Combinatorial Chemistry & High Throughput Screening - Volume 6, Issue 4, 2003
Volume 6, Issue 4, 2003
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Phenotypic Screening of Small Molecule Libraries by High Throughput Cell Imaging
Authors: J.C. Yarrow, Y. Feng, Z.E. Perlman, T. Kirchhausen and T.J. MitchisonWe have developed high throughput fluorescence cell imaging methods to screen chemical libraries for compounds with effects on diverse aspects of cell physiology. We describe screens for compounds that arrest cells in mitosis, that block cell migration, and that block the secretory pathway. Each of these screens yielded specific inhibitors for research use, and the mitosis screen identified Eg5 as a potential target protein for cancer chemotherapy. Cell imaging provides a large amount of information from primary screening data that can be used to distinguish compounds with different effects on cells, and together with automated analysis, to quantitate compound effects.
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A Fluorescent High-Throughput Assay for Double-Stranded DNA: the RediPlate PicoGreen Assay
Authors: R. Batchelor, D. Hagen, I. Johnson and J. BeechemThe fluorescent PicoGreen® reagent for detection and quantitation of double-stranded DNA has been adapted for high-throughput screening: the RediPlate PicoGreen double-stranded DNA assay format. In the RediPlate PicoGreen assay format, the PicoGreen reagent is predistributed and co-dried into either 96- or 384- well microplates with the excipient trehalose. The user resuspends the dried reagents upon adding DNA, and measures the resulting fluorescence after a five minute incubation. Replicate fluorescence measurements on nominally identical wells have less than a 5% coefficient of variation. The assay is linear from 5 to 500 ng / ml DNA in a 200 μl volume. The RediPlate PicoGreen assay format retains the advantages of the original PicoGreen reagent - sensitivity, speed, and specificity - but in a high-throughput format.
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Rapid Assays for Quantitating Cytokine Gene Expression Without Target Amplification
Authors: F.R. Gonzales, A. Lois, T. Sewell, C. LaCerte, B. Gaynor, E. Garcia, M. Jazdzewski, T. Oliver, I. Postor and D. TrainorMany drug discovery efforts are focused on finding candidates that alter gene expression of the cytokines involved in inflammation, allergy, and cell-mediated immunity. Current methods used to evaluate gene expression such as northern blot and RT-PCR are laborious, time-consuming, expensive, and are not conducive to high throughput screening. High Performance Signal Amplification (HPSA™) gene expression assays quantitate mRNA targets directly from cell lysate samples using DNA probe hybridization and fluorescent signal amplification. The assay format eliminates the need for RNA purification prior to testing and does not involve target amplification. The 96 or 384-well microplate formats allow the method to be run manually, by a workstation approach, or with full automation. Cellular mRNA levels are quantitated relative to a standard curve comprised of highly purified in vitro RNA calibrators. The analytical sensitivity is in the low attomole (10 -18 mole) range. This technique was used to monitor the transcription patterns of mRNA encoding TNF-α, IL-1β, and Interferon-γ in human cell lines or primary PBMC treated with inducers such as PMA, ionomycin, and endotoxin. The specificity, precision and reproducibility of the assay are sufficient to provide a reliable screening system. The HPSA gene expression assay system offers a rapid and convenient alternative to more cumbersome, expensive methods.
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Assay Development and High-Throughput Screening of Caspases in Microfluidic Format
More LessCaspase proteases are familiar targets in drug discovery. A common format for screening to identify caspase inhibitors employs fluorogenic or colorimetric tetra-peptide substrates in 96, 384, or 1536 -well microtiter plates. The primary motivation for increasing the number of wells per plate is to reduce the reagent cost per test and increase the throughput of HTS operations. There are significant challenges, however, to moving into or beyond the 1536-well format, such as submicroliter liquid handling, liquid evaporation, increased surface area-to-volume ratios, and the potential for artifacts and interference from small air-borne particles such as lint. Therefore, HTS scientists remain keenly interested in technologies that offer alternatives to the ever-shrinking microtiter plate well. Microfluidic assay technology represents an attractive option that, in theory, consumes only subnanoliter volumes of reagents per test. We have successfully employed a microfluidic assay technology in fluorogenic screening assays for several caspase isoforms utilizing the Caliper Technologies Labchip™ platform. Caspase-3 is used as a representative case to describe microfluidic assay development and initial high-throughput screening results. In addition, microfluidic screening and plate-based screening are compared in terms of reagent consumption, data quality, and ease of operation.
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Fluorescence Assays for High-Throughput Screening of Protein Kinases
Authors: G.J.R. Zaman, A. Garritsen, T. Boer and C.A.A. van BoeckelProtein kinases comprise one of the most important group of targets for drug discovery research today. Methods to identify novel kinase inhibitors by high-throughput screening have evolved rapidly in recent years. An important aspect is the availability of fluorescent probes that can be applied in a homogeneous, or mix-and-measure, assay format. Here, we illustrate the application of fluorescence read-out technologies for kinase targets in light of our own experiences in assay development and high-throughput screening.
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Competitive Fluorescence Polarization Assays for the Detection of Phosphoinositide Kinase and Phosphatase Activity
Authors: B.E. Drees, A. Weipert, H. Hudson, C.G. Ferguson, L. Chakravarty and G.D. PrestwichWe describe the development and implementation of competitive fluorescence polarization (FP) based assays for determining activity of phosphoinositide 3-kinase (PI 3-K) and the type-II SH2-domaincontaining inositol 5-phosphatase (SHIP2). These assays are based on the interaction of specific phosphoinositide binding proteins with fluorophore-labeled phosphoinositide and inositol phosphate tracers. Enzyme reaction products are detected by their ability to compete with the fluorescent tracers for protein binding, leading to an increase in the amount of free tracer and a decrease in polarization (mP) values. A variety of fluorophore-labeled tracers were evaluated, and assay sensitivity and specificity for products of PI 3-K and SHIP2 activity was determined. Assay performance was evaluated using recombinant PI 3-Kα and SHIP2 with diC8-PI(4,5)P2 and diC8-PI(3,4,5)P3 as respective substrates. IC50 values for previously characterized PI 3-K inhibitors were within expected ranges. These assays are homogeneous, sensitive, and rapid, and suitable for HTS applications, and will facilitate screening for novel inhibitors of phosphoinositide kinases and phosphatases in drug development.
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Strategies and Solid-Phase Formats for the Analysis of Protein and Peptide Phosphorylation Employing A Novel Fluorescent Phosphorylation Sensor Dye
Authors: K. Martin, T.H. Steinberg, T. Goodman, B. Schulenberg, J.A. Kilgore, K.R. Gee, J.M. Beechem and W.F. PattonProtein kinases represent one of the largest families of regulatory enzymes, with more than 2,000 of them being encoded for by the human genome. Many cellular processes are regulated by the reversible phosphorylation of proteins and upwards of 30% of the proteins comprising the eukaryotic proteome are likely to be phosphorylated at some point during their existence. In the past, analysis of global protein phosphorylation has been accomplished through radiolabelling of samples with inorganic 32P or [γ-32P] ATP. The approach is limited to specimens amenable to radiolabelling and poses certain safety and disposal problems. Alternatively, immunodetection with antibodies to the common phosphoamino acids may be employed, but the antibodies are relatively expensive and exhibit limited specificity and a certain degree of cross-reactivity. Pro-Q Diamond dye is a new fluorescent phosphosensor technology suitable for the detection of phosphoserine-, phosphothreonine- and phosphotyrosine-containing proteins directly in isoelectric focusing gels, SDS-polyacrylamide gels and two-dimensional gels. Additionally, the technology is appropriate for the detection of phosphoproteins or phosphopeptides arrayed on protein chips or affixed to beads. Dye-stained proteins and peptides can be excited with a laser-based light source of 532 or 543 nm or with a xenon-arc lamp-based system equipped with appropriate band pass filters. Alternatively, ultraviolet light of about 302 nm may be employed, providing that sufficiently long exposure times are used to collect the fluorescence signal. Pro-Q Diamond dye emits maximally at approximately 580 nm. The fluorescence-based detection technology is easy to conduct, cost effective and allows rapid large-scale screening of protein and peptide phosphorylation in a variety of solid-phase assay formats.
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Development of Fluorescence-Based Selective Assays for Serine / Threonine and Tyrosine Phosphatases
Authors: C. Pastula, I. Johnson, J.M. Beechem and W.F. PattonA number of aromatic substrates were evaluated for their ability to detect tyrosine phosphatase and serine / threonine phosphatase activity. Results demonstrated that the fluorinated coumarin DiFMUP is the most sensitive substrate for detecting LAR and PP-2A activity. Using this substrate, selective high-throughput screening assays for serine / threonine and tyrosine phosphatases were developed. Specific inhibitor cocktails were added to each assay to limit the activity of other phosphatases. LAR, CD-45, and PTP-1B all rapidly hydrolyze DiFMUP in the tyrosine phosphatase assay. The activity of non-tyrosine phosphatases is less than 6% of the LAR activity. PP-1 and PP-2A are highly active in the serine / threonine phosphatase assay. Inhibition of LAR and PP-2A in these assays is demonstrated using known inhibitors. Both of these assays are sensitive, robust, kinetic assays that can be used to quantify enzyme activity.
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Homogeneous Fluorescence Assay for Cyclic AMP
More LessThe objective of these studies was to develop a new homogeneous fluorescence assay for determining the concentrations of cAMP in biological samples. The assay is based on a novel general concept of using ligand-dependent sequence-specific DNA binding proteins as sensors for their respective ligands. CAP protein, a bacterial DNA binding protein whose DNA binding activity depends on cAMP, was used to develop the assay. In the presence of cAMP, DNA binding activity of CAP is greatly increased. Signaling of cAMP presence was achieved by detecting cAMP-dependent formation of CAP-DNA complex using a recently developed fluorescence assay for DNA binding proteins (Heyduk, T., and Heyduk, E. Nature Biotechnology 20,171-176, 2002). Both 96-well and 384-well black microplate formats of the assay were developed and used to detect cAMP in low nanomolar concentrations. The assay involves mixing of the sample with the assay solution containing all necessary components for cAMP determination followed by fluorescence intensity readout; no washing or reagent addition steps are necessary. Excellent reproducibility of fluorescence signal change as a function of cAMP concentration was observed. Experiments with HEK 293 cells stimulated with forskolin were performed to demonstrate that the assay could be used for cAMP determination in cellular extracts. In summary, the obtained data fully validated the new homogenous assay for measuring cAMP based on cAMP-dependent DNA binding activity of CAP protein. It is expected that the development of assays for many other ligands of DNA binding proteins will be possible using the same overall assay design developed for cAMP.
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Measuring Intracellular Calcium Fluxes in High Throughput Mode
Authors: C. Chambers, F. Smith, C. Williams, S. Marcos, Z. Liu, P. Hayter, G. Ciaramella, W. Keighley, P. Gribbon and A. SewingThe measurement of intracellular calcium fluxes in real time is widely applied within the pharmaceutical industry to measure the activation of G-protein coupled receptors (GPCR's), either for pharmacological characterisation or to screen for new surrogate ligands. Initially restricted to Gq coupled GPCRs, the introduction of promiscuous and chimeric G-proteins has further widened the application of these assays. The development of new calcium sensitive dyes and assays has provided sensitive, homogeneous assays which can be readily applied to high throughput screening (HTS). In this paper we describe the full automation of this assay type using a fluorometric imaging plate reader (FLIPR™) integrated into a Beckman / Sagian system to establish a simple robotic system that is well suited for the current medium throughput screening in this area of lead discovery. Using a recently completed HTS we discuss important determinants for FLIPR™ based screening, highlight some limitations of the current approach, and look at the requirements for future automated systems capable of keeping up with expanding compound files.
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New Ca2+ Fluoroionophores Based on the BODIPY Fluorophore
Authors: K.R. Gee, A. Rukavishnikov and A. RotheCalcium (Ca2+) fluoroionophores are useful in cell-based functional assays of G-protein coupled receptor (GPCR) activation or ion channel modulation. In this paper we describe new calcium probes that improve or overcome certain deficiencies in existing probes. These new fluoroionophores are based on acylation of amino-BAPTA [BAPTA = glycine, N,N'-(1,2-ethanediyl-bis(oxy-2,1-phenylene)) bis(N-(carboxymethyl))] with fluorescent BODIPY® propionates [BODIPY = 4,4-difluoro-5,7-dimethyl- 4-bora-3a,4a-diaza-s-indacene]. The resulting probes show high affinity to aqueous calcium solutions, and respond to calcium binding with significant fluorescence increases. The BODIPY fluorophores are uncharged and their fluorescence is pH-insensitive. The wide range of excitation / emission wavelength choices available within the BODIPY fluorophore series allows several different colors of new calcium indicators to be prepared. Cell permeable versions respond well with increasing fluorescence intensities in live cells after calcium influx.
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High Throughput Fluorescence-Based Assays for Cyclic ADP-Ribose, NAADP, and Their Metabolic Enzymes
Authors: R.M. Graeff and H. LeeCyclic ADP-ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate (NAADP) are two novel Ca2+ messengers derived respectively from NAD and NADP. Since their discovery in sea urchin eggs, both have now been shown to serve messenger functions in a wide range of cells from plant to human. In this article, a series of fluorimetric assays for cADPR, NAADP and their metabolic enzymes is compiled. The enzyme assay makes use of an analog of NAD, nicotinamide guanine dinucleotide, which is non-fluorescent but is cyclized by the enzymes to a fluorescent analog of cADPR, cyclic GDP-ribose. Other NAD utilizing enzymes are not capable of catalyzing the cyclization and thus produce no interference. The fluorimetric assays for cADPR and NAADP make use of coupled-enzyme amplification and can readily detect nanomolar concentrations of either messenger. All the assays described can be performed in multi-well format, allowing ready automation and use in high throughput screening. An added advantage of these assays is that all the required reagents are commercially available, facilitating general adoption of the techniques by all those who are interested in the physiology and enzymology of the novel Ca2+ signaling pathways mediated by cADPR and NAADP.
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β Galactosidase Enzyme Fragment Complementation as A Novel Technology for High Throughput Screening
Authors: R.M. Eglen and R. SinghIn this review, the applications of β galactosidase complementation are described. αComplementation is a naturally occurring process in bacteria and in engineered cells, and can also occur in eukaryotic cells. Two forms of α complementation have been used in high throughput screening (HTS), in which interacting fragments complement with either low or high affinity. Low affinity complementation is used to monitor protein protein interactions, such as those occurring in homodimerization of the epidermal growth factor receptor (EGFR), and provides a robust screen for detection of EGFR inhibitors. High affinity complementation provides the basis for several HTS assays, in which analytes, such as cAMP or IP3, are detected in crude cell lysates. A development of the latter approach is protein labeling, providing for measurement of cell protein expression and trafficking. Collectively, the use of β galactosidase complementation provides a novel and flexible technology for highly sensitive, homogeneous HTS assay development.
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High Throughput Screening of G-Protein Coupled Receptors via Flow Cytometry
Authors: A. Waller, P. Simons, E.R. Prossnitz, B.S. Edwards and L.A. SklarThe molecular assemblies of signal transduction components, for example kinases and their target proteins or receptor-ligand complexes and intracellular signaling molecules, are critical for biological functions in cells. To better understand the interactions of these molecular assemblies and to screen for new pharmaceutics that could control and modulate these types of interactions, we have focused on developing high throughput approaches for the analysis of G-protein coupled receptors via flow cytometry. Flow cytometry offers a number of advantages including real-time collection of multicomponent data, and together with improvements in sample handling, the high throughput sampling rate is up to 100 samples per minute. For our targets, assemblies of solubilized GPCRs, a screening platform of a dextran bead has proven to be flexible, allowing different surface chemistries on the beads. The bead can be either ligand-labeled or have epitopelinked proteins attached to the bead surface, enabling several molecular assemblies to be constructed and analyzed. A major improvement with this system is that for screening ligands for GPCRs the underlying mechanism of action for these compounds can be investigated and incorporated into the definition of a ‘hit’. Our current screening system is capable of simultaneously distinguishing GPCR agonists and antagonists.
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Established and Emerging Fluorescence-Based Assays for G-Protein Function: Heterotrimeric G-Protein Alpha Subunits and Regulator of G-Protein Signaling (RGS) Proteins
Authors: R.J. Kimple, M.B. Jones, A. Shutes, B.R. Yerxa, D.P. Siderovski and F.S. WillardHeterotrimeric G-proteins are molecular switches that couple serpentine receptors to intracellular effector pathways and the regulation of cell physiology. Ligand-bound receptors cause G-protein alpha subunits to bind guanosine 5'-triphosphate (GTP) and activate effector pathways. Signal termination is facilitated by the intrinsic GTPase activity of G-protein alpha subunits. Regulators of G-protein signaling (RGS) proteins accelerate the GTPase activity of the G-protein alpha subunit, and thus negatively regulate Gprotein- mediated signal transduction. In vitro biochemical assays of heterotrimeric G-proteins commonly include measurements of nucleotide binding, GTPase activity, and interaction with RGS proteins. However, the conventional assays for most of these processes involve radiolabeled guanine nucleotide analogues and scintillation counting. In this article, we focus on fluorescence-based methodologies to study heterotrimeric Gprotein alpha subunit regulation in vitro. Furthermore, we consider the potential of such techniques in highthroughput screening and drug discovery.
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Established and Emerging Fluorescence-Based Assays for G-Protein Function: Ras-Superfamily GTPases
Authors: R.J. Rojas, R.J. Kimple, K.L. Rossman, D.P. Siderovski and J. SondekRas and Rho GTPases are signaling proteins that regulate a variety of physiological events and are intimately linked to the progression of cancer. Recently, a variety of fluorescence-based assays have been refined to monitor activation of these GTPases. This review summarizes current fluorescence-based techniques for studying Ras superfamily GTPases with an emphasis on practical examples and high-throughput applications. These techniques are not only useful for biochemical characterization of Ras superfamily members, but will also facilitate the discovery of small molecule therapeutics designed to inhibit signal transduction mediated by GTPases.
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Volumes & issues
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Volume 28 (2025)
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Volume 27 (2024)
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Volume 26 (2023)
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Volume 25 (2022)
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Volume 24 (2021)
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Volume 23 (2020)
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Volume 22 (2019)
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Volume 21 (2018)
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Volume 20 (2017)
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Volume 19 (2016)
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Volume 18 (2015)
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Volume 17 (2014)
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Volume 16 (2013)
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Volume 15 (2012)
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Volume 14 (2011)
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Volume 13 (2010)
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Volume 12 (2009)
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Volume 11 (2008)
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Volume 10 (2007)
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Volume 9 (2006)
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Volume 8 (2005)
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Volume 7 (2004)
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Volume 6 (2003)
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Volume 5 (2002)
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Volume 4 (2001)
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Volume 3 (2000)
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Label-Free Detection of Biomolecular Interactions Using BioLayer Interferometry for Kinetic Characterization
Authors: Joy Concepcion, Krista Witte, Charles Wartchow, Sae Choo, Danfeng Yao, Henrik Persson, Jing Wei, Pu Li, Bettina Heidecker, Weilei Ma, Ram Varma, Lian-She Zhao, Donald Perillat, Greg Carricato, Michael Recknor, Kevin Du, Huddee Ho, Tim Ellis, Juan Gamez, Michael Howes, Janette Phi-Wilson, Scott Lockard, Robert Zuk and Hong Tan
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