Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

High-throughput screening assays for the identification of chemical probes

Abstract

High-throughput screening (HTS) assays enable the testing of large numbers of chemical substances for activity in diverse areas of biology. The biological responses measured in HTS assays span isolated biochemical systems containing purified receptors or enzymes to signal transduction pathways and complex networks functioning in cellular environments. This Review addresses factors that need to be considered when implementing assays for HTS and is aimed particularly at investigators new to this field. We discuss assay design strategies, the major detection technologies and examples of HTS assays for common target classes, cellular pathways and simple cellular phenotypes. We conclude with special considerations for configuring sensitive, robust, informative and economically feasible HTS assays.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Assay categories and methodologies.
Figure 2: Influence of assay design on the measured biological response.
Figure 3: Assay performance and sensitivity.
Figure 4: Compound effects on assay outputs.

Similar content being viewed by others

References

  1. Zhang, R. et al. A continuous spectrophotometric assay for the hepatitis C virus serine protease. Anal. Biochem. 270, 268–275 (1999).

    CAS  PubMed  Google Scholar 

  2. McDonald, O.B. et al. A scintillation proximity assay for the Raf/MEK/ERK kinase cascade: high-throughput screening and identification of selective enzyme inhibitors. Anal. Biochem. 268, 318–329 (1999).

    CAS  PubMed  Google Scholar 

  3. Seville, M., West, A.B., Cull, M.G. & McHenry, C.S. Fluorometric assay for DNA polymerases and reverse transcriptase. Biotechniques 21, 664–672 (1996).

    CAS  PubMed  Google Scholar 

  4. Verma, R. et al. Ubistatins inhibit proteasome-dependent degradation by binding the ubiquitin chain. Science 306, 117–120 (2004).

    CAS  PubMed  Google Scholar 

  5. Ferrer, M. et al. A fully automated [35S]GTPgammaS scintillation proximity assay for the high-throughput screening of Gi-linked G protein-coupled receptors. Assay Drug Dev. Technol. 1, 261–273 (2003).

    CAS  PubMed  Google Scholar 

  6. Dinger, M.C. & Beck-Sickinger, A.G. in Molecular Biology in Medicinal Chemistry (eds. Dingermann, T., Steinhiber, D. & Folkers, G.) 73–94 (Wiley-VCH Verlag GmbH & Co., Weinheim, Germany, 2004).

    Google Scholar 

  7. Hodder, P., Mull, R., Cassaday, J., Berry, K. & Strulovici, B. Miniaturization of intracellular calcium functional assays to 1536-well plate format using a fluorometric imaging plate reader. J. Biomol. Screen. 9, 417–426 (2004).

    CAS  PubMed  Google Scholar 

  8. Inglese, J. (ed.) Measuring Biological Responses with Automated Microscopy Vol. 414 (Elsevier Academic, San Diego, 2006).

    Google Scholar 

  9. Taylor, D.L., Haskins, J.R. & Giuliano, K.A. (eds.) High Content Screening Vol. 356 (Humana, Totowa, New Jersey, 2006).

    Google Scholar 

  10. Sever, J.L. Application of a microtechnique to viral serological investigations. J. Immunol. 88, 320–329 (1962).

    CAS  PubMed  Google Scholar 

  11. Carroll, S.S., Inglese, J., Mao, S.-S. & Olsen, D.B. in Molecular Cancer Therapeutics: Strategies for Drug Discovery and Development (ed. Prendergast, G.C.) 119–140 (John Wiley & Sons, Inc., Hoboken, New Jersey, USA, 2004).

    Google Scholar 

  12. Wölcke, J. & Ullmann, D. Miniaturized HTS technologies - uHTS. Drug Discov. Today 6, 637–646 (2001).

    PubMed  Google Scholar 

  13. Karvinen, J. et al. Caspase multiplexing: simultaneous homogeneous time-resolved quenching assay (TruPoint) for caspases 1, 3, and 6. Anal. Biochem. 325, 317–325 (2004).

    CAS  PubMed  Google Scholar 

  14. Bandyopadhyay, S. et al. A high-throughput drug screen targeted to the 5′untranslated region of Alzheimer amyloid precursor protein mRNA. J. Biomol. Screen. 11, 469–480 (2006).

    CAS  PubMed  Google Scholar 

  15. Davis, R.E. et al. A cell-based assay for IkappaBalpha stabilization using a two-color dual luciferase-based sensor. Assay Drug Dev. Technol. 5, 85–104 (2007).

    CAS  PubMed  Google Scholar 

  16. O'Boyle, D.R. II et al. Development of a cell-based high-throughput specificity screen using a hepatitis C virus-bovine viral diarrhea virus dual replicon assay. Antimicrob. Agents Chemother. 49, 1346–1353 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Ross, S. et al. High-content screening analysis of the p38 pathway: profiling of structurally related p38alpha kinase inhibitors using cell-based assays. Assay Drug Dev. Technol. 4, 397–409 (2006).

    CAS  PubMed  Google Scholar 

  18. Iversen, P.W., Eastwood, B.J., Sittampalam, G.S. & Cox, K.L. A comparison of assay performance measures in screening assays: signal window, Z' factor, and assay variability ratio. J. Biomol. Screen. 11, 247–252 (2006).

    CAS  PubMed  Google Scholar 

  19. Eastwood, B.J. et al. The minimum significant ratio: a statistical parameter to characterize the reproducibility of potency estimates from concentration-response assays and estimation by replicate-experiment studies. J. Biomol. Screen. 11, 253–261 (2006).

    PubMed  Google Scholar 

  20. Assay Guidance Manual Committee. Assay Guidance Manual Version 4.1 (Eli Lilly and Company and NIH Chemical Genomics Center, Bethesda, Maryland, 2005).

  21. Fluorescence Spectra Viewer (Invitrogen Corporation, Carlsbad, California, 2006). <http://probes.invitrogen.com/servlets/spectraviewer?fileid1=1304dna>

  22. Lakowicz, J.R. Principles of Fluorescence Spectroscopy (Springer, Berlin, 2006).

    Google Scholar 

  23. Owicki, J.C. Fluorescence polarization and anisotropy in high throughput screening: perspectives and primer. J. Biomol. Screen. 5, 297–306 (2000).

    CAS  PubMed  Google Scholar 

  24. Jameson, D.M. & Croney, J.C. Fluorescence polarization: past, present and future. Comb. Chem. High Throughput Screen. 6, 167–176 (2003).

    CAS  PubMed  Google Scholar 

  25. Hemmila, I. & Laitala, V. Progress in lanthanides as luminescent probes. J. Fluoresc. 15, 529–542 (2005).

    CAS  PubMed  Google Scholar 

  26. Trinquet, E. & Mathis, G. Fluorescence technologies for the investigation of chemical libraries. Mol. Biosyst. 2, 380–387 (2006).

    CAS  PubMed  Google Scholar 

  27. Giepmans, B.N., Adams, S.R., Ellisman, M.H. & Tsien, R.Y. The fluorescent toolbox for assessing protein location and function. Science 312, 217–224 (2006).

    CAS  PubMed  Google Scholar 

  28. Haugland, R.P. The Handbook—A Guide to Fluorescent Probes and Labeling Technologies 10th edn. (Eugene, Oregon, 2006).

    Google Scholar 

  29. Medintz, I.L., Uyeda, H.T., Goldman, E.R. & Mattoussi, H. Quantum dot bioconjugates for imaging, labelling and sensing. Nat. Mater. 4, 435–446 (2005).

    CAS  PubMed  Google Scholar 

  30. Haney, S.A., LaPan, P., Pan, J. & Zhang, J. High-content screening moves to the front of the line. Drug Discov. Today 11, 889–894 (2006).

    CAS  PubMed  Google Scholar 

  31. Bowen, W.P. & Wylie, P.G. Application of laser-scanning fluorescence microplate cytometry in high content screening. Assay Drug Dev. Technol. 4, 209–221 (2006).

    CAS  PubMed  Google Scholar 

  32. Fan, F. & Wood, K.V. Bioluminescent assays for high-throughput screening. Assay Drug Dev. Technol. 5, 127–136 (2007).

    CAS  PubMed  Google Scholar 

  33. Nakatsu, T. et al. Structural basis for the spectral difference in luciferase bioluminescence. Nature 440, 372–376 (2006).

    CAS  PubMed  Google Scholar 

  34. Blair, W.S. et al. A novel HIV-1 antiviral high throughput screening approach for the discovery of HIV-1 inhibitors. Antiviral Res. 65, 107–116 (2005).

    CAS  PubMed  Google Scholar 

  35. Hao, W. et al. Development of a novel dicistronic reporter-selectable hepatitis C virus replicon suitable for high-throughput inhibitor screening. Antimicrob. Agents Chemother. 51, 95–102 (2007).

    CAS  PubMed  Google Scholar 

  36. Zlokarnik, G. Fusions to beta-lactamase as a reporter for gene expression in live mammalian cells. Methods Enzymol. 326, 221–244 (2000).

    CAS  PubMed  Google Scholar 

  37. Kunapuli, P. et al. Development of an intact cell reporter gene beta-lactamase assay for G protein-coupled receptors for high-throughput screening. Anal. Biochem. 314, 16–29 (2003).

    CAS  PubMed  Google Scholar 

  38. Oosterom, J., van Doornmalen, E.J., Lobregt, S., Blomenrohr, M. & Zaman, G.J. High-throughput screening using beta-lactamase reporter-gene technology for identification of low-molecular-weight antagonists of the human gonadotropin releasing hormone receptor. Assay Drug Dev. Technol. 3, 143–154 (2005).

    CAS  PubMed  Google Scholar 

  39. Pfleger, K.D. & Eidne, K.A. Illuminating insights into protein-protein interactions using bioluminescence resonance energy transfer (BRET). Nat. Methods 3, 165–174 (2006).

    CAS  PubMed  Google Scholar 

  40. Remy, I. & Michnick, S.W. Mapping biochemical networks with protein-fragment complementation assays. Methods Mol. Biol. 261, 411–426 (2004).

    CAS  PubMed  Google Scholar 

  41. Wu, S. & Liu, B. Application of scintillation proximity assay in drug discovery. BioDrugs 19, 383–392 (2005).

    CAS  PubMed  Google Scholar 

  42. Lavery, P., Brown, M.J. & Pope, A.J. Simple absorbance-based assays for ultra-high throughput screening. J. Biomol. Screen. 6, 3–9 (2001).

    CAS  PubMed  Google Scholar 

  43. Zuck, P. et al. Miniaturization of absorbance assays using the fluorescent properties of white microplates. Anal. Biochem. 342, 254–259 (2005).

    CAS  PubMed  Google Scholar 

  44. Zheng, C.J. et al. Therapeutic targets: progress of their exploration and investigation of their characteristics. Pharmacol. Rev. 58, 259–279 (2006).

    CAS  PubMed  Google Scholar 

  45. Fox, S. et al. High-throughput screening: update on practices and success. J. Biomol. Screen. 11, 864–869 (2006).

    PubMed  Google Scholar 

  46. Hopkins, A.L. & Groom, C.R. The druggable genome. Nat. Rev. Drug Discov. 1, 727–730 (2002).

    CAS  PubMed  Google Scholar 

  47. Pawson, T. & Scott, J.D. Protein phosphorylation in signaling—50 years and counting. Trends Biochem. Sci. 30, 286–290 (2005).

    CAS  PubMed  Google Scholar 

  48. Singh, P., Harden, B.J., Lillywhite, B.J. & Broad, P.M. Identification of kinase inhibitors by an ATP depletion method. Assay Drug Dev. Technol. 2, 161–169 (2004).

    CAS  PubMed  Google Scholar 

  49. Munagala, N. et al. Identification of small molecule ceramide kinase inhibitors using a homogeneous chemiluminescence high throughput assay. Assay Drug Dev. Technol. 5, 65–73 (2007).

    CAS  PubMed  Google Scholar 

  50. Lowery, R.G. & Kleman-Leyer, K. Transcreener: screening enzymes involved in covalent regulation. Expert Opin. Ther. Targets 10, 179–190 (2006).

    CAS  PubMed  Google Scholar 

  51. Charter, N.W., Kauffman, L., Singh, R. & Eglen, R.M. A generic, homogenous method for measuring kinase and inhibitor activity via adenosine 5′-diphosphate accumulation. J. Biomol. Screen. 11, 390–399 (2006).

    CAS  PubMed  Google Scholar 

  52. Sportsman, J.R., Gaudet, E.A. & Boge, A. Immobilized metal ion affinity-based fluorescence polarization (IMAP): advances in kinase screening. Assay Drug Dev. Technol. 2, 205–214 (2004).

    CAS  PubMed  Google Scholar 

  53. Comley, J. Kinase screening and profiling-spoilt for choice. Drug Discov. World 7, 27–50 (2006).

    Google Scholar 

  54. Morgan, A.G., McCauley, T.J., Stanaitis, M.L., Mathrubutham, M. & Millis, S.Z. Development and validation of a fluorescence technology for both primary and secondary screening of kinases that facilitates compound selectivity and site-specific inhibitor determination. Assay Drug Dev. Technol. 2, 171–181 (2004).

    CAS  PubMed  Google Scholar 

  55. Newbatt, Y. et al. Identification of inhibitors of the kinase activity of oncogenic V600E BRAF in an enzyme cascade high-throughput screen. J. Biomol. Screen. 11, 145–154 (2006).

    CAS  PubMed  Google Scholar 

  56. Osmond, R.I. et al. GPCR screening via ERK 1/2: a novel platform for screening G protein-coupled receptors. J. Biomol. Screen. 10, 730–737 (2005).

    CAS  PubMed  Google Scholar 

  57. Eglen, R.M. & Singh, R. Beta galactosidase enzyme fragment complementation as a novel technology for high throughput screening. Comb. Chem. High Throughput Screen. 6, 381–387 (2003).

    CAS  PubMed  Google Scholar 

  58. Zaman, G.J., van der Lee, M.M., Kok, J.J., Nelissen, R.L. & Loomans, E.E. Enzyme fragment complementation binding assay for p38alpha mitogen-activated protein kinase to study the binding kinetics of enzyme inhibitors. Assay Drug Dev. Technol. 4, 411–420 (2006).

    CAS  PubMed  Google Scholar 

  59. Barnett, S.F. et al. Identification and characterization of pleckstrin-homology-domain-dependent and isoenzyme-specific Akt inhibitors. Biochem. J. 385, 399–408 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Leung, D., Abbenante, G. & Fairlie, D.P. Protease inhibitors: current status and future prospects. J. Med. Chem. 43, 305–341 (2000).

    CAS  PubMed  Google Scholar 

  61. Grant, S.K., Sklar, J.G. & Cummings, R.T. Development of novel assays for proteolytic enzymes using rhodamine-based fluorogenic substrates. J. Biomol. Screen. 7, 531–540 (2002).

    CAS  PubMed  Google Scholar 

  62. Auld, D. in Proteolytic Enzymes Tools: and Targets (eds. Stocker, W. & Sterchi, E. E.) 30–48 (Springer-Velag, Berlin Heidelberg, 1999).

    Google Scholar 

  63. Ferrer, M. et al. Miniaturizable homogenous time-resolved fluorescence assay for carboxypeptidase B activity. Anal. Biochem. 317, 94–98 (2003).

    CAS  PubMed  Google Scholar 

  64. Jones, J., Heim, R., Hare, E., Stack, J. & Pollok, B.A. Development and application of a GFP-FRET intracellular caspase assay for drug screening. J. Biomol. Screen. 5, 307–317 (2000).

    CAS  PubMed  Google Scholar 

  65. Whitney, M. et al. A collaborative screening program for the discovery of inhibitors of HCV NS2/3 cis-cleaving protease activity. J. Biomol. Screen. 7, 149–154 (2002).

    CAS  PubMed  Google Scholar 

  66. Lee, J.C. et al. Development of a cell-based assay for monitoring specific hepatitis C virus NS3/4A protease activity in mammalian cells. Anal. Biochem. 316, 162–170 (2003).

    CAS  PubMed  Google Scholar 

  67. Li, Y., Liu, Y.W. & Cordell, B. Novel functional assay for proteases and modulators. Application in beta-secretase studies. Mol. Biotechnol. 18, 1–10 (2001).

    PubMed  Google Scholar 

  68. Olefsky, J.M. Nuclear receptor minireview series. J. Biol. Chem. 276, 36863–36864 (2001).

    CAS  PubMed  Google Scholar 

  69. Zeh, K. et al. Gain-of-function somatic cell lines for drug discovery applications generated by homologous recombination. Assay Drug Dev. Technol. 1, 755–765 (2003).

    CAS  PubMed  Google Scholar 

  70. Sun, S., Almaden, J., Carlson, T.J., Barker, J. & Gehring, M.R. Assay development and data analysis of receptor-ligand binding based on scintillation proximity assay. Metab. Eng. 7, 38–44 (2005).

    CAS  PubMed  Google Scholar 

  71. Parker, G.J., Law, T.L., Lenoch, F.J. & Bolger, R.E. Development of high throughput screening assays using fluorescence polarization: nuclear receptor-ligand-binding and kinase/phosphatase assays. J. Biomol. Screen. 5, 77–88 (2000).

    CAS  PubMed  Google Scholar 

  72. Fung, P. et al. A homogeneous cell-based assay to measure nuclear translocation using beta-galactosidase enzyme fragment complementation. Assay Drug Dev. Technol. 4, 263–272 (2006).

    CAS  PubMed  Google Scholar 

  73. Mackem, S., Baumann, C.T. & Hager, G.L. A glucocorticoid/retinoic acid receptor chimera that displays cytoplasmic/nuclear translocation in response to retinoic acid. A real time sensing assay for nuclear receptor ligands. J. Biol. Chem. 276, 45501–45504 (2001).

    CAS  PubMed  Google Scholar 

  74. Wehrman, T.S., Casipit, C.L., Gewertz, N.M. & Blau, H.M. Enzymatic detection of protein translocation. Nat. Methods 2, 521–527 (2005).

    CAS  PubMed  Google Scholar 

  75. Gowda, K., Marks, B.D., Zielinski, T.K. & Ozers, M.S. Development of a coactivator displacement assay for the orphan receptor estrogen-related receptor-gamma using time-resolved fluorescence resonance energy transfer. Anal. Biochem. 357, 105–115 (2006).

    CAS  PubMed  Google Scholar 

  76. Zhu, Z. et al. Correlation of high-throughput pregnane X receptor (PXR) transactivation and binding assays. J. Biomol. Screen. 9, 533–540 (2004).

    CAS  PubMed  Google Scholar 

  77. Eglen, R.M., Bosse, R. & Reisine, T. Emerging concepts of guanine nucleotide-binding protein-coupled receptor (GPCR) function and implications for high throghput screening. Assay Drug Dev. Technol. 5, 425–451 (2007).

    CAS  PubMed  Google Scholar 

  78. Jacoby, E., Bouhelal, R., Gerspacher, M. & Seuwen, K. The 7 TM G-protein-coupled receptor target family. ChemMedChem 1, 761–782 (2006).

    PubMed  Google Scholar 

  79. Yu, N. et al. Real-time monitoring of morphological changes in living cells by electronic cell sensor arrays: an approach to study G protein-coupled receptors. Anal. Chem. 78, 35–43 (2006).

    CAS  PubMed  Google Scholar 

  80. Handl, H.L. & Gillies, R.J. Lanthanide-based luminescent assays for ligand-receptor interactions. Life Sci. 77, 361–371 (2005).

    CAS  PubMed  Google Scholar 

  81. Kenakin, T. Inverse, protean, and ligand-selective agonism: matters of receptor conformation. FASEB J. 15, 598–611 (2001).

    CAS  PubMed  Google Scholar 

  82. Behan, D.P. & Chalmers, D.T. The use of constitutively active receptors for drug discovery at the G protein-coupled receptor gene pool. Curr. Opin. Drug Discov. Devel. 4, 548–560 (2001).

    CAS  PubMed  Google Scholar 

  83. Labrecque, J. et al. The development of an europium-GTP assay to quantitate chemokine antagonist interactions for CXCR4 and CCR5. Assay Drug Dev. Technol. 3, 637–648 (2005).

    CAS  PubMed  Google Scholar 

  84. Chambers, C. et al. Measuring intracellular calcium fluxes in high throughput mode. Comb. Chem. High Throughput Screen. 6, 355–362 (2003).

    CAS  PubMed  Google Scholar 

  85. Williams, C. cAMP detection methods in HTS: selecting the best from the rest. Nat. Rev. Drug Discov. 3, 125–135 (2004).

    CAS  PubMed  Google Scholar 

  86. Reinscheid, R.K., Kim, J., Zeng, J. & Civelli, O. High-throughput real-time monitoring of Gs-coupled receptor activation in intact cells using cyclic nucleotide-gated channels. Eur. J. Pharmacol. 478, 27–34 (2003).

    CAS  PubMed  Google Scholar 

  87. Adie, E.J. et al. CypHer 5: a generic approach for measuring the activation and trafficking of G protein-coupled receptors in live cells. Assay Drug Dev. Technol. 1, 251–259 (2003).

    CAS  PubMed  Google Scholar 

  88. Charest, P.G., Terrillon, S. & Bouvier, M. Monitoring agonist-promoted conformational changes of beta-arrestin in living cells by intramolecular BRET. EMBO Rep. 6, 334–340 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Karlsson, A.M. et al. Biosensing of opioids using frog melanophores. Biosens. Bioelectron. 17, 331–335 (2002).

    CAS  PubMed  Google Scholar 

  90. Burstein, E.S. et al. Integrative functional assays, chemical genomics and high throughput screening: harnessing signal transduction pathways to a common HTS readout. Curr. Pharm. Des. 12, 1717–1729 (2006).

    CAS  PubMed  Google Scholar 

  91. Liu, A.M. et al. Galpha(16/z) chimeras efficiently link a wide range of G protein-coupled receptors to calcium mobilization. J. Biomol. Screen. 8, 39–49 (2003).

    CAS  PubMed  Google Scholar 

  92. Kostenis, E. Is Galpha16 the optimal tool for fishing ligands of orphan G-protein-coupled receptors? Trends Pharmacol. Sci. 22, 560–564 (2001).

    CAS  PubMed  Google Scholar 

  93. Trinquet, E. et al. D-myo-inositol 1-phosphate as a surrogate of D-myo-inositol 1,4,5-tris phosphate to monitor G protein-coupled receptor activation. Anal. Biochem. 358, 126–135 (2006).

    CAS  PubMed  Google Scholar 

  94. Hamdan, F.F., Audet, M., Garneau, P., Pelletier, J. & Bouvier, M. High-throughput screening of G protein-coupled receptor antagonists using a bioluminescence resonance energy transfer 1-based beta-arrestin2 recruitment assay. J. Biomol. Screen. 10, 463–475 (2005).

    CAS  PubMed  Google Scholar 

  95. Zheng, W., Spencer, R.H. & Kiss, L. High throughput assay technologies for ion channel drug discovery. Assay Drug Dev. Technol. 2, 543–552 (2004).

    CAS  PubMed  Google Scholar 

  96. McDonough, S.I. & Bean, B.P. in Voltage-Gated Ion Channels as Drug Targets Vol. 29 (eds. Triggle, D.J., Gopalakrishnan, M., Rampe, D. & Zheng, W.) 19–35 (Wiley-VCH, Weinheim, Germany, 2006).

    Google Scholar 

  97. Gee, K.R. et al. Chemical and physiological characterization of fluo-4 Ca(2+)-indicator dyes. Cell Calcium 27, 97–106 (2000).

    CAS  PubMed  Google Scholar 

  98. Gonzalez, J.E. & Maher, M.P. Cellular fluorescent indicators and voltage/ion probe reader (VIPR) tools for ion channel and receptor drug discovery. Receptors Channels 8, 283–295 (2002).

    CAS  PubMed  Google Scholar 

  99. Terstappen, G.C. Nonradioactive rubidium ion efflux assay and its applications in drug discovery and development. Assay Drug Dev. Technol. 2, 553–559 (2004).

    CAS  PubMed  Google Scholar 

  100. Finkel, A. et al. Population patch clamp improves data consistency and success rates in the measurement of ionic currents. J. Biomol. Screen. 11, 488–496 (2006).

    CAS  PubMed  Google Scholar 

  101. Wible, B.A. et al. HERG-Lite: a novel comprehensive high-throughput screen for drug-induced hERG risk. J. Pharmacol. Toxicol. Methods 52, 136–145 (2005).

    CAS  PubMed  Google Scholar 

  102. Schwab, D., Fischer, H., Tabatabaei, A., Poli, S. & Huwyler, J. Comparison of in vitro P-glycoprotein screening assays: recommendations for their use in drug discovery. J. Med. Chem. 46, 1716–1725 (2003).

    CAS  PubMed  Google Scholar 

  103. Henrich, C.J. et al. A high-throughput cell-based assay for inhibitors of ABCG2 activity. J. Biomol. Screen. 11, 176–183 (2006).

    CAS  PubMed  Google Scholar 

  104. Wieczorke, R., Dlugai, S., Krampe, S. & Boles, E. Characterisation of mammalian GLUT glucose transporters in a heterologous yeast expression system. Cell. Physiol. Biochem. 13, 123–134 (2003).

    CAS  PubMed  Google Scholar 

  105. Verkman, A.S. Drug discovery in academia. Am. J. Physiol. Cell Physiol. 286, C465–C474 (2004).

    CAS  PubMed  Google Scholar 

  106. Rubin, L.L. & de Sauvage, F.J. Targeting the Hedgehog pathway in cancer. Nat. Rev. Drug Discov. 5, 1026–1033 (2006).

    CAS  PubMed  Google Scholar 

  107. Massoud, T.F., Paulmurugan, R., De, A., Ray, P. & Gambhir, S.S. Reporter gene imaging of protein-protein interactions in living subjects. Curr. Opin. Biotechnol. 18, 31–37 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  108. MacDonald, M.L. et al. Identifying off-target effects and hidden phenotypes of drugs in human cells. Nat. Chem. Biol. 2, 329–337 (2006).

    CAS  PubMed  Google Scholar 

  109. Buttner, F.H., Kumpf, R., Menzel, S., Reulle, D. & Valler, M.J. Evaluation of the InteraX system technology in a high-throughput screening environment. J. Biomol. Screen. 10, 485–494 (2005).

    PubMed  Google Scholar 

  110. Wallrabe, H. & Periasamy, A. Imaging protein molecules using FRET and FLIM microscopy. Curr. Opin. Biotechnol. 16, 19–27 (2005).

    CAS  PubMed  Google Scholar 

  111. Marine, S. et al. A miniaturized cell-based fluorescence resonance energy transfer assay for insulin-receptor activation. Anal. Biochem. 355, 267–277 (2006).

    CAS  PubMed  Google Scholar 

  112. Wolff, M. et al. Automated high content screening for phosphoinositide 3 kinase inhibition using an AKT 1 redistribution assay. Comb. Chem. High Throughput Screen. 9, 339–350 (2006).

    CAS  PubMed  Google Scholar 

  113. Almholt, D.L. et al. Nuclear export inhibitors and kinase inhibitors identified using a MAPK-activated protein kinase 2 redistribution screen. Assay Drug Dev. Technol. 2, 7–20 (2004).

    CAS  PubMed  Google Scholar 

  114. Granas, C. et al. Identification of RAS-mitogen-activated protein kinase signaling pathway modulators in an ERF1 redistribution screen. J. Biomol. Screen. 11, 423–434 (2006).

    PubMed  Google Scholar 

  115. Rickardson, L., Wickstrom, M., Larsson, R. & Lovborg, H. Image-based screening for the identification of novel proteasome inhibitors. J. Biomol. Screen. 12, 203–210 (2007).

    CAS  PubMed  Google Scholar 

  116. Online Mendelian Inheritance of Man (OMIM). (Johns Hopkins University and National Center for Biotechnology Information, National Library of Medicine, 2007). <http://www.ncbi.nlm.nih.gov/omim/>

  117. Habashi, J.P. et al. Losartan, an AT1 antagonist, prevents aortic aneurysm in a mouse model of Marfan syndrome. Science 312, 117–121 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Jarecki, J. et al. Diverse small-molecule modulators of SMN expression found by high-throughput compound screening: early leads towards a therapeutic for spinal muscular atrophy. Hum. Mol. Genet. 14, 2003–2018 (2005).

    CAS  PubMed  Google Scholar 

  119. Welch, E.M. et al. PTC124 targets genetic disorders caused by nonsense mutations. Nature 447, 87–91 (2007).

    CAS  PubMed  Google Scholar 

  120. Bernier, V., Lagace, M., Bichet, D.G. & Bouvier, M. Pharmacological chaperones: potential treatment for conformational diseases. Trends Endocrinol. Metab. 15, 222–228 (2004).

    CAS  PubMed  Google Scholar 

  121. Sazani, P. et al. Nuclear antisense effects of neutral, anionic and cationic oligonucleotide analogs. Nucleic Acids Res. 29, 3965–3974 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. Zhang, X. et al. A potent small molecule inhibits polyglutamine aggregation in Huntington's disease neurons and suppresses neurodegeneration in vivo. Proc. Natl. Acad. Sci. USA 102, 892–897 (2005).

    CAS  PubMed  Google Scholar 

  123. Kenakin, T. Predicting therapeutic value in the lead optimization phase of drug discovery. Nat. Rev. Drug Discov. 2, 429–438 (2003).

    CAS  PubMed  Google Scholar 

  124. Van Der Hee, R.M., Deurholt, T., Gerhardt, C.C. & De Groene, E.M. Comparison of 3 AT1 receptor binding assays: filtration assay, ScreenReady Target, and WGA Flashplate. J. Biomol. Screen. 10, 118–126 (2005).

    CAS  PubMed  Google Scholar 

  125. Wu, X., Glickman, J.F., Bowen, B.R. & Sills, M.A. Comparison of assay technologies for a nuclear receptor assay screen reveals differences in the sets of identified functional antagonists. J. Biomol. Screen. 8, 381–392 (2003).

    CAS  PubMed  Google Scholar 

  126. Inglese, J. et al. Quantitative high-throughput screening: a titration-based approach that efficiently identifies biological activities in large chemical libraries. Proc. Natl. Acad. Sci. USA 103, 11473–11478 (2006).

    CAS  PubMed  Google Scholar 

  127. Burlingham, B. & Widlanski, T. An intuitive look at the relationship of Ki and IC50: a more general use for the Dixon plot. J. Chem. Educ. 80, 214–218 (2003).

    CAS  Google Scholar 

  128. Copeland, R.A. Mechanistic considerations in high-throughput screening. Anal. Biochem. 320, 1–12 (2003).

    CAS  PubMed  Google Scholar 

  129. Leff, P. & Dougall, I.G. Further concerns over Cheng-Prusoff analysis. Trends Pharmacol. Sci. 14, 110–112 (1993).

    CAS  PubMed  Google Scholar 

  130. Wu, G., Yuan, Y. & Hodge, C.N. Determining appropriate substrate conversion for enzymatic assays in high-throughput screening. J. Biomol. Screen. 8, 694–700 (2003).

    CAS  PubMed  Google Scholar 

  131. Knight, S.M., Umezawa, N., Lee, H.S., Gellman, S.H. & Kay, B.K. A fluorescence polarization assay for the identification of inhibitors of the p53–DM2 protein-protein interaction. Anal. Biochem. 300, 230–236 (2002).

    CAS  PubMed  Google Scholar 

  132. Kane, S.A. et al. Development of a binding assay for p53/HDM2 by using homogeneous time-resolved fluorescence. Anal. Biochem. 278, 29–38 (2000).

    CAS  PubMed  Google Scholar 

  133. Zuck, P. et al. Ligand-receptor binding measured by laser-scanning imaging. Proc. Natl. Acad. Sci. USA 96, 11122–11127 (1999).

    CAS  PubMed  Google Scholar 

  134. Zhang, R. et al. Fluorescence polarization assay and inhibitor design for MDM2/p53 interaction. Anal. Biochem. 331, 138–146 (2004).

    CAS  PubMed  Google Scholar 

  135. Parks, D.J. et al. 1,4-Benzodiazepine-2,5-diones as small molecule antagonists of the HDM2-p53 interaction: discovery and SAR. Bioorg. Med. Chem. Lett. 15, 765–770 (2005).

    CAS  PubMed  Google Scholar 

  136. Inglese, J. Engaging science and technology for drug development. Assay Drug Dev. Technol. 1, 1 (2002).

    CAS  PubMed  Google Scholar 

  137. Lundholt, B.K., Heydorn, A., Bjorn, S.P. & Praestegaard, M. A simple cell-based HTS assay system to screen for inhibitors of p53-Hdm2 protein-protein interactions. Assay Drug Dev. Technol. 4, 679–688 (2006).

    CAS  PubMed  Google Scholar 

  138. Peppard, J. et al. Development of a high-throughput screening assay for inhibitors of aggrecan cleavage using luminescent oxygen channeling (AlphaScreen). J. Biomol. Screen. 8, 149–156 (2003).

    CAS  PubMed  Google Scholar 

  139. DeForge, L.E. et al. Substrate capacity considerations in developing kinase assays. Assay Drug Dev. Technol. 2, 131–140 (2004).

    CAS  PubMed  Google Scholar 

  140. Iyer, R., Barrese, A.A. III, Parakh, S., Parker, C.N. & Tripp, B.C. Inhibition profiling of human carbonic anhydrase II by high-throughput screening of structurally diverse, biologically active compounds. J. Biomol. Screen. 11, 782–791 (2006).

    CAS  PubMed  Google Scholar 

  141. Comley, J. Assay Interference, a limiting factor in HTS? Drug Discov. World 4, 91–98 (2003).

    Google Scholar 

  142. Zheng, W. et al. Miniaturization of a hepatitis C virus RNA polymerase assay using a -102 degrees C cooled CCD camera-based imaging system. Anal. Biochem. 290, 214–220 (2001).

    CAS  PubMed  Google Scholar 

  143. Rishton, G.M. Nonleadlikeness and leadlikeness in biochemical screening. Drug Discov. Today 8, 86–96 (2003).

    CAS  PubMed  Google Scholar 

  144. Swift, K., Anderson, S.N. & Matayoshi, E.D. in Advances in Fluorescence Sensing Technology V, Proceedings of SPIE - The International Society for Optical Engineering 4252 47–58 (2001).

    Google Scholar 

  145. Porcari, V., Magnoni, L., Terstappen, G.C. & Fecke, W. A continuous time-resolved fluorescence assay for identification of BACE1 inhibitors. Assay Drug Dev. Technol. 3, 287–297 (2005).

    CAS  PubMed  Google Scholar 

  146. Moger, J., Gribbon, P., Sewing, A. & Winlove, C.P. The application of fluorescence lifetime readouts in high-throughput screening. J. Biomol. Screen. 11, 765–772 (2006).

    CAS  PubMed  Google Scholar 

  147. Feng, B.Y. et al. A high-throughput screen for aggregation-based inhibition in a large compound library. J. Med. Chem. 50, 2385–2390 (2007).

    CAS  PubMed  Google Scholar 

  148. Bakhtiarova, A. et al. Resveratrol inhibits firefly luciferase. Biochem. Biophys. Res. Commun. 351, 481–484 (2006).

    CAS  PubMed  Google Scholar 

  149. Ullman, E.F. et al. Luminescent oxygen channeling immunoassay: measurement of particle binding kinetics by chemiluminescence. Proc. Natl. Acad. Sci. USA 91, 5426–5430 (1994).

    CAS  PubMed  Google Scholar 

  150. Issad, T., Blanquart, C. & Gonzalez-Yanes, C. The use of bioluminescence resonance energy transfer for the study of therapeutic targets: application to tyrosine kinase receptors. Expert Opin. Ther. Targets 11, 541–556 (2007).

    CAS  PubMed  Google Scholar 

  151. Zlokarnik, G. et al. Quantitation of transcription and clonal selection of single living cells with beta-lactamase as reporter. Science 279, 84–88 (1998).

    CAS  PubMed  Google Scholar 

  152. Kumaraswamy, S. et al. Fluorescent-conjugated polymer superquenching facilitates highly sensitive detection of proteases. Proc. Natl. Acad. Sci. USA 101, 7511–7515 (2004).

    CAS  PubMed  Google Scholar 

  153. Kiss, L. et al. High throughput ion-channel pharmacology: planar-array-based voltage clamp. Assay Drug Dev. Technol. 1, 127–135 (2003).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank D. Leja and J. Fekces for illustrations. The authors are supported by the Molecular Libraries Initiative of the NIH Roadmap for Medical Research and the Intramural Research Program of the National Human Genome Research Institute, NIH.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to James Inglese.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Inglese, J., Johnson, R., Simeonov, A. et al. High-throughput screening assays for the identification of chemical probes. Nat Chem Biol 3, 466–479 (2007). https://doi.org/10.1038/nchembio.2007.17

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.2007.17

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing