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Pham QL, Tong NAN, Mathew A, Basuray S, Voronov RS. A compact low-cost low-maintenance open architecture mask aligner for fabrication of multilayer microfluidics devices. BIOMICROFLUIDICS 2018; 12:044119. [PMID: 30174777 PMCID: PMC6105338 DOI: 10.1063/1.5035282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Abstract
A custom-built mask aligner (CBMA), which fundamentally covers all the key features of a commercial mask aligner, while being low cost and light weight and having low power consumption and high accuracy, is constructed. The CBMA is composed of a custom high fidelity light emitting diode light source, a vacuum chuck, a mask holder, high-precision translation and rotation stages, and high resolution digital microscopes. The total cost of the system is under $7500, which is over ten times cheaper than a comparable commercial system. It produces a collimated ultraviolet illumination of 1.8-2.0 mW cm-2 over an area of a standard 4-in. wafer, at the plane of photoresist exposure, and the alignment accuracy is characterized to be <3 μm, which is sufficient for most microfluidic applications. Moreover, this manuscript provides detailed descriptions of the procedures needed to fabricate multilayered master molds using our CBMA. Finally, the capabilities of the CBMA are demonstrated by fabricating two- and three-layer masters for micro-scale devices, commonly encountered in biomicrofluidic applications. The former is a flow-free chemical gradient generator, and the latter is an addressable microfluidic stencil. Scanning electron microscopy is used to confirm that the master molds contain the intended features of different heights.
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Affiliation(s)
- Q. L. Pham
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - N. A. N. Tong
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - A. Mathew
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - S. Basuray
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - R. S. Voronov
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
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2
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nBioChip, a Lab-on-a-Chip Platform of Mono- and Polymicrobial Biofilms for High-Throughput Downstream Applications. mSphere 2017; 2:mSphere00247-17. [PMID: 28680970 PMCID: PMC5489659 DOI: 10.1128/msphere.00247-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 06/08/2017] [Indexed: 12/13/2022] Open
Abstract
With an estimated 80% of infections being associated with a biofilm mode of growth and the ensuing recalcitrance of these biofilms with respect to conventional antibiotic treatment leading to high mortality rates, there is a dire and unmet need for the development of novel approaches to prevent, treat, and control these infections. Both bacteria and fungi are capable of forming biofilms that are inherently fragile and often polymicrobial in nature, which further complicates treatment. In this work, we showcase a nanobiofilm chip as a convenient platform for culturing several hundreds of mono- or polymicrobial biofilms and for susceptibility testing. This platform enables true ultra-high-throughput screening for antimicrobial drug discovery or diagnostics or for addressing fundamental issues in microbiology. Current in vitro techniques for the culture of microorganisms, and particularly of delicate microbial biofilms, are still mostly limited to low-density plates and manual labor and are not amenable to automation and true high-throughput (HT) applications. We have developed a novel fully automated platform for the formation of mono- and polymicrobial biofilms of Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans at the nanoscale level. The nBioChip is robotically printed, robustly handled, and scanned using a standard microarray reader. Using this technique, hundreds to thousands of identical nanobiofilms encapsulated in hydrogel spots were cultured on microscope slides. The spots can withstand the washing steps involved in screening assays. The miniaturized biofilms demonstrated characteristics similar to those displayed by conventionally formed macroscopic biofilms, including (i) three-dimensional architectural features, (ii) synthesis of exopolymeric matrix material, and (iii) elevated resistance to antibiotic treatment. On the basis of our results, the nBioChip can generate reliable high-throughput antimicrobial susceptibility testing (HT-AST) in 12 to 18 h. The chip serves as a proof-of-concept universal platform for high-throughput drug screening and other downstream applications and furthers understanding of microbial interactions in mixed-species communities at the nanoscale level. IMPORTANCE With an estimated 80% of infections being associated with a biofilm mode of growth and the ensuing recalcitrance of these biofilms with respect to conventional antibiotic treatment leading to high mortality rates, there is a dire and unmet need for the development of novel approaches to prevent, treat, and control these infections. Both bacteria and fungi are capable of forming biofilms that are inherently fragile and often polymicrobial in nature, which further complicates treatment. In this work, we showcase a nanobiofilm chip as a convenient platform for culturing several hundreds of mono- or polymicrobial biofilms and for susceptibility testing. This platform enables true ultra-high-throughput screening for antimicrobial drug discovery or diagnostics or for addressing fundamental issues in microbiology.
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Hu H, Lee J, Wang M, Xu N, Chen H, Duan Q, Wang L. Study on mass transfer of droplets in narrow space. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2015.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Fleury L, Faux C, Santos C, Ballereau S, Génisson Y, Ausseil F. Development of a CERT START Domain-Ceramide HTRF Binding Assay and Application to Pharmacological Studies and Screening. ACTA ACUST UNITED AC 2015; 20:779-87. [PMID: 25716975 DOI: 10.1177/1087057115573402] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/09/2015] [Indexed: 11/16/2022]
Abstract
Sphingomyelin (SM) metabolism deregulation was recently associated with cell metastasis and chemoresistance, and several pharmacological strategies targeting SM metabolism have emerged. The ceramide (Cer) generated in the endoplasmic reticulum (ER) is transferred to the Golgi apparatus to be transformed into SM. CERamide Transfer (CERT) protein is responsible for the nonvesicular trafficking of Cer to Golgi. Blocking the CERT-mediated ER-to-Golgi Cer transfer is an interesting antioncogenic therapeutic approach. Here, we developed a protein-lipid interaction assay for the identification of new CERT-Cer interaction inhibitors. Frequently used for protein-protein interaction by enzymatic and analyte dosage assays, homogeneous time-resolved fluorescence technology was adapted for the first time to a lipid-protein binding assay. This test was developed for high-throughput screening, and a library of 672 molecules was screened. Seven hits were identified, and their inhibitory effect quantified by EC50 measurements showed binding inhibition three orders of magnitude more potent than that of HPA12, the unique known CERT antagonist to date. Each compound was tested on an independent test, confirming its high affinity and pharmacological potential.
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Affiliation(s)
| | - Céline Faux
- Unité de Service et de Recherche CNRS, Toulouse, France
| | - Cécile Santos
- LSPCMIB, CNRS-Université Paul Sabatier-Toulouse III, Toulouse, France
| | | | - Yves Génisson
- LSPCMIB, CNRS-Université Paul Sabatier-Toulouse III, Toulouse, France
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5
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Anti-epidermal growth factor receptor tyrosine kinase activities of traditional Chinese medicine for cancer treatment. Eur J Integr Med 2014. [DOI: 10.1016/j.eujim.2014.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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6
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Considerations for the design and reporting of enzyme assays in high-throughput screening applications. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.pisc.2013.12.001] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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7
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Abstract
BACKGROUND Homogeneous time-resolved fluorescence (HTRF) is a fluorescence resonance energy transfer-based technology used to measure bimolecular interactions. It has been applied successfully to kinase assays and has become an important tool in kinase drug discovery. OBJECTIVE This article reviews the current status of HTRF technology in biochemical and cellular kinase assays. METHODS Recent literature and meeting reports on HTRF kinase assays are reviewed, and their principles, advantages and drawbacks, current status and the potential applications in kinase drug discovery are discussed. RESULTS/CONCLUSION HTRF kinase assays are homogeneous, robust, sensitive, easy to miniaturize and high-throughput. This assay format is versatile, as both peptide and protein substrates can be used, and high ATP concentrations are tolerated, which enables the assay to be performed under conditions mimicking the physiological environment. HTRF kinase assays have been applied to both high-throughput screening and compound mechanistic studies. Besides protein kinases, the technology has now been expanded into the lipid kinase family. Furthermore, the utility of HTRF technology in cellular assays is emerging. HTRF kinase assays are a great addition to the toolbox for kinase drug discovery.
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Affiliation(s)
- Yong Jia
- Group Leader Genomics Institute of the Novartis Research Foundation, Department of Kinase Biology, 10675 John J Hopkins Dr, San Diego, CA 92121, USA +858 812 1728 ; +858 812 1918 ;
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Takagi T, Shum D, Parisi M, Santos RE, Radu C, Calder P, Rizvi Z, Frattini MG, Djaballah H. Comparison of luminescence ADP production assay and radiometric scintillation proximity assay for Cdc7 kinase. Comb Chem High Throughput Screen 2012; 14:669-87. [PMID: 21564015 DOI: 10.2174/138620711796504442] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 03/19/2011] [Accepted: 04/26/2011] [Indexed: 12/20/2022]
Abstract
Several assay technologies have been successfully adapted and used in HTS to screen for protein kinase inhibitors; however, emerging comparative analysis studies report very low hit overlap between the different technologies, which challenges the working assumption that hit identification is not dependent on the assay method of choice. To help address this issue, we performed two screens on the cancer target, Cdc7-Dbf4 heterodimeric protein kinase, using a direct assay detection method measuring [(33)P]-phosphate incorporation into the substrate and an indirect method measuring residual ADP production using luminescence. We conducted the two screens under similar conditions, where in one, we measured [(33)P]-phosphate incorporation using scintillation proximity assay (SPA), and in the other, we detected luminescence signal of the ATP-dependent luciferase after regenerating ATP from residual ADP (LUM). Surprisingly, little or no correlation were observed between the positives identified by the two methods; at a threshold of 30% inhibition, 25 positives were identified in the LUM screen whereas the SPA screen only identified two positives, Tannic acid and Gentian violet, with Tannic acid being common to both. We tested 20 out of the 25 positive compounds in secondary confirmatory study and confirmed 12 compounds including Tannic acid as Cdc7-Dbf4 kinase inhibitors. Gentian violet, which was only positive in the SPA screen, inhibited luminescence detection and categorized as a false positive. This report demonstrates the strong impact in detection format on the success of a screening campaign and the importance of carefully designed confirmatory assays to eliminate those compounds that target the detection part of the assay.
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Affiliation(s)
- Toshimitsu Takagi
- HTS Core Facility, Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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Development of an online p38α mitogen-activated protein kinase binding assay and integration of LC-HR-MS. Anal Bioanal Chem 2010; 398:1771-80. [PMID: 20730527 PMCID: PMC2943585 DOI: 10.1007/s00216-010-4087-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 07/28/2010] [Accepted: 08/02/2010] [Indexed: 11/19/2022]
Abstract
A high-resolution screening method was developed for the p38α mitogen-activated protein kinase to detect and identify small-molecule binders. Its central role in inflammatory diseases makes this enzyme a very important drug target. The setup integrates separation by high-performance liquid chromatography with two parallel detection techniques. High-resolution mass spectrometry gives structural information to identify small molecules while an online enzyme binding detection method provides data on p38α binding. The separation step allows the individual assessment of compounds in a mixture and links affinity and structure information via the retention time. Enzyme binding detection was achieved with a competitive binding assay based on fluorescence enhancement which has a simple principle, is inexpensive, and is easy to interpret. The concentrations of p38α and the fluorescence tracer SK&F86002 were optimized as well as incubation temperature, formic acid content of the LC eluents, and the material of the incubation tubing. The latter notably improved the screening of highly lipophilic compounds. For optimization and validation purposes, the known kinase inhibitors BIRB796, TAK715, and MAPKI1 were used among others. The result is a high-quality assay with Z′ factors around 0.8, which is suitable for semi-quantitative affinity measurements and applicable to various binding modes. Furthermore, the integrated approach gives affinity data on individual compounds instead of averaged ones for mixtures. P38 α online screening platform ![]()
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Horton RA, Vogel KW. Multiplexing Terbium- and Europium-Based TR-FRET Readouts to Increase Kinase Assay Capacity. ACTA ACUST UNITED AC 2010; 15:1008-15. [DOI: 10.1177/1087057110368993] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Identification and characterization of kinase inhibitor potency and selectivity is often an iterative process in which a library of compounds is first screened against a single kinase, and hits from that screen are then profiled against other kinases to determine specificity. By developing kinase assays that employ either a terbium- or a europium-based time-resolved fluorescence resonance energy transfer (TR-FRET) readout, one can take advantage of the distinct emission properties of these labels to develop assays for 2 kinases that can be performed simultaneously in the same well. This not only increases the information content provided per assay well but can immediately provide information on compound specificity. The authors have applied this strategy to the development of multiplexed assays for 2 examples systems: EGFR and IKKβ, as well as lipid kinase family members mTOR and PIK3C3. They demonstrate the ability of these multiplexed assays to characterize selective kinase inhibitors in a dose-response mode, with no difference in results obtained from traditional single kinase assays performed separately.
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11
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Doti N, Marasco D, Pedone C, Sabatella M, Ruvo M. Optimizing a kinase assay for IKKbeta on an HTS station. ACTA ACUST UNITED AC 2010; 14:1263-8. [PMID: 19773587 DOI: 10.1177/1087057109345527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Using a commercially available time-resolved fluorescence resonance energy transfer (TR-FRET)-based assay for IKKbeta, the authors have automated the assay procedure on a high-throughput screening station to carry out screening campaigns on multiwell plates. They have determined the Z' factor and optimized volumes, times, and time-resolved fluorescence parameters. They have also compared 2 kinases with different fusion tags, the influence of different enzyme/substrate ratios and of DMSO presence at different concentration. The authors found that glutathione S-transferase (GST)-fused IKKbeta shows better signal-to-noise (S/N) ratios over the poly-histidine-tagged variant. The substrate can be used at 50 nM with optimal performances when the enzyme is used at 2 nM. DMSO at 0.2% and 1% only slightly affects the S/N ratio, whereas when used at 2%, the final concentration deriving from a 50-fold dilution from a 5-mM stock solution in pure solvent, S/N undergoes a decrease of about 15%. Under the optimized conditions, the assay Z' factor calculated over 192 data points has an optimized value of 0.881 and allows the testing of 94 molecules in quadruplicate in 140 min.
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Affiliation(s)
- Nunzianna Doti
- Istituto di Biostrutture e Bioimmagini, CNR, 80134 Napoli, Italy
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12
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Tanaka K, Koresawa M, Iida M, Fukasawa K, Stec E, Cassaday J, Chase P, Rickert K, Hodder P, Takagi T, Komatani H. Multiplexed random peptide library and phospho-specific antibodies facilitate human polo-like kinase 1 inhibitor screen. Assay Drug Dev Technol 2010; 8:47-62. [PMID: 20085455 PMCID: PMC3532019 DOI: 10.1089/adt.2009.0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the challenges to develop time-resolved fluorescence resonance energy transfer (TR-FRET) assay for serine/threonine (Ser/Thr) protein kinase is to select an optimal peptide substrate and a specific phosphor Ser/Thr antibody. This report describes a multiplexed random screen-based development of TR-FRET assay for ultra-high-throughput screening (uHTS) of small molecule inhibitors for a potent cancer drug target polo-like kinase 1 (Plk1). A screen of a diverse peptide library in a 384-well plate format identified several highly potent substrates that share the consensus motif for phosphorylation by Plk1. Their potencies were comparable to FKD peptide, a designed peptide substrate derived from well-described Plk1 substrate Cdc25C. A specific anti-phosphor Ser/Thr antibody p(S/T)F antibody that detects the phosphorylation of FKD peptide was screened out of 87 antibodies with time-resolved fluorometry technology in a 96-well plate format. Using FKD peptide and p(S/T)F antibody, we successfully developed a robust TR-FRET assay in 384-well plate format, and further miniaturized this assay to 1,536-well plate format to perform uHTS. We screened about 1.2 million compounds for Plk1 inhibitors using a Plk1 deletion mutant that only has the kinase domain and subsequently screened the same compound library using a full-length active-mutant Plk1. These uHTSs identified a number of hit compounds, and some of them had selectivity to either the deletion mutant or the full-length protein. Our results prove that a combination of random screen for substrate peptide and phospho-specific antibodies is very powerful strategy to develop TR-FRET assays for protein kinases.
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Affiliation(s)
- Kenji Tanaka
- Tsukuba Research Institute, Banyu Pharmaceutical Co., Ltd., Tsukuba, Japan.
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13
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Mathis G, Bazin H. Stable Luminescent Chelates and Macrocyclic Compounds. LANTHANIDE LUMINESCENCE 2010. [DOI: 10.1007/4243_2010_5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Giera M, Heus F, Janssen L, Kool J, Lingeman H, Irth H. Microfractionation Revisited: A 1536 Well High Resolution Screening Assay. Anal Chem 2009; 81:5460-6. [DOI: 10.1021/ac900622b] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Giera
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Ferry Heus
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Laura Janssen
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jeroen Kool
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Henk Lingeman
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Hubertus Irth
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Habig M, Blechschmidt A, Dressler S, Hess B, Patel V, Billich A, Ostermeier C, Beer D, Klumpp M. Efficient elimination of nonstoichiometric enzyme inhibitors from HTS hit lists. ACTA ACUST UNITED AC 2009; 14:679-89. [PMID: 19470716 DOI: 10.1177/1087057109336586] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-throughput screening often identifies not only specific, stoichiometrically binding inhibitors but also undesired compounds that unspecifically interfere with the targeted activity by nonstoichiometrically binding, unfolding, and/or inactivating proteins. In this study, the effect of such unwanted inhibitors on several different enzyme targets was assessed based on screening results for over a million compounds. In particular, the shift in potency on variation of enzyme concentration was used as a means to identify nonstoichiometric inhibitors among the screening hits. These potency shifts depended on both compound structure and target enzyme. The approach was confirmed by statistical analysis of thousands of dose-response curves, which showed that the potency of competitive and therefore clearly stoichiometric inhibitors was not affected by increasing enzyme concentration. Light-scattering measurements of thermal protein unfolding further verified that compounds that stabilize protein structure by stoichiometric binding show the same potency irrespective of enzyme concentration. In summary, measuring inhibitor IC(50) values at different enzyme concentrations is a simple, cost-effective, and reliable method to identify and eliminate compounds that inhibit a specific target enzyme via nonstoichiometric mechanisms.
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Affiliation(s)
- Michael Habig
- Lead Finding Platform, Protein Structure Unit, Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Basel, Switzerland
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16
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Hong L, Quinn CM, Jia Y. Evaluating the utility of the HTRF Transcreener ADP assay technology: a comparison with the standard HTRF assay technology. Anal Biochem 2009; 391:31-8. [PMID: 19406097 DOI: 10.1016/j.ab.2009.04.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 04/20/2009] [Accepted: 04/22/2009] [Indexed: 01/13/2023]
Abstract
The HTRF (homogeneous time-resolved fluorescence) Transcreener ADP assay is a new kinase assay technology marketed by Cis-Bio International (Bagnols-Cèze, France). It measures kinase activity by detecting the formation of ADP using a monoclonal antibody and HTRF detection principles. In this article, we compare this technology with a standard HTRF kinase assay using EGFR [L858R/T790M] mutant enzyme as a case study. We demonstrate that the HTRF Transcreener ADP assay generated similar kinetic constants and inhibitor potency compared with the standard HTRF assay. However, the smaller dynamic window and lower Z' factor of the HTRF Transcreener ADP assay make this format less preferable for high-throughput screening. Based on the assay principle, the HTRF Transcreener ADP assay can detect both kinase and ATPase activities simultaneously. The ability to probe ATPase activity opens up new avenues for assaying kinases with intrinsic ATPase activity without the need to identify substrates, and this can speed up the drug discovery process. However, caution must be exercised because any contaminating ATPase activity will result in an invalid assay. The inability to tolerate high concentrations of ATP in the assay will also limit the application of this technology, especially in compound mechanistic studies such as ATP competition. Overall, the HTRF Transcreener ADP assay provides a new alternative tool to complement existing assay technologies for drug discovery.
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Affiliation(s)
- Lin Hong
- Department of Kinase Biology/Oncology, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
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17
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Eglen RM, Reisine T. The Current Status of Drug Discovery Against the Human Kinome. Assay Drug Dev Technol 2009; 7:22-43. [DOI: 10.1089/adt.2008.164] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Richard M. Eglen
- Bio-discovery, PerkinElmer Life and Analytical Sciences, Waltham, Massachusetts
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18
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Dufau I, Lazzari A, Samson A, Pouny I, Ausseil F. Optimization of a homogeneous assay for kinase inhibitors in plant extracts. Assay Drug Dev Technol 2008; 6:673-82. [PMID: 19035848 DOI: 10.1089/adt.2008.143] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
To identify natural and original kinase inhibitors from plant extracts, we have developed and compared a heterogeneous enzyme-linked immunosorbent assay (ELISA) and a homogeneous time-resolved fluorescence (HTRF, Cisbio International, Bagnols/Cèze, France) assay. Kinase affinity for the ATP substrate was determined in both assays, and the same [ATP]/ATP Km ratio was used in each case to enable the identification of ATP competitive and noncompetitive inhibitors. Assays were then used to screen the same collection of chemical compounds and plant extracts. The intra-assay correlation analysis of each technology showed a very good screening precision in HTRF and an acceptable one in ELISA. When the two methods were compared, a poor correlation was obtained with a higher hit rate in the ELISA. We then performed a detailed study of the ELISA hits and showed that they also presented a strong antioxidant activity, associated with high adsorption into microplate wells, which interfered with the horseradish peroxidase-based detection system. These hits were then flagged as false-positives. We also showed that many plant extracts presented this kind of activity and that this interference could explain the lack of correlation between the assays. These findings suggest that assay design should be carefully adapted to the substances to be screened and that interferences should be extensively considered before any assay development process and comparison studies. In spite of a few interferences, our results showed that a homogeneous-phase assay like the HTRF assay could be more efficiently used for plant extract screening than a heterogeneous-phase assay like ELISA.
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Affiliation(s)
- Isabelle Dufau
- Centre de Criblage Pharmacologique, CNRS--Pierre Fabre Joint Service Unit 2646, Toulouse, France
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Abstract
High-throughput screening (HTS) is a well-established process in lead discovery for pharma and biotech companies and is now also being set up for basic and applied research in academia and some research hospitals. Since its first advent in the early to mid-1990s, the field of HTS has seen not only a continuous change in technology and processes but also an adaptation to various needs in lead discovery. HTS has now evolved into a quite mature discipline of modern drug discovery. Whereas in previous years, much emphasis has been put toward a steady increase in capacity ("quantitative increase") via various strategies in the fields of automation and miniaturization, the past years have seen a steady shift toward higher content and quality ("quality increase") for these biological test systems. Today, many experts in the field see HTS at the crossroads with the need to decide either toward further increase in throughput or more focus toward relevance of biological data. In this article, the authors describe the development of HTS over the past decade and point out their own ideas for future directions of HTS in biomedical research. They predict that the trend toward further miniaturization will slow down with the implementation of 384-well, 1536-well, and 384 low-volume-well plates. The authors predict that, ultimately, each hit-finding strategy will be much more project related, tailor-made, and better integrated into the broader drug discovery efforts.
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Affiliation(s)
- Lorenz M Mayr
- Novartis Institutes of BioMedical Research, Center of Proteomic Chemistry, Basel, Switzerland.
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Jia Y, Gu XJ, Brinker A, Warmuth M. Measuring the tyrosine kinase activity: a review of biochemical and cellular assay technologies. Expert Opin Drug Discov 2008; 3:959-78. [DOI: 10.1517/17460441.3.8.959] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Yong Jia
- Group Leader Genomics Institute of the Novartis Research Foundation, Department of Kinase Biology, 10675 John J. Hopkins Dr, San Diego, CA 92121, USA ;
| | - Xiang-ju Gu
- Group Leader Genomics Institute of the Novartis Research Foundation, Department of Lead Discovery, 10675 John J. Hopkins Dr, San Diego, CA 92121, USA
| | - Achim Brinker
- Associate Director Genomics Institute of the Novartis Research Foundation, Department of Lead Discovery, 10675 John J. Hopkins Dr, San Diego, CA 92121, USA
| | - Markus Warmuth
- Director Genomics Institute of the Novartis Research Foundation, Department of Kinase Biology, 10675 John J. Hopkins Dr, San Diego, CA 92121, USA
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Graf C, Klumpp M, Habig M, Rovina P, Billich A, Baumruker T, Oberhauser B, Bornancin F. Targeting ceramide metabolism with a potent and specific ceramide kinase inhibitor. Mol Pharmacol 2008; 74:925-32. [PMID: 18612076 DOI: 10.1124/mol.108.048652] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Ceramide kinase (CerK) produces the bioactive lipid ceramide-1-phosphate (C1P) and appears as a key enzyme for controlling ceramide levels. In this study, we discovered and characterized adamantane-1-carboxylic acid (2-benzoylamino-benzothiazol-6-yl)amide (NVP-231), a potent, specific, and reversible CerK inhibitor that competitively inhibits binding of ceramide to CerK. NVP-231 is active in the low nanomolar range on purified as well as cellular CerK and abrogates phosphorylation of ceramide, resulting in decreased endogenous C1P levels. When combined with another ceramide metabolizing inhibitor, such as tamoxifen, NVP-231 synergistically increased ceramide levels and reduced cell growth. Therefore, NVP-231 represents a novel and promising compound for controlling ceramide metabolism that may provide insight into CerK physiological function.
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Affiliation(s)
- Christine Graf
- Novartis Institutes for BioMedical Research, Vienna, Austria
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Schröter T, Minond D, Weiser A, Dao C, Habel J, Spicer T, Chase P, Baillargeon P, Scampavia L, Schürer S, Chung C, Mader C, Southern M, Tsinoremas N, LoGrasso P, Hodder P. Comparison of miniaturized time-resolved fluorescence resonance energy transfer and enzyme-coupled luciferase high-throughput screening assays to discover inhibitors of Rho-kinase II (ROCK-II). ACTA ACUST UNITED AC 2008; 13:17-28. [PMID: 18227223 DOI: 10.1177/1087057107310806] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Kinases are important drug discovery targets for a wide variety of therapeutic indications; consequently, the measurement of kinase activity remains a common high-throughput screening (HTS) application. Recently, enzyme-coupled luciferase-kinase (LK) format assays have been introduced. This format measures luminescence resulting from metabolism of adenosine triphosphate (ATP) via a luciferin/luciferase-coupled reaction. In the research presented here, 1536-well format time-resolved fluorescence resonance energy transfer (TR-FRET) and LK assays were created to identify novel Rho-associated kinase II (ROCK-II) inhibitors. HTS campaigns for both assays were conducted in this miniaturized format. It was found that both assays were able to consistently reproduce the expected pharmacology of inhibitors known to be specific to ROCK-II (fasudil IC50: 283 +/- 27 nM and 336 +/- 54 nM for TR-FRET and LK assays, respectively; Y-27632 IC50: 133 +/- 7.8 nM and 150 +/- 22 nM for TR-FRET and LK assays, respectively). In addition, both assays proved robust for HTS efforts, demonstrating excellent plate Z' values during the HTS campaign (0.84 +/- 0.03; 0.72 +/- 0.05 for LK and TR-FRET campaigns, respectively). Both formats identified scaffolds of known and novel ROCK-II inhibitors with similar sensitivity. A comparison of the performance of these 2 assay formats in an HTS campaign was enabled by the existence of a subset of 25,000 compounds found in both our institutional and the Molecular Library Screening Center Network screening files. Analysis of the HTS campaign results based on this subset of common compounds showed that both formats had comparable total hit rates, hit distributions, amount of hit clusters, and format-specific artifact. It can be concluded that both assay formats are suitable for the discovery of ROCK-II inhibitors, and the choice of assay format depends on reagents and/or screening technology available.
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Affiliation(s)
- Thomas Schröter
- Department of Molecular Therapeutics and Drug Discovery, Scripps Florida, Jupiter, Florida 33458, USA
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23
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Sharlow ER, Leimgruber S, Yellow-Duke A, Barrett R, Wang QJ, Lazo JS. Development, validation and implementation of immobilized metal affinity for phosphochemicals (IMAP)-based high-throughput screening assays for low-molecular-weight compound libraries. Nat Protoc 2008; 3:1350-63. [PMID: 18714303 DOI: 10.1038/nprot.2008.111] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes assay development, validation and implementation of automated immobilized metal affinity for phosphochemicals (IMAP)-based fluorescence polarization (FP) and time-resolved fluorescence resonance energy transfer (TR-FRET) high-throughput screening (HTS) assays for identification of low-molecular-weight kinase inhibitors. Both procedures are performed in miniaturized kinase reaction volumes and involve the stepwise addition of test or control compounds, enzyme and substrate/ATP. Kinase reactions are stopped by subsequent addition of IMAP-binding buffer. Assay attributes of the IMAP FP and TR-FRET methodologies are described. HTS assays developed using these procedures should result in Z-factors and low assay variability necessary for robust HTS assays. Providing that the required reagents and equipment are available, one scientist should be able to develop a 384-well, miniaturized HTS assay in approximately 6-8 weeks. Specific automated HTS assay conditions will determine the number of assay plates processed in a screening session, but two scientists should expect to process between 100 and 150 assay plates in one 8-h screening day.
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Affiliation(s)
- Elizabeth R Sharlow
- Drug Discovery Institute, Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
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Sharlow ER, Leimgruber S, Ying Shun T, Lazo JS. Development and implementation of a miniaturized high-throughput time-resolved fluorescence energy transfer assay to identify small molecule inhibitors of polo-like kinase 1. Assay Drug Dev Technol 2007; 5:723-35. [PMID: 18181689 PMCID: PMC7026857 DOI: 10.1089/adt.2007.102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Polo-like kinase (Plk) 1 is a key enzyme involved in regulating the mammalian cell cycle that is also a validated anticancer drug target. Nonetheless, there are relatively few readily available potent and selective small molecule inhibitors of Plk1. To increase the availability of pharmacologically valuable Plk1 inhibitors, we describe herein the development, variability assessment, validation, and implementation of a 384-well automated, miniaturized high-throughput time-resolved fluorescence energy transfer screening assay designed to identify Plk1 kinase inhibitors. Using a small molecule library of pharmaceutically active compounds to gauge high-throughput assay robustness and reproducibility, we found nine general kinase inhibitors, including H-89, which was selected as the minimum control. We then interrogated a 97,101 compound library from the National Institutes of Health repository for small molecule inhibitors of Plk1 kinase activity. The initial primary hit rate in a single 10 microM concentration format was 0.21%. Hit compounds were subjected to concentration-response confirmation and interference assays. Identified in the screen were seven compounds with 50% inhibitory concentration (IC50) values below 1 microM, 20 compounds with IC50 values between 1 microM and 5 microM, and eight compounds with IC50 values between 5 and 10 microM, which could be assigned to seven distinct chemotype classes. Hit compounds were also examined for their ability to inhibit other kinases such as protein kinase D, focal adhesion kinase, rho-associated coiled coil protein kinase 2, c-jun NH2-terminal kinase 3, and protein kinase A via experimentation or data-mining. These compounds should be useful as probes for the biological activity of Plk1 and as leads for the development of new selective inhibitors of Plk1.
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Affiliation(s)
- Elizabeth R. Sharlow
- Department of Pharmacology, University of Pittsburgh, Pittsburgh, PA
- Pittsburgh Molecular Libraries Screening Center, University of Pittsburgh, Pittsburgh, PA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA
| | - Stephanie Leimgruber
- Pittsburgh Molecular Libraries Screening Center, University of Pittsburgh, Pittsburgh, PA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA
| | - Tong Ying Shun
- Pittsburgh Molecular Libraries Screening Center, University of Pittsburgh, Pittsburgh, PA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA
| | - John S. Lazo
- Department of Pharmacology, University of Pittsburgh, Pittsburgh, PA
- Pittsburgh Molecular Libraries Screening Center, University of Pittsburgh, Pittsburgh, PA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA
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Mathias U, Jung M. Determination of drug–serum protein interactions via fluorescence polarization measurements. Anal Bioanal Chem 2007; 388:1147-56. [PMID: 17554529 DOI: 10.1007/s00216-007-1351-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 05/04/2007] [Accepted: 05/08/2007] [Indexed: 10/23/2022]
Abstract
New fast methods for the determination of pharmacokinetic behaviour of potential drug candidates are receiving increasing interest. We present a new homogeneous method for the determination of drug binding and drug competition for human serum albumin and alpha(1)-acid glycoprotein that is amenable to high-throughput-screening. It is based on selective fluorescent probes and the measurement of fluorescence polarization. This leads to decreased interference with fluorescent drugs as compared with previously published methods based on similar probes and the measurement of fluorescence intensity. The binding of highly fluorescent drugs that still interfere with the probes can be measured by simply titrating the drugs in a two-component system with the serum protein. The assay may also be used to discover strongly binding protein ligands that are interesting for drug-targeting strategies. Additionally, binding data could be obtained from larger libraries of compounds for in silico predictive pharmacokinetics. Figure Fluorescence polarization displacement titration of dansylsarcosine (3D-structure as insert) bound to human serum albumin (HSA) by naproxene.
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Affiliation(s)
- Ulf Mathias
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr 25, Freiburg, Germany
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26
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Abstract
In the development of high throughput screening (HTS) as a central paradigm of drug discovery, fluorescence has generally been adopted as the favored methodology. Nevertheless, luminescence has maintained a prominent position among certain assay formats, most notably genetic reporters. Recently, there has been growing partiality for luminescent assays across a wider range of applications due to their sensitivity, broad linearity, and robustness to library compounds and complex biological samples. This trend has been fostered by the development of several new assay designs for diverse targets such as kinases, cytochrome p450s, proteases, apoptosis, and cytotoxicity. This review addresses recent progress made in the use of bioluminescent assays for HTS, highlighting new detection capabilities brought about by engineering luciferase genes, enzymes, and substrates. In genetic reporter applications, modifications to the luciferase genes have improved assay sensitivity by substantially increasing expression efficiency and enhanced response dynamics by reducing expression lifetime. The performance of assays based on detection of ATP and luciferin has been enhanced by modifications to the luciferase enzyme that increase its chemical and physical stability. Detection of ATP allows rapid analysis of cell metabolism and enzymatic processes coupled to ATP metabolism. Because luciferins are not naturally associated with mammalian physiology, assays for luciferin detection utilize synthetic derivatives designed to yield luminescence only when coupled with specific target enzymes. Finally, new methods for modulating the specific activity of luciferases are leading to the development of intracellular biosensors for dynamic detection of physiological processes.
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Affiliation(s)
- Frank Fan
- Promega Corporation, Madison, WI 53711, USA.
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