Hamamoto
- Division of Molecular Modification and Cancer Biology, National Cancer Center, Tokyo, Japan
| | - Hye Won Lee
- Department of Pathology, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Keun Hur
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
| | - Mi-Young Son
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea.
- Department of Biological Science, Sungkyunkwan University, Suwon, Republic of Korea.
| | - Dae-Soo Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea.
| | - Hyun-Soo Cho
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea.
- Department of Biological Science, Sungkyunkwan University, Suwon, Republic of Korea.
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8
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Zimmermann RA, Fischer TR, Schwickert M, Nidoieva Z, Schirmeister T, Kersten C. Chemical Space Virtual Screening against Hard-to-Drug RNA Methyltransferases DNMT2 and NSUN6. Int J Mol Sci 2023; 24:ijms24076109. [PMID: 37047081 PMCID: PMC10094593 DOI: 10.3390/ijms24076109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
Targeting RNA methyltransferases with small molecules as inhibitors or tool compounds is an emerging field of interest in epitranscriptomics and medicinal chemistry. For two challenging RNA methyltransferases that introduce the 5-methylcytosine (m5C) modification in different tRNAs, namely DNMT2 and NSUN6, an ultra-large commercially available chemical space was virtually screened by physicochemical property filtering, molecular docking, and clustering to identify new ligands for those enzymes. Novel chemotypes binding to DNMT2 and NSUN6 with affinities down to KD,app = 37 µM and KD,app = 12 µM, respectively, were identified using a microscale thermophoresis (MST) binding assay. These compounds represent the first molecules with a distinct structure from the cofactor SAM and have the potential to be developed into activity-based probes for these enzymes. Additionally, the challenges and strategies of chemical space docking screens with special emphasis on library focusing and diversification are discussed.
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Affiliation(s)
- Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Zarina Nidoieva
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
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9
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Tredup C, Ndreshkjana B, Schneider NS, Tjaden A, Kemas AM, Youhanna S, Lauschke VM, Berger BT, Krämer A, Berger LM, Röhm S, Knapp S, Farin HF, Müller S. Deep Annotation of Donated Chemical Probes (DCP) in Organotypic Human Liver Cultures and Patient-Derived Organoids from Tumor and Normal Colorectum. ACS Chem Biol 2023; 18:822-836. [PMID: 36944371 PMCID: PMC10127199 DOI: 10.1021/acschembio.2c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Well-characterized small molecules are essential tools for studying the biology and therapeutic relevance of a target protein. However, many compounds reported in the literature and routinely studied in biomedical research lack the potency and selectivity required for mechanistic cellular studies on the function of a given protein. Furthermore, commercially available compounds often do not include useful tools developed by industry as part of their research and development efforts, as they frequently remain proprietary. The freely available donated chemical probe (DCP) library, fueled by generous donations of compounds from industry and academia, enables easy access to a steadily growing collection of these valuable and well-characterized tools. Here, we provide a systematic description of the current DCP library collection and their associated comprehensive characterization data, including a variety of in vitro and cellular assays. Of note, we characterized the set in relevant human primary models by employing hepatotoxicity screening in primary human liver spheroids and viability screening in patient-derived colorectal cancer organoids and matched normal-adjacent epithelium. Taken together, the DCP library represents a well-annotated, openly available collection of tool compounds for studying a wide range of targets, including kinases, G-protein-coupled receptors, and ion channels. As such, it represents a unique resource for the biomedical research community.
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Affiliation(s)
- Claudia Tredup
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Benardina Ndreshkjana
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596Frankfurt am Main, Germany
| | - Natalie S Schneider
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Aurino M Kemas
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65Stockholm, Sweden
| | - Sonia Youhanna
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65Stockholm, Sweden
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376Stuttgart, Germany
- University of Tübingen, 72074Tübingen, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main60596, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Sandra Röhm
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main60596, Germany
| | - Henner F Farin
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main60596, Germany
- German Cancer Consortium (DKTK), Heidelberg69120, Germany
- German Cancer Research Center (DKFZ), 69120Heidelberg, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
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10
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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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11
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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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12
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Barghout SH, Mann MK, Aman A, Yu Y, Alteen MG, Schimmer AD, Schapira M, Arrowsmith CH, Barsyte-Lovejoy D. Combinatorial Anticancer Drug Screen Identifies Off-Target Effects of Epigenetic Chemical Probes. ACS Chem Biol 2022; 17:2801-2816. [PMID: 36084291 DOI: 10.1021/acschembio.2c00451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Anticancer drug response is determined by genetic and epigenetic mechanisms. To identify the epigenetic regulators of anticancer drug response, we conducted a chemical epigenetic screen using chemical probes that target different epigenetic modulators. In this screen, we tested 31 epigenetic probes in combination with 14 mechanistically diverse anticancer agents and identified 8 epigenetic probes that significantly potentiate the cytotoxicity of TAK-243, a first-in-class ubiquitin-activating enzyme (UBA1) inhibitor evaluated in several solid and hematologic malignancies. These probes are TP-472, GSK864, A-196, UNC1999, SGC-CBP30, and PFI-4 (and its related analogues GSK6853 and GSK5959), and they target BRD9/7, mutant IDH1, SUV420H1/2, EZH2/1, p300/CBP, and BRPF1B, respectively. In contrast to epigenetic probes, negative control compounds did not have a significant impact on TAK-243 cytotoxicity. Potentiation of TAK-243 cytotoxicity was associated with reduced ubiquitylation and induction of apoptosis. Mechanistically, these epigenetic probes exerted their potentiation by inhibiting the efflux transporter ATP-binding cassette subfamily G member 2 (ABCG2) without inducing significant changes in the ubiquitylation pathways or ABCG2 expression levels. As assessed by docking analysis, the identified probes could potentially interact with ABCG2. Based on these data, we have developed a cell-based assay that can quantitatively evaluate ABCG2 inhibition by drug candidates. In conclusion, our study identifies epigenetic probes that profoundly potentiate TAK-243 cytotoxicity through off-target ABCG2 inhibition. We also provide experimental evidence that several negative control compounds cannot exclude a subset of off-target effects of chemical probes. Finally, potentiation of TAK-243 cytotoxicity can serve as a quantitative measure of ABCG2-inhibitory activity.
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Affiliation(s)
- Samir H Barghout
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology & Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Pharmacology & Toxicology, Faculty of Pharmacy, Tanta University, Tanta 31111, Egypt
| | - Mandeep K Mann
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology & Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Yifan Yu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology & Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Matthew G Alteen
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Aaron D Schimmer
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology & Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology & Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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13
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Němec V, Schwalm MP, Müller S, Knapp S. PROTAC degraders as chemical probes for studying target biology and target validation. Chem Soc Rev 2022; 51:7971-7993. [PMID: 36004812 DOI: 10.1039/d2cs00478j] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule degraders such as PROTACs (PROteolysis TArgeting Chimeras) have emerged as new promising pharmacological modalities and the first PROTAC drug candidates are now studied clinically. The catalytic properties of PROTACs, acting as chemical degraders of a protein of interest (POI), represent an attractive new strategy for drug development. The development and characterization of PROTACs requires an array of additional assay systems that track the degradation pathway leading ultimately to degradation of the POI, identifying critical steps for PROTAC optimization. In addition to their exciting translational potential, PROTACs represent versatile chemical tools that considerably expanded our chemical biology toolbox and significantly enlarged the proteome that can be modulated by small molecules. Similar to conventional chemical probes, PROTACs used as chemical probes in target validation require comprehensive characterization. As a consequence, PROTAC-specific quality criteria should be defined by the chemical biology community. These criteria need to comprise additional or alternative parameters compared to those for conventional occupancy-driven chemical probes, such as the maximum level of target degradation (Dmax), confirmation of a proteasome dependent degradation mechanism and, importantly, also kinetic parameters of POI degradation. The kinetic aspects are particularly relevant for PROTACs that harbor covalent binding moieties. Here, we review recent progress in the development of assay systems for PROTAC characterization and suggest a set of criteria for PROTACs as high quality chemical probes.
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Affiliation(s)
- Václav Němec
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany
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14
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Chemical biology and pharmacology of histone lysine methylation inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194840. [PMID: 35753676 DOI: 10.1016/j.bbagrm.2022.194840] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 12/20/2022]
Abstract
Histone lysine methylation is a post-translational modification that plays a key role in the epigenetic regulation of a broad spectrum of biological processes. Moreover, the dysregulation of histone lysine methyltransferases (KMTs) has been implicated in the pathogenesis of several diseases particularly cancer. Due to their pathobiological importance, KMTs have garnered immense attention over the last decade as attractive therapeutic targets. These endeavors have culminated in tens of chemical probes that have been used to interrogate many aspects of histone lysine methylation. Besides, over a dozen inhibitors have been advanced to clinical trials, including the EZH2 inhibitor tazemetostat approved for the treatment of follicular lymphoma and advanced epithelioid sarcoma. In this Review, we highlight the chemical biology and pharmacology of KMT inhibitors and targeted protein degraders focusing on the clinical development of EZH1/2, DOT1L, Menin-MLL, and WDR5-MLL inhibitors. We also briefly discuss the pharmacologic targeting of other KMTs.
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15
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16
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Yang X, Dickmander RJ, Bayati A, Taft-Benz SA, Smith JL, Wells CI, Madden EA, Brown JW, Lenarcic EM, Yount BL, Chang E, Axtman AD, Baric RS, Heise MT, McPherson PS, Moorman NJ, Willson TM. Host Kinase CSNK2 is a Target for Inhibition of Pathogenic SARS-like β-Coronaviruses. ACS Chem Biol 2022; 17:1937-1950. [PMID: 35723434 PMCID: PMC9236220 DOI: 10.1021/acschembio.2c00378] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inhibition of the protein kinase CSNK2 with any of 30 specific and selective inhibitors representing different chemotypes, blocked replication of pathogenic human, bat, and murine β-coronaviruses. The potency of in-cell CSNK2A target engagement across the set of inhibitors correlated with antiviral activity and genetic knockdown confirmed the essential role of the CSNK2 holoenzyme in β-coronavirus replication. Spike protein endocytosis was blocked by CSNK2A inhibition, indicating that antiviral activity was due in part to a suppression of viral entry. CSNK2A inhibition may be a viable target for the development of anti-SARS-like β-coronavirus drugs.
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Affiliation(s)
- Xuan Yang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
| | - Rebekah J Dickmander
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Armin Bayati
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Sharon A Taft-Benz
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Emily A Madden
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jason W Brown
- Takeda San Diego, San Diego, California 92121, United States
| | - Erik M Lenarcic
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Edcon Chang
- Takeda San Diego, San Diego, California 92121, United States
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
| | - Ralph S Baric
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mark T Heise
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Peter S McPherson
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Nathaniel J Moorman
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Timothy M Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
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17
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Proj M, Knez D, Sosič I, Gobec S. Redox active or thiol reactive? Optimization of rapid screens to identify less evident nuisance compounds. Drug Discov Today 2022; 27:1733-1742. [PMID: 35301150 DOI: 10.1016/j.drudis.2022.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/03/2022] [Accepted: 03/11/2022] [Indexed: 01/01/2023]
Abstract
Compounds that exhibit assay interference or undesirable mechanisms of bioactivity are routinely encountered in assays at various stages of drug discovery. We observed that assays for the investigation of thiol-reactive and redox-active compounds have not been collected in a comprehensive review. Here, we review these assays and subject them to experimental optimization to improve their reliability. We demonstrate the usefulness of our assay cascade by assaying a library of bioactive compounds, chemical probes, and a set of approved drugs. These high-throughput assays should complement the array of wet-lab and in silico assays during the initial stages of hit discovery campaigns to pursue only hit compounds with tractable mechanisms of action. Teaser: We provide an overview of assays to detect redox active and thiol reactive compounds and the robust protocols for identification of nuisance compounds during early stages of drug discovery programs.
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Affiliation(s)
- Matic Proj
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Askerceva 7, SI-1000 Ljubljana, Slovenia
| | - Damijan Knez
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Askerceva 7, SI-1000 Ljubljana, Slovenia
| | - Izidor Sosič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Askerceva 7, SI-1000 Ljubljana, Slovenia.
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Askerceva 7, SI-1000 Ljubljana, Slovenia.
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18
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Levit Kaplan A, Strachan RT, Braz JM, Craik V, Slocum S, Mangano T, Amabo V, O'Donnell H, Lak P, Basbaum AI, Roth BL, Shoichet BK. Structure-Based Design of a Chemical Probe Set for the 5-HT 5A Serotonin Receptor. J Med Chem 2022; 65:4201-4217. [PMID: 35195401 DOI: 10.1021/acs.jmedchem.1c02031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 5-HT5A receptor (5-HT5AR), for which no selective agonists and a few antagonists exist, remains the least understood serotonin receptor. A single commercial antagonist, SB-699551, has been widely used to investigate the 5-HT5AR function in neurological disorders, including pain, but this molecule has substantial liabilities as a chemical probe. Accordingly, we sought to develop an internally controlled probe set. Docking over 6 million molecules against a 5-HT5AR homology model identified 5 mid-μM ligands, one of which was optimized to UCSF678, a 42 nM arrestin-biased partial agonist at the 5-HT5AR with a more restricted off-target profile and decreased assay liabilities versus SB-699551. Site-directed mutagenesis supported the docked pose of UCSF678. Surprisingly, analogs of UCSF678 that lost the 5-HT5AR activity revealed that 5-HT5AR engagement is nonessential for alleviating pain, contrary to studies with less-selective ligands. UCSF678 and analogs constitute a selective probe set with which to study the function of the 5-HT5AR.
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Affiliation(s)
- Anat Levit Kaplan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - Ryan T Strachan
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Joao M Braz
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, United States
| | - Veronica Craik
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, United States
| | - Samuel Slocum
- National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Thomas Mangano
- National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Vanessa Amabo
- National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Henry O'Donnell
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - Allan I Basbaum
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, United States
| | - Bryan L Roth
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States.,National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States.,Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
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19
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Yang X, Dickmander RJ, Bayati A, Taft-Benz SA, Smith JL, Wells CI, Madden EA, Brown JW, Lenarcic EM, Yount BL, Chang E, Axtman AD, Baric RS, Heise MT, McPherson PS, Moorman NJ, Willson TM. Host kinase CSNK2 is a target for inhibition of pathogenic β-coronaviruses including SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35018375 PMCID: PMC8750650 DOI: 10.1101/2022.01.03.474779] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Inhibition of the protein kinase CSNK2 with any of 30 specific and selective inhibitors representing different chemotypes, blocked replication of pathogenic human and murine β-coronaviruses. The potency of in-cell CSNK2A target engagement across the set of inhibitors correlated with antiviral activity and genetic knockdown confirmed the essential role of the CSNK2 holoenzyme in β-coronavirus replication. Spike protein uptake was blocked by CSNK2A inhibition, indicating that antiviral activity was due in part to a suppression of viral entry. CSNK2A inhibition may be a viable target for development of new broad spectrum anti-β-coronavirus drugs.
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Affiliation(s)
- Xuan Yang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States
| | - Rebekah J Dickmander
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Armin Bayati
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Sharon A Taft-Benz
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Emily A Madden
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason W Brown
- Takeda San Diego, San Diego, CA 92121, United States
| | - Erik M Lenarcic
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Edcon Chang
- Takeda San Diego, San Diego, CA 92121, United States
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Ralph S Baric
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Mark T Heise
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Peter S McPherson
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Nathaniel J Moorman
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Timothy M Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States
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20
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Sailer A, Meiring JCM, Heise C, Pettersson LN, Akhmanova A, Thorn‐Seshold J, Thorn‐Seshold O. Pyrrole Hemithioindigo Antimitotics with Near-Quantitative Bidirectional Photoswitching that Photocontrol Cellular Microtubule Dynamics with Single-Cell Precision*. Angew Chem Int Ed Engl 2021; 60:23695-23704. [PMID: 34460143 PMCID: PMC8596636 DOI: 10.1002/anie.202104794] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/23/2021] [Indexed: 11/07/2022]
Abstract
We report the first cellular application of the emerging near-quantitative photoswitch pyrrole hemithioindigo, by rationally designing photopharmaceutical PHTub inhibitors of the cytoskeletal protein tubulin. PHTubs allow simultaneous visible-light imaging and photoswitching in live cells, delivering cell-precise photomodulation of microtubule dynamics, and photocontrol over cell cycle progression and cell death. This is the first acute use of a hemithioindigo photopharmaceutical for high-spatiotemporal-resolution biological control in live cells. It additionally demonstrates the utility of near-quantitative photoswitches, by enabling a dark-active design to overcome residual background activity during cellular photopatterning. This work opens up new horizons for high-precision microtubule research using PHTubs and shows the cellular applicability of pyrrole hemithioindigo as a valuable scaffold for photocontrol of a range of other biological targets.
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Affiliation(s)
- Alexander Sailer
- Department of PharmacyLudwig-Maximilians University of MunichButenandtstrasse 781377MunichGermany
| | - Joyce C. M. Meiring
- Department of BiologyUtrecht UniversityPadualaan 83584UtrechtThe Netherlands
| | - Constanze Heise
- Department of PharmacyLudwig-Maximilians University of MunichButenandtstrasse 781377MunichGermany
| | - Linda N. Pettersson
- Department of PharmacyLudwig-Maximilians University of MunichButenandtstrasse 781377MunichGermany
| | - Anna Akhmanova
- Department of BiologyUtrecht UniversityPadualaan 83584UtrechtThe Netherlands
| | - Julia Thorn‐Seshold
- Department of PharmacyLudwig-Maximilians University of MunichButenandtstrasse 781377MunichGermany
| | - Oliver Thorn‐Seshold
- Department of PharmacyLudwig-Maximilians University of MunichButenandtstrasse 781377MunichGermany
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21
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Sailer A, Meiring JCM, Heise C, Pettersson LN, Akhmanova A, Thorn‐Seshold J, Thorn‐Seshold O. Pyrrole Hemithioindigo Antimitotics with Near‐Quantitative Bidirectional Photoswitching that Photocontrol Cellular Microtubule Dynamics with Single‐Cell Precision**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Alexander Sailer
- Department of Pharmacy Ludwig-Maximilians University of Munich Butenandtstrasse 7 81377 Munich Germany
| | - Joyce C. M. Meiring
- Department of Biology Utrecht University Padualaan 8 3584 Utrecht The Netherlands
| | - Constanze Heise
- Department of Pharmacy Ludwig-Maximilians University of Munich Butenandtstrasse 7 81377 Munich Germany
| | - Linda N. Pettersson
- Department of Pharmacy Ludwig-Maximilians University of Munich Butenandtstrasse 7 81377 Munich Germany
| | - Anna Akhmanova
- Department of Biology Utrecht University Padualaan 8 3584 Utrecht The Netherlands
| | - Julia Thorn‐Seshold
- Department of Pharmacy Ludwig-Maximilians University of Munich Butenandtstrasse 7 81377 Munich Germany
| | - Oliver Thorn‐Seshold
- Department of Pharmacy Ludwig-Maximilians University of Munich Butenandtstrasse 7 81377 Munich Germany
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22
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Serafim RAM, Elkins JM, Zuercher WJ, Laufer SA, Gehringer M. Chemical Probes for Understudied Kinases: Challenges and Opportunities. J Med Chem 2021; 65:1132-1170. [PMID: 34477374 DOI: 10.1021/acs.jmedchem.1c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over 20 years after the approval of the first-in-class protein kinase inhibitor imatinib, the biological function of a significant fraction of the human kinome remains poorly understood while most research continues to be focused on few well-validated targets. Given the strong genetic evidence for involvement of many kinases in health and disease, the understudied fraction of the kinome holds a large and unexplored potential for future therapies. Specific chemical probes are indispensable tools to interrogate biology enabling proper preclinical validation of novel kinase targets. In this Perspective, we highlight recent case studies illustrating the development of high-quality chemical probes for less-studied kinases and their application in target validation. We spotlight emerging techniques and approaches employed in the generation of chemical probes for protein kinases and beyond and discuss the associated challenges and opportunities.
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Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - William J Zuercher
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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23
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Škuta C, Southan C, Bartůněk P. Will the chemical probes please stand up? RSC Med Chem 2021; 12:1428-1441. [PMID: 34447939 PMCID: PMC8372204 DOI: 10.1039/d1md00138h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022] Open
Abstract
In 2005, the NIH Molecular Libraries Program (MLP) undertook the identification of tool compounds to expand biological insights, now termed small-molecule chemical probes. This inspired other organisations to initiate similar efforts from 2010 onwards. As a central focus of the Probes & Drugs portal (P&D), we have standardised, integrated and compared sets of declared probe compounds harvested from 12 different sources. This turned out to be challenging and revealed unexpected anomalies. Results in this work address key questions including; a) individual and total structure counts, b) overlaps between sources, c) comparisons with selected PubChem sources and d) investigating the probe coverage of druggable targets. In addition, we developed new high-level scoring schemes to filter collections down to probes of higher quality. This generated 548 high-quality chemical probes (HQCP) covering 447 distinct protein targets. This HQCP collection has been added to the P&D portal and will be regularly updated as established sources expand and new ones release data.
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Affiliation(s)
- Ctibor Škuta
- CZ-OPENSCREEN, National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the Czech Academy of Sciences Vídeňská 1083 142 20 Prague 4 Czech Republic
| | - Christopher Southan
- Deanery of Biomedical Sciences, University of Edinburgh Edinburgh EH8 9XD UK
| | - Petr Bartůněk
- CZ-OPENSCREEN, National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the Czech Academy of Sciences Vídeňská 1083 142 20 Prague 4 Czech Republic
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24
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Clegg MA, Theodoulou NH, Bamborough P, Chung CW, Craggs PD, Demont EH, Gordon LJ, Liwicki GM, Phillipou A, Tomkinson NCO, Prinjha RK, Humphreys PG. Optimization of Naphthyridones into Selective TATA-Binding Protein Associated Factor 1 (TAF1) Bromodomain Inhibitors. ACS Med Chem Lett 2021; 12:1308-1317. [PMID: 34413961 DOI: 10.1021/acsmedchemlett.1c00294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022] Open
Abstract
Bromodomain containing proteins and the acetyl-lysine binding bromodomains contained therein are increasingly attractive targets for the development of novel epigenetic therapeutics. To help validate this target class and unravel the complex associated biology, there has been a concerted effort to develop selective small molecule bromodomain inhibitors. Herein we describe the structure-based efforts and multiple challenges encountered in optimizing a naphthyridone template into selective TAF1(2) bromodomain inhibitors which, while unsuitable as chemical probes themselves, show promise for the future development of small molecules to interrogate TAF1(2) biology. Key to this work was the introduction and modulation of the basicity of a pendant amine which had a substantial impact on not only bromodomain selectivity but also cellular target engagement.
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Affiliation(s)
- Michael A. Clegg
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Natalie H. Theodoulou
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Paul Bamborough
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Chun-wa Chung
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Peter D. Craggs
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | | | - Laurie J. Gordon
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Gemma M. Liwicki
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Alex Phillipou
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Nicholas C. O. Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Rab K. Prinjha
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
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