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Hua L, Wang D, Wang K, Wang Y, Gu J, Zhang Q, You Q, Wang L. Design of Tracers in Fluorescence Polarization Assay for Extensive Application in Small Molecule Drug Discovery. J Med Chem 2023; 66:10934-10958. [PMID: 37561645 DOI: 10.1021/acs.jmedchem.3c00881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Development of fluorescence polarization (FP) assays, especially in a competitive manner, is a potent and mature tool for measuring the binding affinities of small molecules. This approach is suitable for high-throughput screening (HTS) for initial ligands and is also applicable for further study of the structure-activity relationships (SARs) of candidate compounds for drug discovery. Buffer and tracer, especially rational design of the tracer, play a vital role in an FP assay system. In this perspective, we provided different kinds of approaches for tracer design based on successful cases in recent years. We classified these tracers by different types of ligands in tracers, including peptide, nucleic acid, natural product, and small molecule. To make this technology accessible for more targets, we briefly described the basic theory and workflow, followed by highlighting the design and application of typical FP tracers from a perspective of medicinal chemistry.
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Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Danni Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Keran Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jinying Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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2
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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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3
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Ligand Discovery: High-Throughput Binding: Fluorescence Polarization (Anisotropy). Methods Mol Biol 2021. [PMID: 33877601 DOI: 10.1007/978-1-0716-1197-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
High-throughput assays based on fluorescence polarization (or fluorescence anisotropy) technology have often been employed for primary hit-finding in drug discovery. These binding assays provide a homogeneous format and consistent performance and offer advantages over some other optical methods. Developments in assay design and improvements in fluorescent probes have enabled the application of the technique to even complex biological systems. Here we describe the practical considerations for development of FP assays applied in high-throughput screening, including fluorophore selection, assay design, data analysis, and approaches for detecting compound interference.
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4
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Pallesen JS, Narayanan D, Tran KT, Solbak SMØ, Marseglia G, Sørensen LME, Høj LJ, Munafò F, Carmona RMC, Garcia AD, Desu HL, Brambilla R, Johansen TN, Popowicz GM, Sattler M, Gajhede M, Bach A. Deconstructing Noncovalent Kelch-like ECH-Associated Protein 1 (Keap1) Inhibitors into Fragments to Reconstruct New Potent Compounds. J Med Chem 2021; 64:4623-4661. [PMID: 33818106 DOI: 10.1021/acs.jmedchem.0c02094] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Targeting the protein-protein interaction (PPI) between nuclear factor erythroid 2-related factor 2 (Nrf2) and Kelch-like ECH-associated protein 1 (Keap1) is a potential therapeutic strategy to control diseases involving oxidative stress. Here, six classes of known small-molecule Keap1-Nrf2 PPI inhibitors were dissected into 77 fragments in a fragment-based deconstruction reconstruction (FBDR) study and tested in four orthogonal assays. This gave 17 fragment hits of which six were shown by X-ray crystallography to bind in the Keap1 Kelch binding pocket. Two hits were merged into compound 8 with a 220-380-fold stronger affinity (Ki = 16 μM) relative to the parent fragments. Systematic optimization resulted in several novel analogues with Ki values of 0.04-0.5 μM, binding modes determined by X-ray crystallography, and enhanced microsomal stability. This demonstrates how FBDR can be used to find new fragment hits, elucidate important ligand-protein interactions, and identify new potent inhibitors of the Keap1-Nrf2 PPI.
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Affiliation(s)
- Jakob S Pallesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Dilip Narayanan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kim T Tran
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Sara M Ø Solbak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Giuseppe Marseglia
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.,Food and Drug Department, University of Parma, Parco Area delle Scienze 27/a, 43124 Parma, Italy
| | - Louis M E Sørensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lars J Høj
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Federico Munafò
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Rosa M C Carmona
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anthony D Garcia
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.,École Nationale Supérieure de Chimie de Rennes, 11 Allée de Beaulieu, CS 50837, Rennes Cedex 7 35708, France
| | - Haritha L Desu
- The Miami Project to Cure Paralysis, Dept. Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
| | - Roberta Brambilla
- The Miami Project to Cure Paralysis, Dept. Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida 33136, United States.,Department of Neurobiology Research, Institute of Molecular Medicine, and BRIDGE-Brain Research Inter Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, DK-5000 Odense, Denmark
| | - Tommy N Johansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Michael Gajhede
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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5
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Vinegoni C, Feruglio PF, Gryczynski I, Mazitschek R, Weissleder R. Fluorescence anisotropy imaging in drug discovery. Adv Drug Deliv Rev 2019; 151-152:262-288. [PMID: 29410158 PMCID: PMC6072632 DOI: 10.1016/j.addr.2018.01.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
Abstract
Non-invasive measurement of drug-target engagement can provide critical insights in the molecular pharmacology of small molecule drugs. Fluorescence polarization/fluorescence anisotropy measurements are commonly employed in protein/cell screening assays. However, the expansion of such measurements to the in vivo setting has proven difficult until recently. With the advent of high-resolution fluorescence anisotropy microscopy it is now possible to perform kinetic measurements of intracellular drug distribution and target engagement in commonly used mouse models. In this review we discuss the background, current advances and future perspectives in intravital fluorescence anisotropy measurements to derive pharmacokinetic and pharmacodynamic measurements in single cells and whole organs.
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Affiliation(s)
- Claudio Vinegoni
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Paolo Fumene Feruglio
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona, Italy
| | - Ignacy Gryczynski
- University of North Texas Health Science Center, Institute for Molecular Medicine, Fort Worth, TX, United States
| | - Ralph Mazitschek
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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6
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Tereshchenkov AG, Shishkina AV, Karpenko VV, Chertkov VA, Konevega AL, Kasatsky PS, Bogdanov AA, Sumbatyan NV. New Fluorescent Macrolide Derivatives for Studying Interactions of Antibiotics and Their Analogs with the Ribosomal Exit Tunnel. BIOCHEMISTRY (MOSCOW) 2017; 81:1163-1172. [PMID: 27908240 DOI: 10.1134/s0006297916100138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Novel fluorescent derivatives of macrolide antibiotics related to tylosin bearing rhodamine, fluorescein, Alexa Fluor 488, BODIPY FL, and nitrobenzoxadiazole (NBD) residues were synthesized. The formation of complexes of these compounds with 70S E. coli ribosomes was studied by measuring the fluorescence polarization depending on the ribosome amount at constant concentration of the fluorescent substance. With the synthesized fluorescent tylosin derivatives, the dissociation constants for ribosome complexes with several known antibiotics and macrolide analogs previously obtained were determined. It was found that the fluorescent tylosin derivatives containing BODIPY FL and NBD groups could be used to screen the binding of novel antibiotics to bacterial ribosomes in the macrolide-binding site.
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Affiliation(s)
- A G Tereshchenkov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.
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7
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Blommel P, Hanson GT, Vogel KW. Multiplexing Fluorescence Polarization Assays to Increase Information Content Per Screen: Applications for Screening Steroid Hormone Receptors. ACTA ACUST UNITED AC 2016; 9:294-302. [PMID: 15191646 DOI: 10.1177/1087057104264420] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As the push to reduce cost per well in high-throughput screening reaches the practical limitations of liquid handling, future cost savings will likely arise from an increase in information content per well. One strategy to increase information content is to perform discreet assays against multiple targets in a single well. In such assays, reagent usage and liquid handling steps do not scale-up in direct proportion to the increase in information content, providing for a simple method to increase data points per screen without further reductions in assay volume. The authors have used tracers incorporating the spectrally distinct fluorophores fluorescein and TAMRA to develop a high-throughput assay to identify selective estrogen receptor α or proges-terone receptor ligands. Selectivity is assessed immediately in this assay, with no requirement for separate follow-up screening to determine selectivity. This methodology is easily adaptable to other target classes.
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Affiliation(s)
- Paul Blommel
- Invitrogen Drug Discovery Solutions, 501 Charmany Drive, Madison, WI 53719, USA
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8
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Harris A, Cox S, Burns D, Norey C. Miniaturization of Fluorescence Polarization Receptor-Binding Assays Using CyDye-Labeled Ligands. ACTA ACUST UNITED AC 2016; 8:410-20. [PMID: 14567793 DOI: 10.1177/1087057103256319] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fluorescence polarization (FP) is an established technique for the study of biological interactions and is frequently used in the high-throughput screening (HTS) of potential new drug targets. This work describes the miniaturization of FP receptor assays to 1536-well formats for use in HTS. The FP assays were initially developed in 384-well microplates using CyDye-labeled nonpeptide and peptide ligands. Receptor expression levels varied from ∼1 to 10 pmols receptor per mg protein, and ligand concentrations were in the 0.5- to 1.0-nM range. The FP assays were successfully miniaturized to 1536-well formats using Cy3B-labeled ligands, significantly reducing reagent consumption, particularly the receptor source, without compromising assay reliability. Z' factor values determined for the FP receptor assays in both 384- and 1536-well formats were found to be > 0.5, indicating the assays to be robust, reliable, and suitable for HTS purposes.
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Affiliation(s)
- Alison Harris
- Amersham Biosciences, UK Limited, The Maynard Centre, Buckinghamshire, UK
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9
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Jäger S, Garbow N, Kirsch A, Preckel H, Gandenberger FU, Herrenknecht K, Rüdiger M, Hutchinson JP, Bingham RP, Ramon F, Bardera A, Martin J. A Modular, Fully Integrated Ultra-High-Throughput Screening System Based on Confocal Fluorescence Analysis Techniques. ACTA ACUST UNITED AC 2016; 8:648-59. [PMID: 14711390 DOI: 10.1177/1087057103258475] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The rapid increase in size of compound libraries, as well as new targets emerging from the Human Genome Project, require progress in ultra-high-throughput screening (uHTS) systems. In a joint effort with scientists and engineers from the biotech and the pharmaceutical industry, a modular, fully integrated system for miniaturized uHTS was developed. The goal was to achieve high data quality in small assay volumes (1-4 μL) combined with reliable and unattended operation. Two new confocal fluorescence readers have been designed. One of the instruments is a 4-channel confocal fluorescence reader, measuring with 4 objectives in parallel. The fluorescence readout is based on single-molecule detection methods, allowing high sensitivity at low tracer concentrationsand delivering an information-rich output. The other instrument isa confocal fluorescence im aging reader, where the imagesare analyzed in terms of generic patternsand quantified in units of intensity per pixel. Both readers are spanning the application range from assays with isolated targets in homogenous solution or membrane vesiclebased assays (4-channel reader) to cell-based assays (imaging reader). Results from a comprehensive test on these assay types demonstrate the high quality and robustness of this screening system.
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Affiliation(s)
- Stefan Jäger
- Evotec OAI/Evotec Technologies, Hamburg, Germany.
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10
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Abstract
Steady-state measurements of fluorescence polarization have been widely adopted in the field of high-throughput screening for the study of biomolecular interactions. This chapter reviews the basic theory of fluorescence polarization, the underlying principle for using fluorescence polarization to study interactions between small-molecule fluorophores and macromolecular targets, and representative applications of fluorescence polarization in high-throughput screening.
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Affiliation(s)
- Xinyi Huang
- Immunology, Inflammation and Infectious Diseases Discovery and Translational Area Roche Pharma Research & Early Development, Roche Innovation Center Shanghai, Roche R&D Center (China) Ltd, 720 Cai Lun Road, Bldg 5, Pudong, Shanghai, 201203, China.
| | - Ann Aulabaugh
- Immunology, Inflammation and Infectious Diseases Discovery and Translational Area Roche Pharma Research & Early Development, Roche Innovation Center Shanghai, Roche R&D Center (China) Ltd, 720 Cai Lun Road, Bldg 5, Pudong, Shanghai, 201203, China
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11
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Kosa NM, Foley TL, Burkart MD. Fluorescent techniques for discovery and characterization of phosphopantetheinyl transferase inhibitors. J Antibiot (Tokyo) 2013; 67:113-20. [PMID: 24192555 DOI: 10.1038/ja.2013.106] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/26/2013] [Accepted: 09/13/2013] [Indexed: 11/09/2022]
Abstract
Phosphopantetheinyl transferase (PPTase; E.C. 2.7.8.-) activates biosynthetic pathways that synthesize both primary and secondary metabolites in bacteria. Inhibitors of these enzymes have the potential to serve as antibiotic compounds that function through a unique mode of action and possess clinical utility. Here we report a direct and continuous assay for this enzyme class based upon monitoring polarization of a fluorescent phosphopantetheine analog as it is transferred from a low-molecular weight CoA substrate to higher-molecular weight protein acceptor. We demonstrate the utility of this method for the biochemical characterization of PPTase Sfp, a canonical representative from this class. We also establish the portability of this technique to other homologs by adapting the assay to function with the human PPTase, a target for which a microplate detection method does not currently exist. Comparison of these targets provides a basis to predict the therapeutic index of inhibitor candidates and offers a valuable characterization of enzyme activity.
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Affiliation(s)
- Nicolas M Kosa
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Timothy L Foley
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, CA, USA
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12
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Jude KM, Hartland A, Berger JM. Real-time detection of DNA topological changes with a fluorescently labeled cruciform. Nucleic Acids Res 2013; 41:e133. [PMID: 23680786 PMCID: PMC3711437 DOI: 10.1093/nar/gkt413] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Topoisomerases are essential cellular enzymes that maintain the appropriate topological status of DNA and are the targets of several antibiotic and chemotherapeutic agents. High-throughput (HT) analysis is desirable to identify new topoisomerase inhibitors, but standard in vitro assays for DNA topology, such as gel electrophoresis, are time-consuming and are not amenable to HT analysis. We have exploited the observation that closed-circular DNA containing an inverted repeat can release the free energy stored in negatively supercoiled DNA by extruding the repeat as a cruciform. We inserted an inverted repeat containing a fluorophore-quencher pair into a plasmid to enable real-time monitoring of plasmid supercoiling by a bacterial topoisomerase, Escherichia coli gyrase. This substrate produces a fluorescent signal caused by the extrusion of the cruciform and separation of the labels as gyrase progressively underwinds the DNA. Subsequent relaxation by a eukaryotic topoisomerase, human topo IIα, causes reintegration of the cruciform and quenching of fluorescence. We used this approach to develop a HT screen for inhibitors of gyrase supercoiling. This work demonstrates that fluorescently labeled cruciforms are useful as general real-time indicators of changes in DNA topology that can be used to monitor the activity of DNA-dependent motor proteins.
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Affiliation(s)
- Kevin M Jude
- Department of Molecular and Cellular Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720-3220, USA
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13
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Breuer S, Chang MW, Yuan J, Torbett BE. Identification of HIV-1 inhibitors targeting the nucleocapsid protein. J Med Chem 2012; 55:4968-77. [PMID: 22587465 DOI: 10.1021/jm201442t] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The HIV-1 nucleocapsid (NC) is a RNA/DNA binding protein encoded within the Gag polyprotein, which is critical for the selection and chaperoning of viral genomic RNA during virion assembly. RNA/DNA binding occurs through a highly conserved zinc-knuckle motif present in NC. Given the necessity of NC-viral RNA/DNA interaction for viral replication, identification of compounds that disrupt the NC-RNA/DNA interaction may have value as an antiviral strategy. To identify small molecules that disrupt NC-viral RNA/DNA binding, a high-throughput fluorescence polarization assay was developed and a library of 14,400 diverse, druglike compounds was screened. Compounds that disrupted NC binding to a fluorescence-labeled DNA tracer were next evaluated by differential scanning fluorimetry to identify compounds that must bind to NC or Gag to impart their effects. Two compounds were identified that inhibited NC-DNA interaction, specifically bound NC with nanomolar affinity, and showed modest anti-HIV-1 activity in ex vivo cell assays.
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Affiliation(s)
- Sebastian Breuer
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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14
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Joensson HN, Zhang C, Uhlén M, Andersson-Svahn H. A homogeneous assay for protein analysis in droplets by fluorescence polarization. Electrophoresis 2012; 33:436-9. [PMID: 22228311 DOI: 10.1002/elps.201100350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 10/10/2011] [Accepted: 10/11/2011] [Indexed: 11/10/2022]
Abstract
We present a novel homogeneous ("mix-incubate-read") droplet microfluidic assay for specific protein detection in picoliter volumes by fluorescence polarization (FP), for the first time demonstrating the use of FP in a droplet microfluidic assay. Using an FP-based assay we detect streptavidin concentrations as low as 500 nM and demonstrate that an FP assay allows us to distinguish droplets containing 5 μM rabbit IgG from droplets without IgG with an accuracy of 95%, levels relevant for hybridoma screening. This adds to the repertoire of droplet assay techniques a direct protein detection method which can be performed entirely inside droplets without the need for labeling of the analyte molecules.
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Affiliation(s)
- Haakan N Joensson
- Division of Nanobiotechnology, Royal Institute of Technology (KTH), Albanova University Center, Stockholm, Sweden.
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15
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Geiss BJ, Stahla-Beek HJ, Hannah AM, Gari HH, Henderson BR, Saeedi BJ, Keenan SM. A high-throughput screening assay for the identification of flavivirus NS5 capping enzyme GTP-binding inhibitors: implications for antiviral drug development. ACTA ACUST UNITED AC 2011; 16:852-61. [PMID: 21788392 DOI: 10.1177/1087057111412183] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There are no effective antivirals currently available for the treatment of flavivirus infection in humans. As such, the identification and characterization of novel drug target sites are critical to developing new classes of antiviral drugs. The flavivirus NS5 N-terminal capping enzyme (CE) is vital for the formation of the viral RNA cap structure, which directs viral polyprotein translation and stabilizes the 5' end of the viral genome. The structure of the flavivirus CE has been solved, and a detailed understanding of the CE-guanosine triphosphate (GTP) and CE-RNA cap interactions is available. Because of the essential nature of the interaction for viral replication, disrupting CE-GTP binding is an attractive approach for drug development. The authors have previously developed a robust assay for monitoring CE-GTP binding in real time. They adapted this assay for high-throughput screening and performed a pilot screen of 46 323 commercially available compounds. A number of small-molecule inhibitors capable of displacing a fluorescently labeled GTP in vitro were identified, and a second functional assay was developed to identify false positives. The results presented indicate that the flavivirus CE cap-binding site is a valuable new target site for antiviral drug discovery and should be further exploited for broad-spectrum anti-flaviviral drug development.
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Affiliation(s)
- Brian J Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
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16
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Johnson RL, Hwang JY, Arnold LA, Huang R, Wichterman J, Augustinaite I, Austin CP, Inglese J, Guy RK, Huang W. A quantitative high-throughput screen identifies novel inhibitors of the interaction of thyroid receptor beta with a peptide of steroid receptor coactivator 2. JOURNAL OF BIOMOLECULAR SCREENING 2011; 16:618-27. [PMID: 21482722 PMCID: PMC3162318 DOI: 10.1177/1087057111402199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The thyroid hormone receptors (TR) are members of the nuclear hormone receptor (NHR) superfamily that regulate development, growth, and metabolism. Upon ligand binding, TR releases bound corepressors and recruits coactivators to modulate target gene expression. Steroid receptor coactivator 2 (SRC2) is an important coregulator that interacts with TRβ to activate gene transcription. To identify novel inhibitors of the TRβ and SRC2 interaction, the authors performed a quantitative high-throughput screen (qHTS) of a TRβ-SRC2 fluorescence polarization assay against more than 290 000 small molecules. The qHTS assayed compounds at 6 concentrations up to 92 µM to generate titration-response curves and determine the potency and efficacy of all compounds. The qHTS data set enabled the characterization of actives for structure-activity relationships as well as for potential artifacts such as fluorescence interference. Selected qHTS actives were tested in the screening assay using fluoroprobes labeled with Texas Red or fluorescein. The retest identified 19 series and 4 singletons as active in both assays with 40% or greater efficacy, free of compound interference, and not toxic to mammalian cells. Selected compounds were tested as independent samples, and a methylsulfonylnitrobenzoate series inhibited the TRβ-SRC2 interaction with 5 µM IC(50). This series represents a new class of thyroid hormone receptor-coactivator modulators.
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Affiliation(s)
- Ronald L Johnson
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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17
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Shapiro A, Jahic H, Prasad S, Ehmann D, Thresher J, Gao N, Hajec L. A homogeneous, high-throughput fluorescence anisotropy-based DNA supercoiling assay. ACTA ACUST UNITED AC 2011; 15:1088-98. [PMID: 20930214 DOI: 10.1177/1087057110378624] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The degree of supercoiling of DNA is vital for cellular processes, such as replication and transcription. DNA topology is controlled by the action of DNA topoisomerase enzymes. Topoisomerases, because of their importance in cellular replication, are the targets of several anticancer and antibacterial drugs. In the search for new drugs targeting topoisomerases, a biochemical assay compatible with automated high-throughput screening (HTS) would be valuable. Gel electrophoresis is the standard method for measuring changes in the extent of supercoiling of plasmid DNA when acted upon by topoisomerases, but this is a low-throughput and laborious method. A medium-throughput method was described previously that quantitatively distinguishes relaxed and supercoiled plasmids by the difference in their abilities to form triplex structures with an immobilized oligonucleotide. In this article, the authors describe a homogeneous supercoiling assay based on triplex formation in which the oligonucleotide strand is labeled with a fluorescent dye and the readout is fluorescence anisotropy. The new assay requires no immobilization, filtration, or plate washing steps and is therefore well suited to HTS for inhibitors of topoisomerases. The utility of this assay is demonstrated with relaxation of supercoiled plasmid by Escherichia coli topoisomerase I, supercoiling of relaxed plasmid by E. coli DNA gyrase, and inhibition of gyrase by fluoroquinolones and nalidixic acid.
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18
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Bach A, Stuhr-Hansen N, Thorsen TS, Bork N, Moreira IS, Frydenvang K, Padrah S, Christensen SB, Madsen KL, Weinstein H, Gether U, Strømgaard K. Structure-activity relationships of a small-molecule inhibitor of the PDZ domain of PICK1. Org Biomol Chem 2010; 8:4281-8. [PMID: 20668766 DOI: 10.1039/c0ob00025f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently, we described the first small-molecule inhibitor, (E)-ethyl 2-cyano-3-(3,4-dichlorophenyl)acryloylcarbamate (1), of the PDZ domain of protein interacting with Calpha-kinase 1 (PICK1), a potential drug target against brain ischemia, pain and cocaine addiction. Herein, we explore structure-activity relationships of 1 by introducing subtle modifications of the acryloylcarbamate scaffold and variations of the substituents on this scaffold. The configuration around the double bond of 1 and analogues was settled by a combination of X-ray crystallography, NMR and density functional theory calculations. Thereby, docking studies were used to correlate biological affinities with structural considerations for ligand-protein interactions. The most potent analogue obtained in this study showed an improvement in affinity compared to 1 and is currently a lead in further studies of PICK1 inhibition.
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Affiliation(s)
- Anders Bach
- Department of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
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19
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Baumann S, Schoof S, Bolten M, Haering C, Takagi M, Shin-ya K, Arndt HD. Molecular Determinants of Microbial Resistance to Thiopeptide Antibiotics. J Am Chem Soc 2010; 132:6973-81. [DOI: 10.1021/ja909317n] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sascha Baumann
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Sebastian Schoof
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Marcel Bolten
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Claudia Haering
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Motoki Takagi
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kazuo Shin-ya
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hans-Dieter Arndt
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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20
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NMR methods in fragment screening: theory and a comparison with other biophysical techniques. Drug Discov Today 2009; 14:1051-7. [DOI: 10.1016/j.drudis.2009.07.013] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/23/2009] [Accepted: 07/27/2009] [Indexed: 11/19/2022]
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21
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Abstract
Steady-state measurements of fluorescence polarization have been widely adopted in the field of high-throughput screening for the study of biomolecular interactions. This chapter reviews the basic theory of fluorescence polarization, the underlying principle for using fluorescence polarization to study interactions between small-molecule fluorophores and macromolecular targets, and representative applications of fluorescence polarization in high-throughput screening.
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Affiliation(s)
- Xinyi Huang
- Chemical and Screening Sciences, Wyeth Research, Collegeville, PA, USA
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22
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Simeonov A, Jadhav A, Thomas CJ, Wang Y, Huang R, Southall NT, Shinn P, Smith J, Austin CP, Auld DS, Inglese J. Fluorescence Spectroscopic Profiling of Compound Libraries. J Med Chem 2008; 51:2363-71. [DOI: 10.1021/jm701301m] [Citation(s) in RCA: 211] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anton Simeonov
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
| | - Ajit Jadhav
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
| | - Craig J. Thomas
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
| | - Yuhong Wang
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
| | - Ruili Huang
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
| | - Noel T. Southall
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
| | - Paul Shinn
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
| | - Jeremy Smith
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
| | - Christopher P. Austin
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
| | - Douglas S. Auld
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
| | - James Inglese
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-3370
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23
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Sathuluri RR, Yamamura S, Tamiya E. Microsystems technology and biosensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 109:285-350. [PMID: 17999038 DOI: 10.1007/10_2007_078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This review addresses the recent developments in miniaturized microsystems or lab-on-a-chip devices for biosensing of different biomolecules: DNA, proteins, small molecules, and cells, especially at the single-molecule and single-cell level. In order to sense these biomolecules with sensitivity we have fabricated chip devices with respect to the biomolecule to be analyzed. The details of the fabrication are also dealt with in this review. We mainly developed microarray and microfluidic chip devices for DNA, protein, and cell analyses. In addition, we have introduced the porous anodic alumina layer chip with nanometer scale and gold nanoparticles for label-free sensing of DNA and protein interactions. We also describe the use of microarray and microfluidic chip devices for cell-based assays and single-cell analysis in drug discovery research.
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Affiliation(s)
- Ramachandra Rao Sathuluri
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
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24
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Capelle MAH, Gurny R, Arvinte T. High throughput screening of protein formulation stability: practical considerations. Eur J Pharm Biopharm 2006; 65:131-48. [PMID: 17107777 DOI: 10.1016/j.ejpb.2006.09.009] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 09/01/2006] [Accepted: 09/18/2006] [Indexed: 11/28/2022]
Abstract
The formulation of protein drugs is a difficult and time-consuming process, mainly due to the complexity of protein structure and the very specific physical and chemical properties involved. Understanding protein degradation pathways is essential for the success of a biopharmaceutical drug. The present review concerns the application of high throughput screening techniques in protein formulation development. A protein high throughput formulation (HTF) platform is based on the use of microplates. Basically, the HTF platform consists of two parts: (i) sample preparation and (ii) sample analysis. Sample preparation involves automated systems for dispensing the drug and the formulation ingredients in both liquid and powder form. The sample analysis involves specific methods developed for each protein to investigate physical and chemical properties of the formulations in microplates. Examples are presented of the use of protein intrinsic fluorescence for the analysis of protein aqueous properties (e.g., conformation and aggregation). Different techniques suitable for HTF analysis are discussed and some of the issues concerning implementation are presented with reference to the use of microplates.
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Affiliation(s)
- Martinus A H Capelle
- Department of Pharmaceutics and Biopharmaceutics, University of Geneva, University of Lausanne, CH-1211 Geneva 4, Switzerland
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25
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Horton RA, Strachan EA, Vogel KW, Riddle SM. A substrate for deubiquitinating enzymes based on time-resolved fluorescence resonance energy transfer between terbium and yellow fluorescent protein. Anal Biochem 2006; 360:138-43. [PMID: 17118327 DOI: 10.1016/j.ab.2006.06.031] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 06/26/2006] [Indexed: 11/16/2022]
Abstract
Deubiquitinating enzymes (DUBs) proteolytically cleave ubiquitin from ubiquitinated proteins, and inhibition of DUBs that rescue oncogenic proteins from proteasomal degradation is of emerging therapeutic interest. Recently, USP2 and UCH37 have been shown to deubiquitinate tumor-growth-promoting proteins, and other DUBs have been shown to be overexpressed in cancer cells. Therefore inhibition of DUBs is of interest as a potential therapeutic strategy for treating cancer. DUBs require the presence of properly folded ubiquitin protein in the substrate for efficient proteolysis, which precludes the use of synthetic peptide substrates in DUB activity assays. Because of the requirement for full-length ubiquitin, substrates suitable for use in fluorescent assays to identify or study DUB inhibitors have been difficult to prepare. We describe the development of a time-resolved fluorescence resonance energy transfer (FRET)-based DUB substrate that incorporates full-length ubiquitin that is site-specifically labeled using genetically encoded yellow fluorescent protein (YFP) and a chemically attached terbium donor. The intact substrate shows a high degree of FRET between terbium and YFP, whereas DUB-dependent cleavage leads to a decrease in FRET.
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Affiliation(s)
- Robert A Horton
- Invitrogen Discovery Sciences, 501 Charmany Drive, Madison, WI 53719, USA
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26
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Li J, Kim IH, Roche ED, Beeman D, Lynch AS, Ding CZ, Ma Z. Design, synthesis, and biological evaluation of BODIPY®–erythromycin probes for bacterial ribosomes. Bioorg Med Chem Lett 2006; 16:794-7. [PMID: 16309904 DOI: 10.1016/j.bmcl.2005.11.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 11/08/2005] [Accepted: 11/08/2005] [Indexed: 11/22/2022]
Abstract
BODIPY-erythromycin probes of bacterial ribosomes were designed and synthesized by attaching a BODIPY fluorophore to the 4''- and 9-positions of the erythromycin structure. The probes exhibited excellent binding affinity to bacterial ribosomes and competed with erythromycin and other drugs whose binding sites are in the same vicinity of the 50S subunit. The synthetic fluorescent probe 5 was successfully adapted in our ultra high-throughput screening (uHTS) to identify novel ribosome inhibitors.
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Affiliation(s)
- Jing Li
- Department of Medicinal Chemistry, Cumbre Inc., 1502 Viceroy Dr., Dallas, TX 75235, USA
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27
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Tirat A, Schilb A, Riou V, Leder L, Gerhartz B, Zimmermann J, Worpenberg S, Eidhoff U, Freuler F, Stettler T, Mayr L, Ottl J, Leuenberger B, Filipuzzi I. Synthesis and characterization of fluorescent ubiquitin derivatives as highly sensitive substrates for the deubiquitinating enzymes UCH-L3 and USP-2. Anal Biochem 2005; 343:244-55. [PMID: 15963938 DOI: 10.1016/j.ab.2005.04.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Revised: 04/07/2005] [Accepted: 04/13/2005] [Indexed: 10/25/2022]
Abstract
Deubiquitinating enzymes (DUBs) catalyze the removal of attached ubiquitin molecules from amino groups of target proteins. The large family of DUBs plays an important role in the regulation of the intracellular homeostasis of different proteins and influences therefore key events such as cell division, apoptosis, etc. The DUB family members UCH-L3 and USP2 are believed to inhibit the degradation of various tumor-growth-promoting proteins by removing the trigger for degradation. Inhibitors of these enzymes should therefore lead to enhanced degradation of oncoproteins and may thus stop tumor growth. To develop an enzymatic assay for the search of UCH-L3 and USP2 inhibitors, C-terminally labeled ubiquitin substrates were enzymatically synthesized. We have used the ubiquitin-activating enzyme E1 and one of the ubiquitin-conjugating enzymes E2 to attach a fluorescent lysine derivative to the C terminus of ubiquitin. Since only the epsilon-NH(2) group of the lysine derivatives was free and reactive, the conjugates closely mimic the isopeptide bond between the ubiquitin and the lysine side chains of the targeted proteins. Various substrates were synthesized by this approach and characterized enzymatically with the two DUBs. The variant consisting of the fusion protein between the large N-terminal NusA tag and the ubiquitin which was modified with alpha-NH(2)-tetramethylrhodamin-lysine, was found to give the highest dynamic range in a fluorescence polarization readout. Therefore we have chosen this substrate for the development of a miniaturized, fluorescence-polarization-based high-throughput screening assay.
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Affiliation(s)
- Aline Tirat
- Discovery Technologies, Novartis Institutes for Biomedical Research, CH-4058 Basel, Switzerland
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28
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Yan K, Hunt E, Berge J, May E, Copeland RA, Gontarek RR. Fluorescence polarization method to characterize macrolide-ribosome interactions. Antimicrob Agents Chemother 2005; 49:3367-72. [PMID: 16048949 PMCID: PMC1196252 DOI: 10.1128/aac.49.8.3367-3372.2005] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A fluorescence polarization assay is described that measures the binding of fluorescently labeled erythromycin to 70S ribosomes from Escherichia coli and the displacement of the erythromycin from these ribosomes. The assay has been validated with several macrolide derivatives and other known antibiotics. We demonstrate that this assay is suitable for determining the dissociation constants of novel compounds that have binding sites overlapping those of macrolides. This homogeneous binding assay provides a valuable tool for defining structure-activity relationships among compounds during the discovery and development of new ribosome-targeting drugs.
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Affiliation(s)
- Kang Yan
- 1250 South Collegeville Road, Collegeville, PA 19426, USA.
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29
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Zuck P, O'Donnell GT, Cassaday J, Chase P, Hodder P, Strulovici B, Ferrer M. Miniaturization of absorbance assays using the fluorescent properties of white microplates. Anal Biochem 2005; 342:254-9. [PMID: 15949786 DOI: 10.1016/j.ab.2005.04.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Revised: 04/18/2005] [Accepted: 04/20/2005] [Indexed: 11/30/2022]
Abstract
Miniaturization of high-throughput screening (HTS) assays has several obvious advantages, including increased throughput and lower cost by reduction in reagent consumption. Although absorbance assays are widely used in research laboratories, their application for HTS in a low-volume format has been met with mixed success because they are difficult to miniaturize. Challenges for the miniaturization of absorbance assays include low signal due to short path lengths and meniscus distortions in small well sizes. Here we describe a method to miniaturize absorbance assays to standard, white, low-volume 384-well and 1536-well microplates using a fluorometric plate reader for detection. The premise of this absorbance assay is based on the fluorescent properties of white microplates and the ability of a colored product to quench the fluorescence signal from the plate by absorbing either the excitation light or the emission light. This method was applied to the detection of inorganic phosphate using Quinaldine red and Malachite green dyes and to the monitoring of alkaline phosphatase hydrolysis of p-nitrophenyl phosphate. These assays can be carried out in low volumes, give robust screening statistics, and can be accomplished with a simple, inexpensive fluorometric plate reader.
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Affiliation(s)
- Paul Zuck
- Department of Automated Biotechnology, Merck and Company, 502 Louise Lane, North Wales, PA 19454, USA.
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30
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Göhler T, Jäger S, Warnecke G, Yasuda H, Kim E, Deppert W. Mutant p53 proteins bind DNA in a DNA structure-selective mode. Nucleic Acids Res 2005; 33:1087-100. [PMID: 15722483 PMCID: PMC549414 DOI: 10.1093/nar/gki252] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite the loss of sequence-specific DNA binding, mutant p53 (mutp53) proteins can induce or repress transcription of mutp53-specific target genes. To date, the molecular basis for transcriptional modulation by mutp53 is not understood, but increasing evidence points to the possibility that specific interactions of mutp53 with DNA play an important role. So far, the lack of a common denominator for mutp53 DNA binding, i.e. the existence of common sequence elements, has hampered further characterization of mutp53 DNA binding. Emanating from our previous discovery that DNA structure is an important determinant of wild-type p53 (wtp53) DNA binding, we analyzed the binding of various mutp53 proteins to oligonucleotides mimicking non-B DNA structures. Using various DNA-binding assays we show that mutp53 proteins bind selectively and with high affinity to non-B DNA. In contrast to sequence-specific and DNA structure-dependent binding of wtp53, mutp53 DNA binding to non-B DNA is solely dependent on the stereo-specific configuration of the DNA, and not on DNA sequence. We propose that DNA structure-selective binding of mutp53 proteins is the basis for the well-documented interaction of mutp53 with MAR elements and for transcriptional activities mediates by mutp53.
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Affiliation(s)
- Thomas Göhler
- Department of Tumor Virology, Heinrich-Pette-InstituteMartinistrasse 52, 20251 Hamburg, Germany
| | - Stefan Jäger
- Evotec OAISchnackenburgallee 114, 22525 Hamburg, Germany
| | - Gabriele Warnecke
- Department of Tumor Virology, Heinrich-Pette-InstituteMartinistrasse 52, 20251 Hamburg, Germany
| | - Hideyo Yasuda
- School of Life Science, Tokyo University of Pharmacy and Life ScienceHorinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Ella Kim
- Department of Tumor Virology, Heinrich-Pette-InstituteMartinistrasse 52, 20251 Hamburg, Germany
- Neuro-Oncology Group, Department of Neurosurgery, University of Schleswig-HolsteinCampus Luebeck, Ratzeburger Allee 160, 23583 Luebeck, Germany
| | - Wolfgang Deppert
- Department of Tumor Virology, Heinrich-Pette-InstituteMartinistrasse 52, 20251 Hamburg, Germany
- To whom correspondence should be addressed. Tel: +49 (0)4048051 261; Fax: +49 (0)4048051 117;
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Cooper M, Ebner A, Briggs M, Burrows M, Gardner N, Richardson R, West R. Cy3B: improving the performance of cyanine dyes. J Fluoresc 2005; 14:145-50. [PMID: 15615040 DOI: 10.1023/b:jofl.0000016286.62641.59] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The spectral properties of a rigidified trimethine cyanine dye, Cy3B have been characterised. This probe has excellent fluorescent properties, good water solubility and can be bioconjugated. The emission properties of this fluorophore have also been investigated upon conjugation to an antibody. This study compared the conjugated emission properties of Cy3B with other commercially available fluorophores emitting at similar wavelengths.
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Affiliation(s)
- Michael Cooper
- Amersham Biosciences, Discovery Systems, The Maynard Centre, Whitchurch, Cardiff, CF14 7YT, United Kingdom.
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32
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Minshull J, Govindarajan S, Cox T, Ness JE, Gustafsson C. Engineered protein function by selective amino acid diversification. Methods 2005; 32:416-27. [PMID: 15003604 DOI: 10.1016/j.ymeth.2003.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2003] [Indexed: 11/16/2022] Open
Abstract
Almost all protein engineering methods rely upon making changes to naturally occurring proteins that already possess some of the desired properties. This will probably remain the case as long as we lack a complete understanding of the way that an amino acid sequence gives rise to a protein with a precisely defined biological function. Common to all methods for altering an existing protein is the selection of a subset of amino acids in the protein for variation and a choice of which substitutions to make at each position. Variants are then tested empirically and further variants are created based upon their performance. Differences between protein engineering methods are the ways in which amino acids are chosen for variation, the protocols followed for creating the variants, and how information regarding variant properties is used in creating subsequent variants. In this article, we describe these differences and provide examples of how the experimental parameters of specific projects determine which method is most suitable.
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Eccleston JF, Hutchinson JP, Jameson DM. Fluorescence-Based Assays. PROGRESS IN MEDICINAL CHEMISTRY 2005; 43:19-48. [PMID: 15850822 DOI: 10.1016/s0079-6468(05)43002-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- John F Eccleston
- National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK
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Abstract
Fluorescence-based detection technologies are frequently applied in biological testing, due to their unique advantages in setting up homogeneous, sensitive assays in miniaturized formats. However, the wide application of these readouts has highlighted challenges in reagent design and problems with interference from biological reagents and compounds. Here, we summarize the current application of fluorescence-based detection methodologies, focusing on the problems faced by assay developers and on solutions to reduce false positive and negative results in fluorescence-based HTS.
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Affiliation(s)
- Philip Gribbon
- Lead Discovery Technologies, Pfizer Global Research and Development, Ramsgate Road, Sandwich, UK CT13 9NJ.
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Turek-Etienne TC, Small EC, Soh SC, Xin TA, Gaitonde PV, Barrabee EB, Hart RF, Bryant RW. Evaluation of fluorescent compound interference in 4 fluorescence polarization assays: 2 kinases, 1 protease, and 1 phosphatase. JOURNAL OF BIOMOLECULAR SCREENING 2003; 8:176-84. [PMID: 12844438 DOI: 10.1177/1087057103252304] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
With the increasing use of fluorescence-based assays in high-throughput screening (HTS), the possibility of interference by fluorescent compounds needs to be considered. To investigate compound interference, a well-defined sample set of biologically active compounds, LOPAC, was evaluated using 4 fluorescein-based fluorescence polarization (FP) assays. Two kinase assays, a protease assay, and a phosphatase assay were studied. Fluorescent compound interference and light scattering were observed in both mixture- and single-compound testing under certain circumstances. In the kinase assays, which used low levels (1-3 nM) of fluorophore, an increase in total fluorescence, an abnormal decrease in mP readings, and negative inhibition values were attributed to compound fluorescence. Light scattering was observed by an increase in total fluorescence and minimal reduction in mP, leading to false positives. The protease and phosphatase assays, which used a higher concentration of fluorophore (20-1200 nM) than the kinase assays, showed minimal interference from fluorescent compounds, demonstrating that an increase in the concentration of the fluorophore minimized potential fluorescent compound interference. The data also suggests that mixtures containing fluorescent compounds can result in either false negatives that can mask a potential "hit" or false positives, depending on the assay format. Cy dyes (e.g., Cy3B and Cy5 ) excite and emit further into the red region than fluorescein and, when used in place of fluorescein in kinase 1, eliminate fluorescence interference and light scattering by LOPAC compounds. This work demonstrates that fluorescent compound and light scattering interferences can be overcome by increasing the fluorophore concentration in an assay or by using longer wavelength dyes.
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Affiliation(s)
- Tammy C Turek-Etienne
- New Lead Discovery, Schering-Plough Research Institute K15 4/4800 B421C, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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Abstract
Recent advances in new analysis and prediction concepts in informatics, statistics and computational chemistry have drawn attention to mining the enormous flood of information generated from ultra-high-throughput screening (uHTS) and early drug discovery more effectively. This review analyses current infrastructure and process concepts in data analysis, storage and mining, with a particular focus on high-throughput technologies. It also provides examples of how these techniques have been applied successfully together with underlying reasons for these developments.
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Affiliation(s)
- Nicolas Fay
- Evotec OAI, Schnackenburgallee 114, D-22525 Hamburg, Germany.
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