1
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Pierrat OA, Liu M, Collie GW, Shetty K, Rodrigues MJ, Le Bihan YV, Gunnell EA, McAndrew PC, Stubbs M, Rowlands MG, Yahya N, Shehu E, Talbot R, Pickard L, Bellenie BR, Cheung KMJ, Drouin L, Innocenti P, Woodward H, Davis OA, Lloyd MG, Varela A, Huckvale R, Broccatelli F, Carter M, Galiwango D, Hayes A, Raynaud FI, Bryant C, Whittaker S, Rossanese OW, Hoelder S, Burke R, van Montfort RLM. Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays. Sci Rep 2022; 12:18633. [PMID: 36329085 PMCID: PMC9633773 DOI: 10.1038/s41598-022-23264-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
By suppressing gene transcription through the recruitment of corepressor proteins, B-cell lymphoma 6 (BCL6) protein controls a transcriptional network required for the formation and maintenance of B-cell germinal centres. As BCL6 deregulation is implicated in the development of Diffuse Large B-Cell Lymphoma, we sought to discover novel small molecule inhibitors that disrupt the BCL6-corepressor protein-protein interaction (PPI). Here we report our hit finding and compound optimisation strategies, which provide insight into the multi-faceted orthogonal approaches that are needed to tackle this challenging PPI with small molecule inhibitors. Using a 1536-well plate fluorescence polarisation high throughput screen we identified multiple hit series, which were followed up by hit confirmation using a thermal shift assay, surface plasmon resonance and ligand-observed NMR. We determined X-ray structures of BCL6 bound to compounds from nine different series, enabling a structure-based drug design approach to improve their weak biochemical potency. We developed a time-resolved fluorescence energy transfer biochemical assay and a nano bioluminescence resonance energy transfer cellular assay to monitor cellular activity during compound optimisation. This workflow led to the discovery of novel inhibitors with respective biochemical and cellular potencies (IC50s) in the sub-micromolar and low micromolar range.
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Affiliation(s)
- Olivier A Pierrat
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Manjuan Liu
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Gavin W Collie
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Kartika Shetty
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Matthew J Rodrigues
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Yann-Vaï Le Bihan
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Emma A Gunnell
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - P Craig McAndrew
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Mark Stubbs
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Martin G Rowlands
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Norhakim Yahya
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Erald Shehu
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Rachel Talbot
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Lisa Pickard
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Benjamin R Bellenie
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Kwai-Ming J Cheung
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ludovic Drouin
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Paolo Innocenti
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Hannah Woodward
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Owen A Davis
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Matthew G Lloyd
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ana Varela
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Rosemary Huckvale
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Fabio Broccatelli
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Michael Carter
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - David Galiwango
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Angela Hayes
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Florence I Raynaud
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Christopher Bryant
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Steven Whittaker
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Olivia W Rossanese
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Swen Hoelder
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Rosemary Burke
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Rob L M van Montfort
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK.
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK.
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2
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Henderson MJ, Holbert MA, Simeonov A, Kallal LA. High-Throughput Cellular Thermal Shift Assays in Research and Drug Discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:137-147. [PMID: 31566060 PMCID: PMC10915787 DOI: 10.1177/2472555219877183] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Thermal shift assays (TSAs) can reveal changes in protein structure, due to a resultant change in protein thermal stability. Since proteins are often stabilized upon binding of ligand molecules, these assays can provide a readout for protein target engagement. TSA has traditionally been applied using purified proteins and more recently has been extended to study target engagement in cellular environments with the emergence of cellular thermal shift assays (CETSAs). The utility of CETSA in confirming molecular interaction with targets in a more native context, and the desire to apply this technique more broadly, has fueled the emergence of higher-throughput techniques for CETSA (HT-CETSA). Recent studies have demonstrated that HT-CETSA can be performed in standard 96-, 384-, and 1536-well microtiter plate formats using methods such as beta-galactosidase and NanoLuciferase reporters and AlphaLISA assays. HT-CETSA methods can be used to select and characterize compounds from high-throughput screens and to prioritize compounds in lead optimization by facilitating dose-response experiments. In conjunction with cellular and biochemical activity assays for targets, HT-CETSA can be a valuable addition to the suite of assays available to characterize molecules of interest. Despite the successes in implementing HT-CETSA for a diverse set of targets, caveats and challenges must also be recognized to avoid overinterpretation of results. Here, we review the current landscape of HT-CETSA and discuss the methodologies, practical considerations, challenges, and applications of this approach in research and drug discovery. Additionally, a perspective on potential future directions for the technology is presented.
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Affiliation(s)
- Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Marc A Holbert
- Protein, Cellular, & Structural Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Lorena A Kallal
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, Collegeville, PA, USA
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target Validation. Angew Chem Int Ed Engl 2019; 58:17930-17952. [DOI: 10.1002/anie.201812164] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/08/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
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4
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemische Epigenetik: der Einfluss chemischer und chemo‐biologischer Techniken auf die Zielstruktur‐Validierung von Bromodomänen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
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5
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Zhang Y, Loh C, Chen J, Mainolfi N. Targeted protein degradation mechanisms. DRUG DISCOVERY TODAY. TECHNOLOGIES 2019; 31:53-60. [PMID: 31200860 DOI: 10.1016/j.ddtec.2019.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
Targeted protein degradation mediated by small molecule degraders represents an exciting new therapeutic opportunity to eliminate disease-causing proteins. These molecules recruit E3 ubiquitin ligases to the protein of interest and mediate its ubiquitination and subsequent proteolysis by the proteasome. Significant advancements have been made in the discovery and development of clinically relevant degraders. In this review we will focus on the recent progress in understanding ternary complex formation and structures, ubiquitination, and other critical factors that govern the efficiency of degraders both in vitro and in vivo. With deeper knowledges of these areas, the field is building guiding principles to reduce the level of empiricism and to identify therapeutically relevant degraders more rationally and efficiently.
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Affiliation(s)
- Yi Zhang
- Kymera Therapeutics, 300 Technology Square, Cambridge, MA, 02139, USA
| | - Christine Loh
- Kymera Therapeutics, 300 Technology Square, Cambridge, MA, 02139, USA
| | - Jesse Chen
- Kymera Therapeutics, 300 Technology Square, Cambridge, MA, 02139, USA
| | - Nello Mainolfi
- Kymera Therapeutics, 300 Technology Square, Cambridge, MA, 02139, USA.
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6
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Nguyen D, Lemos C, Wortmann L, Eis K, Holton SJ, Boemer U, Moosmayer D, Eberspaecher U, Weiske J, Lechner C, Prechtl S, Suelzle D, Siegel F, Prinz F, Lesche R, Nicke B, Nowak-Reppel K, Himmel H, Mumberg D, von Nussbaum F, Nising CF, Bauser M, Haegebarth A. Discovery and Characterization of the Potent and Highly Selective (Piperidin-4-yl)pyrido[3,2- d]pyrimidine Based in Vitro Probe BAY-885 for the Kinase ERK5. J Med Chem 2019; 62:928-940. [PMID: 30563338 DOI: 10.1021/acs.jmedchem.8b01606] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The availability of a chemical probe to study the role of a specific domain of a protein in a concentration- and time-dependent manner is of high value. Herein, we report the identification of a highly potent and selective ERK5 inhibitor BAY-885 by high-throughput screening and subsequent structure-based optimization. ERK5 is a key integrator of cellular signal transduction, and it has been shown to play a role in various cellular processes such as proliferation, differentiation, apoptosis, and cell survival. We could demonstrate that inhibition of ERK5 kinase and transcriptional activity with a small molecule did not translate into antiproliferative activity in different relevant cell models, which is in contrast to the results obtained by RNAi technology.
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Affiliation(s)
- Duy Nguyen
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Clara Lemos
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Lars Wortmann
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Knut Eis
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Simon J Holton
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Ulf Boemer
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Dieter Moosmayer
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Uwe Eberspaecher
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Joerg Weiske
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Christian Lechner
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Stefan Prechtl
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Detlev Suelzle
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Franziska Siegel
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Florian Prinz
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Ralf Lesche
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Barbara Nicke
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | | | - Herbert Himmel
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Dominik Mumberg
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Franz von Nussbaum
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Carl F Nising
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Marcus Bauser
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Andrea Haegebarth
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
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7
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Moustakim M, Felce SL, Zaarour N, Farnie G, McCann FE, Brennan PE. Target Identification Using Chemical Probes. Methods Enzymol 2018; 610:27-58. [PMID: 30390803 DOI: 10.1016/bs.mie.2018.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical probes are small molecules with potency and selectivity for a single or small number of protein targets. A good chemical probe engages its target intracellularly and is accompanied by a chemically similar, but inactive molecule to be used as a negative control in cellular phenotypic screening. The utility of these chemical probes is ultimately governed by how well they are developed and characterized. Chemical probes either as single entities, or in chemical probes sets are being increasingly used to interrogate the biological relevance of a target in a disease model. This chapter lays out the core properties of chemical probes, summarizes the seminal and emerging techniques used to demonstrate robust intracellular target engagement. Translation of target engagement assays to disease-relevant phenotypic assays using primary patient-derived cells and tissues is also reviewed. Two examples of epigenetic chemical probe discovery and utility are presented whereby target engagement pointed to novel disease associations elucidated from poorly understood protein targets. Finally, a number of examples are discussed whereby chemical probe sets, or "chemogenomic libraries" are used to illuminate new target-disease links which may represent future directions for chemical probe utility.
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Affiliation(s)
- Moses Moustakim
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Suet Ling Felce
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Nancy Zaarour
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom; Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Gillian Farnie
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom.
| | - Fiona E McCann
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom; Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom.
| | - Paul E Brennan
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom.
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8
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A widely-applicable high-throughput cellular thermal shift assay (CETSA) using split Nano Luciferase. Sci Rep 2018; 8:9472. [PMID: 29930256 PMCID: PMC6013488 DOI: 10.1038/s41598-018-27834-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/08/2018] [Indexed: 11/15/2022] Open
Abstract
Assessment of the interactions between a drug and its protein target in a physiologically relevant cellular environment constitutes a major challenge in the pre-clinical drug discovery space. The Cellular Thermal Shift Assay (CETSA) enables such an assessment by quantifying the changes in the thermal stability of proteins upon ligand binding in intact cells. Here, we present the development and validation of a homogeneous, standardized, target-independent, and high-throughput (384- and 1536-well formats) CETSA platform that uses a split Nano Luciferase approach (SplitLuc CETSA). The broad applicability of the assay was demonstrated for diverse targets, and its performance was compared with independent biochemical and cell-based readouts using a set of well-characterized inhibitors. Moreover, we investigated the utility of the platform as a primary assay for high-throughput screening. The SplitLuc CETSA presented here enables target engagement studies for medium and high-throughput applications. Additionally, it provides a rapid assay development and screening platform for targets where phenotypic or other cell-based assays are not readily available.
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9
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Shaw J, Leveridge M, Norling C, Karén J, Molina DM, O'Neill D, Dowling JE, Davey P, Cowan S, Dabrowski M, Main M, Gianni D. Determining direct binders of the Androgen Receptor using a high-throughput Cellular Thermal Shift Assay. Sci Rep 2018; 8:163. [PMID: 29317749 PMCID: PMC5760633 DOI: 10.1038/s41598-017-18650-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023] Open
Abstract
Androgen Receptor (AR) is a key driver in prostate cancer. Direct targeting of AR has valuable therapeutic potential. However, the lack of disease relevant cellular methodologies capable of discriminating between inhibitors that directly bind AR and those that instead act on AR co-regulators has made identification of novel antagonists challenging. The Cellular Thermal Shift Assay (CETSA) is a technology enabling confirmation of direct target engagement with label-free, endogenous protein in living cells. We report the development of the first high-throughput CETSA assay (CETSA HT) to identify direct AR binders in a prostate cancer cell line endogenously expressing AR. Using this approach, we screened a pharmacology library containing both compounds reported to directly engage AR, and compounds expected to target AR co-regulators. Our results show that CETSA HT exclusively identifies direct AR binders, differentiating them from co-regulator inhibitors where other cellular assays measuring functional responses cannot. Using this CETSA HT approach we can derive apparent binding affinities for a range of AR antagonists, which represent an intracellular measure of antagonist-receptor Ki performed for the first time in a label-free, disease-relevant context. These results highlight the potential of CETSA HT to improve the success rates for novel therapeutic interventions directly targeting AR.
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Affiliation(s)
- Joseph Shaw
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK.
| | - Mathew Leveridge
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK
| | | | | | | | - Daniel O'Neill
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK
| | - James E Dowling
- Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 35 Gatehouse Park, Waltham, MA, USA
| | - Paul Davey
- Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK
| | - Suzanna Cowan
- Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK
| | | | - Martin Main
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK
| | - Davide Gianni
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK.
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10
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McNulty DE, Bonnette WG, Qi H, Wang L, Ho TF, Waszkiewicz A, Kallal LA, Nagarajan RP, Stern M, Quinn AM, Creasy CL, Su DS, Graves AP, Annan RS, Sweitzer SM, Holbert MA. A High-Throughput Dose-Response Cellular Thermal Shift Assay for Rapid Screening of Drug Target Engagement in Living Cells, Exemplified Using SMYD3 and IDO1. SLAS DISCOVERY 2017; 23:34-46. [DOI: 10.1177/2472555217732014] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A persistent problem in early small-molecule drug discovery is the frequent lack of rank-order correlation between biochemical potencies derived from initial screens using purified proteins and the diminished potency and efficacy observed in subsequent disease-relevant cellular phenotypic assays. The introduction of the cellular thermal shift assay (CETSA) has bridged this gap by enabling assessment of drug target engagement directly in live cells based on ligand-induced changes in protein thermal stability. Initial success in applying CETSA across multiple drug target classes motivated our investigation into replacing the low-throughput, manually intensive Western blot readout with a quantitative, automated higher-throughput assay that would provide sufficient capacity to use CETSA as a primary hit qualification strategy. We introduce a high-throughput dose-response cellular thermal shift assay (HTDR-CETSA), a single-pot homogenous assay adapted for high-density microtiter plate format. The assay features titratable BacMam expression of full-length target proteins fused to the DiscoverX 42 amino acid ePL tag in HeLa suspension cells, facilitating enzyme fragment complementation–based chemiluminescent quantification of ligand-stabilized soluble protein. This simplified format can accommodate determination of full-dose CETSA curves for hundreds of individual compounds/analyst/day in replicates. HTDR-CETSA data generated for substrate site and alternate binding mode inhibitors of the histone-lysine N-methyltransferase SMYD3 in HeLa suspension cells demonstrate excellent correlation with rank-order potencies observed in cellular mechanistic assays and direct translation to target engagement of endogenous Smyd3 in cancer-relevant cell lines. We envision this workflow to be generically applicable to HTDR-CETSA screening spanning a wide variety of soluble intracellular protein target classes.
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11
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Identification of PARP14 inhibitors using novel methods for detecting auto-ribosylation. Biochem Biophys Res Commun 2017; 486:626-631. [DOI: 10.1016/j.bbrc.2017.03.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/13/2017] [Indexed: 12/19/2022]
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12
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Nicholas DA, Andrieu G, Strissel KJ, Nikolajczyk BS, Denis GV. BET bromodomain proteins and epigenetic regulation of inflammation: implications for type 2 diabetes and breast cancer. Cell Mol Life Sci 2017; 74:231-243. [PMID: 27491296 PMCID: PMC5222701 DOI: 10.1007/s00018-016-2320-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/16/2016] [Accepted: 07/29/2016] [Indexed: 12/18/2022]
Abstract
Chronic inflammation drives pathologies associated with type 2 diabetes (T2D) and breast cancer. Obesity-driven inflammation may explain increased risk and mortality of breast cancer with T2D reported in the epidemiology literature. Therapeutic approaches to target inflammation in both T2D and cancer have so far fallen short of the expected improvements in disease pathogenesis or outcomes. The targeting of epigenetic regulators of cytokine transcription and cytokine signaling offers one promising, untapped approach to treating diseases driven by inflammation. Recent work has deeply implicated the Bromodomain and Extra-Terminal domain (BET) proteins, which are acetylated histone "readers", in epigenetic regulation of inflammation. This review focuses on inflammation associated with T2D and breast cancer, and the possibility of targeting BET proteins as an approach to regulating inflammation in the clinic. Understanding inflammation in the context of BET protein regulation may provide a basis for designing promising therapeutics for T2D and breast cancer.
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Affiliation(s)
- Dequina A Nicholas
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA
- Department of Microbiology, Training Program in Inflammatory Disorders, 72 East Concord Street, K520, Boston, MA, 02118, USA
| | - Guillaume Andrieu
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA
| | - Katherine J Strissel
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA
| | - Barbara S Nikolajczyk
- Department of Microbiology, Training Program in Inflammatory Disorders, 72 East Concord Street, K520, Boston, MA, 02118, USA
| | - Gerald V Denis
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA.
- Section of Hematology/Oncology, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, 72 East Concord Street, K520, Boston, MA, 02118, USA.
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13
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Abstract
The cellular thermal shift assay (CETSA) was introduced in 2013 as a means to assess drug binding in complex environments such as cell lysates, live cells, and even tissues. The assay principle relies on the well-proven biophysical concept of ligand-induced thermal stabilization of proteins, which in CETSA applications is measured as a persistent presence of soluble protein at elevated temperatures. Given its recent development, we have just started to learn about the benefits and pitfalls of the method as it is applied to a growing number of protein target classes, the majority of which are intracellular soluble proteins. One of the early technology developments concerned the transfer of the original assay procedure from PCR tubes and Western blot detection of soluble protein to a homogeneous assay in high-density microplates. A move to high-throughput formats is essential for a more systematic application in drug discovery settings, as well as in academic efforts for validating chemical probes through studies of structure-activity relationships. This perspective aims at providing an overview of knowledge gained in microplate formatting of CETSA and makes an attempt at forecasting future applications.
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Affiliation(s)
- Brinton Seashore-Ludlow
- 1 Chemical Biology Consortium Sweden, Science for Life Laboratories, Stockholm, Sweden.,2 Department of Medical Biochemistry and Biophysics, Division of Translational Medicine and Chemical Biology, Karolinska Institutet, Solna, Sweden
| | - Thomas Lundbäck
- 1 Chemical Biology Consortium Sweden, Science for Life Laboratories, Stockholm, Sweden.,2 Department of Medical Biochemistry and Biophysics, Division of Translational Medicine and Chemical Biology, Karolinska Institutet, Solna, Sweden
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14
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Small-Molecule Target Engagement in Cells. Cell Chem Biol 2016; 23:435-41. [DOI: 10.1016/j.chembiol.2016.03.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 01/03/2023]
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15
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Abstract
The impressive advances in the generation and interpretation of functional omics data have greatly contributed to a better understanding of the (patho-)physiology of many biological systems and led to a massive increase in the number of specific targets and phenotypes to investigate in both basic and applied research. The obvious complexity revealed by these studies represents a major challenge to the research community and asks for improved target characterisation strategies with the help of reliable, high-quality assays. Thus, the use of living cells has become an integral part of many research activities because the cellular context more closely represents target-specific interrelations and activity patterns. Although still predominant, the use of traditional two-dimensional (2D) monolayer cell culture models has been gradually complemented by studies based on three-dimensional (3D) spheroid (Sutherland 1988) and other 3D tissue culture systems (Santos et al. 2012; Matsusaki et al. 2014) in an attempt to employ model systems more closely representing the microenvironment of cells in the body. Hence, quite a variety of state-of-the-art cell culture models are available for the generation of novel chemical probes or the identification of starting points for drug development in translational research and pharma drug discovery. In order to cope with these information-rich formats and their increasing technical complexity, cell-based assay development has become a scientific research topic in its own right and is used to ensure the provision of significant, reliable and high-quality data outlasting any discussions related to the current "irreproducibility epidemic" (Dolgin 2014; Prinz et al. 2011; Schatz 2014). At the same time the use of cells in microplate assay formats has become state of the art and greatly facilitates rigorous cell-based assay development by providing the researcher with the opportunity to address the multitude of factors affecting the actual assay results in a systematic fashion and a timely manner. This microplate-based assay development strategy should result in the setting up of more robust and reliable test systems that ensure and increase the confidence in the statistical significance of the actual data generated. And, although assay miniaturisation is essential in order to achieve this, most, if not all, cell-based assays can be easily reformatted and adapted to be used in this format in a straightforward manner. This synopsis aims at summarising valuable, general observations made when implementing a diverse set of functional cellular in vitro assays at Bayer Pharma AG without claiming to deeply review all of the literature available in each and every detail. In addition, phenotypic assays (Moffat et al. 2014) or label-free detection methods (Minor 2008) are not discussed. Although this essay tries to cover the most relevant technological developments in the field, it nevertheless may express personal preferences and peculiarities of the author's approach to state-of-the-art cell-based assay development. For additional reviews covering the actual field, see Wunder et al. (2008) and Michelini et al. (2010).
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Affiliation(s)
- Gernot Langer
- Bayer Healthcare, Bayer Pharma AG, Lead Discovery Berlin - Screening, Müllerstr. 178, 13353, Berlin, Germany.
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16
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Target engagement and drug residence time can be observed in living cells with BRET. Nat Commun 2015; 6:10091. [PMID: 26631872 PMCID: PMC4686764 DOI: 10.1038/ncomms10091] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/30/2015] [Indexed: 12/18/2022] Open
Abstract
The therapeutic action of drugs is predicated on their physical engagement with cellular targets. Here we describe a broadly applicable method using bioluminescence resonance energy transfer (BRET) to reveal the binding characteristics of a drug with selected targets within intact cells. Cell-permeable fluorescent tracers are used in a competitive binding format to quantify drug engagement with the target proteins fused to Nanoluc luciferase. The approach enabled us to profile isozyme-specific engagement and binding kinetics for a panel of histone deacetylase (HDAC) inhibitors. Our analysis was directed particularly to the clinically approved prodrug FK228 (Istodax/Romidepsin) because of its unique and largely unexplained mechanism of sustained intracellular action. Analysis of the binding kinetics by BRET revealed remarkably long intracellular residence times for FK228 at HDAC1, explaining the protracted intracellular behaviour of this prodrug. Our results demonstrate a novel application of BRET for assessing target engagement within the complex milieu of the intracellular environment.
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17
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Johnson GR, Li J, Shariff A, Rohde GK, Murphy RF. Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules. PLoS Comput Biol 2015; 11:e1004614. [PMID: 26624011 PMCID: PMC4704559 DOI: 10.1371/journal.pcbi.1004614] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/19/2015] [Indexed: 12/23/2022] Open
Abstract
Characterizing the spatial distribution of proteins directly from microscopy images is a difficult problem with numerous applications in cell biology (e.g. identifying motor-related proteins) and clinical research (e.g. identification of cancer biomarkers). Here we describe the design of a system that provides automated analysis of punctate protein patterns in microscope images, including quantification of their relationships to microtubules. We constructed the system using confocal immunofluorescence microscopy images from the Human Protein Atlas project for 11 punctate proteins in three cultured cell lines. These proteins have previously been characterized as being primarily located in punctate structures, but their images had all been annotated by visual examination as being simply "vesicular". We were able to show that these patterns could be distinguished from each other with high accuracy, and we were able to assign to one of these subclasses hundreds of proteins whose subcellular localization had not previously been well defined. In addition to providing these novel annotations, we built a generative approach to modeling of punctate distributions that captures the essential characteristics of the distinct patterns. Such models are expected to be valuable for representing and summarizing each pattern and for constructing systems biology simulations of cell behaviors.
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Affiliation(s)
- Gregory R. Johnson
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Center for Bioimage Informatics, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jieyue Li
- Center for Bioimage Informatics, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Aabid Shariff
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Center for Bioimage Informatics, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Gustavo K. Rohde
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Center for Bioimage Informatics, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Robert F. Murphy
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Center for Bioimage Informatics, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Departments of Biological Sciences and Machine Learning, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Faculty of Biology and Freiburg Institute for Advanced Studies, Albert Ludwig University of Freiburg, Freiburg, Germany
- * E-mail:
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18
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Romero FA, Taylor AM, Crawford TD, Tsui V, Côté A, Magnuson S. Disrupting Acetyl-Lysine Recognition: Progress in the Development of Bromodomain Inhibitors. J Med Chem 2015; 59:1271-98. [PMID: 26572217 DOI: 10.1021/acs.jmedchem.5b01514] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bromodomains, small protein modules that recognize acetylated lysine on histones, play a significant role in the epigenome, where they function as "readers" that ultimately determine the functional outcome of the post-translational modification. Because the initial discovery of selective BET inhibitors have helped define the role of that protein family in oncology and inflammation, BET bromodomains have continued to garner the most attention of any other bromodomain. More recently, non-BET bromodomain inhibitors that are potent and selective have been disclosed for ATAD2, CBP, BRD7/9, BRPF, BRPF/TRIM24, CECR2, SMARCA4, and BAZ2A/B. Such novel inhibitors can be used to probe the physiological function of these non-BET bromodomains and further understanding of their role in certain disease states. Here, we provide an update to the progress in identifying selective bromodomain inhibitors and their use as biological tools, as well as our perspective on the field.
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Affiliation(s)
- F Anthony Romero
- Discovery Chemistry, Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Alexander M Taylor
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Terry D Crawford
- Discovery Chemistry, Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Vickie Tsui
- Discovery Chemistry, Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Alexandre Côté
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven Magnuson
- Discovery Chemistry, Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
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19
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Doyle SK, Pop MS, Evans HL, Koehler AN. Advances in discovering small molecules to probe protein function in a systems context. Curr Opin Chem Biol 2015; 30:28-36. [PMID: 26615565 DOI: 10.1016/j.cbpa.2015.10.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 12/15/2022]
Abstract
High throughput screening (HTS) has historically been used for drug discovery almost exclusively by the pharmaceutical industry. Due to a significant decrease in costs associated with establishing a high throughput facility and an exponential interest in discovering probes of development and disease associated biomolecules, HTS core facilities have become an integral part of most academic and non-profit research institutions over the past decade. This major shift has led to the development of new HTS methodologies extending beyond the capabilities and target classes used in classical drug discovery approaches such as traditional enzymatic activity-based screens. In this brief review we describe some of the most interesting developments in HTS technologies and methods for chemical probe discovery.
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Affiliation(s)
- Shelby K Doyle
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marius S Pop
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helen L Evans
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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20
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Zhan Y, Kost-Alimova M, Shi X, Leo E, Bardenhagen JP, Shepard HE, Appikonda S, Vangamudi B, Zhao S, Tieu TN, Jiang S, Heffernan TP, Marszalek JR, Toniatti C, Draetta G, Tyler J, Barton M, Jones P, Palmer WS, Geck Do MK, Andersen JN. Development of novel cellular histone-binding and chromatin-displacement assays for bromodomain drug discovery. Epigenetics Chromatin 2015; 8:37. [PMID: 26396593 PMCID: PMC4578755 DOI: 10.1186/s13072-015-0026-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/01/2015] [Indexed: 01/09/2023] Open
Abstract
Background Proteins that ‘read’ the histone code are central elements in epigenetic control and bromodomains, which bind acetyl-lysine motifs, are increasingly recognized as potential mediators of disease states. Notably, the first BET bromodomain-based therapies have entered clinical trials and there is a broad interest in dissecting the therapeutic relevance of other bromodomain-containing proteins in human disease. Typically, drug development is facilitated and expedited by high-throughput screening, where assays need to be sensitive, robust, cost-effective and scalable. However, for bromodomains, which lack catalytic activity that otherwise can be monitored (using classical enzymology), the development of cell-based, drug-target engagement assays has been challenging. Consequently, cell biochemical assays have lagged behind compared to other protein families (e.g., histone deacetylases and methyltransferases). Results Here, we present a suite of novel chromatin and histone-binding assays using AlphaLISA, in situ cell extraction and fluorescence-based, high-content imaging. First, using TRIM24 as an example, the homogenous, bead-based AlphaScreen technology was modified from a biochemical peptide-competition assay to measure binding of the TRIM24 bromodomain to endogenous histone H3 in cells (AlphaLISA). Second, a target agnostic, high-throughput imaging platform was developed to quantify the ability of chemical probes to dissociate endogenous proteins from chromatin/nuclear structures. While overall nuclear morphology is maintained, the procedure extracts soluble, non-chromatin-bound proteins from cells with drug-target displacement visualized by immunofluorescence (IF) or microscopy of fluorescent proteins. Pharmacological evaluation of these assays cross-validated their utility, sensitivity and robustness. Finally, using genetic and pharmacological approaches, we dissect domain contribution of TRIM24, BRD4, ATAD2 and SMARCA2 to chromatin binding illustrating the versatility/utility of the in situ cell extraction platform. Conclusions In summary, we have developed two novel complementary and cell-based drug-target engagement assays, expanding the repertoire of pharmacodynamic assays for bromodomain tool compound development. These assays have been validated through a successful TRIM24 bromodomain inhibitor program, where a micromolar lead molecule (IACS-6558) was optimized using cell-based assays to yield the first single-digit nanomolar TRIM24 inhibitor (IACS-9571). Altogether, the assay platforms described herein are poised to accelerate the discovery and development of novel chemical probes to deliver on the promise of epigenetic-based therapies. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0026-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanai Zhan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Maria Kost-Alimova
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Xi Shi
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Elisabetta Leo
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Jennifer P Bardenhagen
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Hannah E Shepard
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Srikanth Appikonda
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Bhavatarini Vangamudi
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Shuping Zhao
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Trang N Tieu
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Shiming Jiang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Joseph R Marszalek
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Carlo Toniatti
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Giulio Draetta
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Jessica Tyler
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Michelle Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Philip Jones
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Wylie S Palmer
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Mary K Geck Do
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Jannik N Andersen
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA.,XTuit Pharmaceuticals, 700 Main Street, Cambridge, MA 02139 USA
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21
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Jung M, Gelato KA, Fernández-Montalván A, Siegel S, Haendler B. Targeting BET bromodomains for cancer treatment. Epigenomics 2015; 7:487-501. [PMID: 26077433 DOI: 10.2217/epi.14.91] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The bromodomain and extraterminal (BET) subfamily of bromodomain-containing proteins has emerged in the last few years as an exciting, novel target group. BRD4, the best studied BET protein, is implicated in a number of hematological and solid tumors. This is linked to its role in modulating transcription elongation of essential genes involved in cell cycle and apoptosis such as c-Myc and BCL2. Potent BET inhibitors with promising antitumor efficacy in a number of preclinical cancer models have been identified in recent years. This led to clinical studies focusing mostly on the treatment of leukemia and lymphoma, and first encouraging signs of efficacy have already been reported. Here we discuss the biology of BRD4, its known interaction partners and implication in different tumor types. Further, we summarize the current knowledge on BET bromodomain inhibitors.
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Affiliation(s)
- Marie Jung
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany.,Institute of Chemistry & Biochemistry, Free University, D-14195 Berlin, Germany
| | - Kathy A Gelato
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany
| | | | - Stephan Siegel
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany
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