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High-Throughput and In Silico Screening in Drug Discovery

  • Nandu Thrithamarassery Gangadharan
  • Ananda Baskaran Venkatachalam
  • Shiburaj SugathanEmail author
Chapter

Abstract

The process of drug discovery involves multiple branches of science. Discovery of novel molecule with biological modulation activity is a time-consuming and expensive process. High-throughput and in silico tools can reduce time and cost in drug discovery. The aim of high-throughput screening is to identify bioactive molecule from large compound collection and further development of active compounds to leads. There are two types of assay in high-throughput drug discovery: biochemical- and cell-based assays. Choice of assay depends on nature of target and assay feasibilities. Assay method should detect active compound from chemical library. Assay optimization and validation steps reduce false-positive and false-negative results. The assay results must be statistically validated to ensure reliability of results. The good assay design and implementation will give optimal results.In silico tools in drug discovery facilitate hit identification, hit to lead development, and optimization of druggability (improvement absorption, distribution, metabolism, excretion, and toxicity properties). High-throughput and in silico screening can be streamlined for hit identification and lead development. Streamlining of these methods reduces cost and time of drug discovery process. The wise use of these high-throughput methods can lead to discovery of drug with good potency and low toxicity profile.

Keywords

Drug discovery In silico High throughput 

References

  1. Abraham VC, Taylor DL, Haskins JR (2004) High content screening applied to large-scale cell biology. Trends Biotechnol 22:15–22PubMedCrossRefGoogle Scholar
  2. Acker MG, Auld DS (2014) Considerations for the design and reporting of enzyme assays in high-throughput screening applications. Perspect Sci 1:56–73CrossRefGoogle Scholar
  3. Alpha B, Lehn JM, Mathis G (1987) Angew Chem Int Ed 26:266Google Scholar
  4. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 5:403–410CrossRefGoogle Scholar
  5. An WF, Tolliday N (2010) Cell-based assays for high-throughput screening. Mol Biotechnol 45:180–186PubMedCrossRefGoogle Scholar
  6. Auld DS, Farmen MW, Kahl SD, Aidas K, Kevin LM, Chahrzad M, Jeffrey RW (2012) Receptor binding assays for HTS and drug discovery. In: Sittampalam GS, Coussens NP, Nelson H, Arkin M, Auld D, Austin C, Bejcek B, Glicksman M, Inglese J, Iversen PW, Li Z, McGee J, McManus O, Minor L, Napper A, Peltier JM, Riss T, Trask Jr OJ, Weidner J (eds) Assay guidance manual [Internet]. EliLilly & Company and the National Center for Advancing Translational Science, National Center for Biotechnology Information, BethesdaGoogle Scholar
  7. Auld DS, Veith H, Cali JJ (2013) Bioluminescent assays for cytochrome P450 enzymes. Methods Mol Biol 987:1–9PubMedCrossRefGoogle Scholar
  8. Bandyopadhyay S, Ni J, Ruggiero A, Walshe K, Rogers MS, Chattopadhyay N, Glicksman MA, Rogers JT (2006) A high-throughput drug screen targeted to the 5’untranslated region of Alzheimer amyloid precursor protein mRNA. J Biomol Screen 11:469–480PubMedCrossRefGoogle Scholar
  9. Barnum D, Greene J, Smellie A, Sprague P (1996) Identification of common functional configurations among molecules. J Chem Inf Comput Sci 36:563–571PubMedCrossRefGoogle Scholar
  10. Böhm HJ (1992) LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput Aided Mol Des 6:593–606PubMedCrossRefGoogle Scholar
  11. Braun RD, Lanzen JL, Snyder SA, Dewhirst MW (2001) Comparison of tumor and normal tissue oxygen tension measurements using OxyLite or microelectrodes in rodents. Am J Physiol Heart Circ Physiol 280:H2533–H2544PubMedGoogle Scholar
  12. Brooijmans N, Kuntz ID (2003) Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct 32:335–373PubMedCrossRefGoogle Scholar
  13. Buchan DW, Ward SM, Lobley AE, Nugent TC, Bryson K, Jones DT (2010) Protein annotation and modelling servers at University College London. Nucleic Acids Res 38:W563–568Google Scholar
  14. Burt DA (1986) Receptor binding methodology and analysis. In: O’Brien RA (ed) Receptor binding in drug research. Marcel Dekker, New York, pp 3–29Google Scholar
  15. Carnero A (2006) High throughput screening in drug discovery. Clin Transl Oncol 8:482–490Google Scholar
  16. Carroll SS, Inglese J, Mao SS, Olsen DB (2004) Drug screening: assay development issues. In: Prendergast GC (ed) Molecular cancer therapeutics: strategies for drug discovery and development. Wiley, Hoboken, pp 119–140CrossRefGoogle Scholar
  17. Chambers C, Smith F, Williams C, Marcos S, Liu ZH, Hayter P, Ciaramella G, Keighley W, Gribbon P, Sewing A (2003) Measuring intracellular calcium fluxes in high throughput mode. Comb Chem High Throughput Screen 6:355–362PubMedCrossRefGoogle Scholar
  18. Chen J, Lai L (2006) Pocket v.2: further developments on receptor-based pharmacophore modeling. J Chem Inf Model 46:2684–2691PubMedCrossRefGoogle Scholar
  19. Coma I, Clark L, Diez E, Harper G, Herranz J, Hofmann G, Lennon M, Richmond N, Valmaseda M, Macarron R (2009a) Process validation and screen reproducibility in high-throughput screening. J Biomol Screen 14:66–76PubMedCrossRefGoogle Scholar
  20. Coma I, Herranz J, Martin J (2009b) Statistics and decision making in high-throughput screening. Methods Mol Biol 565:69–106PubMedCrossRefGoogle Scholar
  21. Copeland RA (2003) Mechanistic considerations in high-throughput screening. Anal Biochem 320:1–12Google Scholar
  22. Davis RE, Zhang YQ, Southall N, Staudt LM, Austin CP, Inglese J, Auld DS (2007) A cell-based assay for Ikappa Balpha stabilization using a two-color dual luciferase-based sensor. Assay Drug Dev Technol 5:85–103PubMedCrossRefGoogle Scholar
  23. Desmarais W, Bienvenue DL, Bzymek KP, Petsko GA, Ringe D, Holz RC (2006) The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica. J Biol Inorg Chem 11:398–408PubMedCrossRefGoogle Scholar
  24. Desmet J, De Maeyer M, Hazes B, Lasters I (1992) The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356:539–542PubMedCrossRefGoogle Scholar
  25. DeWitte RS, Shakhnovich E (1997) SMoG: De novo design method based on simple, fast and accurate free energy estimates. J Am Chem Soc 119:4608–4617CrossRefGoogle Scholar
  26. Dias R, de Azevedo WF (2008) Molecular docking algorithms. Curr Drug Targets 9:1040–1047PubMedCrossRefGoogle Scholar
  27. Dinger MC, Beck-Sickinger AG (2004) Reporter gene assay systems for the investigation of G-protein-coupled receptors. In: Dingermann T, Steinhilber D, Folkers G (eds) Molecular biology in medicinal chemistry. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, pp 73–94Google Scholar
  28. Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA (2006) PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 20:647–671PubMedCrossRefGoogle Scholar
  29. Ebert AD, Svendsen CN (2010) Human stem cells and drug screening: opportunities and challenges. Nat Rev Drug Discov 9:367–372PubMedCrossRefGoogle Scholar
  30. Eglen RM, Singh R (2003) Beta galactosidase enzyme fragment complementation as a novel technology for high throughput screening. Comb Chem High Throughput Screen 6:381–387PubMedCrossRefGoogle Scholar
  31. Eglen RM, Bosse R, Reisine T (2007) Emerging concepts of guanine nucleotide-binding protein-coupled receptor (GPCR) function and implications for high throughput screening. Assay Drug Dev Technol 5:425–451PubMedCrossRefGoogle Scholar
  32. Ewing TJ, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 15:411–428PubMedCrossRefGoogle Scholar
  33. Fan F, Wood KV (2007) Bioluminescent assays for high-throughput screening. Assay Drug Dev Technol 5:127–136PubMedCrossRefGoogle Scholar
  34. Ferrer M, Kolodin GD, Zuck P, Peltier R, Berry K, Mandala SM, Rosen H, Ota H, Ozaki S, Inglese J, Strulovici B (2003) A fully automated [35S]GTP gamma S scintillation proximity assay for the high-throughput screening of Gi-linked G protein-coupled receptors. Assay Drug Dev Technol 1:261–273PubMedCrossRefGoogle Scholar
  35. Ferrer M, Maiolo J, Kratz P, Jackowski JL, Murphy DJ, Delagrave S, Inglese J (2005) Directed evolution of PDZ variants to generate high-affinity detection reagents. Protein Eng Des Sel 18:165–173PubMedCrossRefGoogle Scholar
  36. Finkel A, Maiolo J, Kratz P, Jackowski JL, Murphy DJ, Delagrave S, Inglese J (2006) Population patch clamp improves data consistency and success rates in the measurement of ionic currents. J Biomol Screen 11:488–496PubMedCrossRefGoogle Scholar
  37. Friesner RA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750–1759PubMedCrossRefGoogle Scholar
  38. Fung P, Peng K, Kobel P, Dotimas H, Kauffman L, Olson K, Eglen RM (2006) A homogeneous cell-based assay to measure nuclear translocationusing beta-galactosidase enzyme fragment complementation. Assay Drug Dev Technol 4:263–72Google Scholar
  39. Funk OF, Kettmann V, Drimal J, Langer T (2004) Chemical function based pharmacophore generation of endothelin-A selective receptor antagonists. J Med Chem 47:2750–2760PubMedCrossRefGoogle Scholar
  40. Gee KR, Brown KA, Chen WN, Bishop-Stewart J, Gray D, Johnson I (2000) Chemical and physiological characterization of fluo-4 Ca(2+)-indicator dyes. Cell Calcium 27:97–106PubMedCrossRefGoogle Scholar
  41. Glickman F, McGee J, Napper A (2004) Assay development for protein kinase enzymes. In: Sittampalam GS, Coussens NP, Nelson H, Arkin M, Auld D, Austin C, Bejcek B, Glicksman M, Inglese J, Iversen PW, Li Z, McGee J, McManus O, Minor L, Napper A, Peltier JM, Riss T, Trask Jr OJ, Weidner J (eds) Assay guidance manual [Internet]. EliLilly & Company and the National Center for Advancing Translational Science, National Center for Biotechnology Information, BethesdaGoogle Scholar
  42. González JE, Maher MP (2002) Cellular fluorescent indicators and voltage/ion probe reader (VIPR TM): tools for ion channel and receptor drug discovery. Recept Channels 8:283–295PubMedCrossRefGoogle Scholar
  43. González JE, González J, Oades K, Leychkis Y (1999) Cell-based assays and instrumentation for screening ion-channel targets. Drug Discov Today 4:431–439PubMedCrossRefGoogle Scholar
  44. Gowda K, Marks BD, Zielinski TK, Ozers MS (2006) Development of a coactivator displacement assay for the orphan receptor estrogen-related receptor-gamma using time-resolved fluorescence resonance energy transfer. Anal Biochem 357:105–115PubMedCrossRefGoogle Scholar
  45. Halperin I, Ma B, Wolfson H, Nussinov R (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Protein Eng Des Sel 47:409–443CrossRefGoogle Scholar
  46. Hamdan FF, Audet M, Garneau P, Pelletier J, Bouvier M (2005) High-throughput screening of G protein-coupled receptor antagonists using a bioluminescence resonance energy transfer 1-based beta-arrestin2 recruitment assay. J Biomol Screen 10:463–475PubMedCrossRefGoogle Scholar
  47. Haney SA, LaPan P, Pan J, Zhang J (2006) High-content screening moves to the front of the line. Drug Discov Today 11:889–894Google Scholar
  48. Hemmilä I, Dakubu S, Mukkala VM et al (1984) Europium as a label in time-resolved immunofluorometric assays. Anal Biochem 137:335–343PubMedCrossRefGoogle Scholar
  49. Hillisch A, Pineda LF, Hilgenfeld R (2004) Utility of homology models in the drug discovery process. Drug Discov Today 9:659–669PubMedCrossRefGoogle Scholar
  50. Hogg DS, Boden P, Lawton G, Kozlowski RZ (2006) Ion channel drug targets – unlocking the potential. Drug Discov World 7:83–92Google Scholar
  51. Hopkins AL, Groom CR (2002) The druggable genome. Nat Rev Drug Discov 1:727–730PubMedCrossRefGoogle Scholar
  52. Hughes JD, Blagg J, Price DA, Bailey S, Decrescenzo GA, Devraj RV, Ellsworth E, Fobian YM, Gibbs ME, Gilles RW, Greene N, Huang E, Krieger-Burke T, Loesel J, Wager T, Whiteley L, Zhang Y (2008) Physiochemical drug properties associated with in vivo toxicological outcomes. Bioorg Med Chem Lett 18:4872–4875PubMedCrossRefGoogle Scholar
  53. Inglese J (2006) Measuring biological responses with automated microscopy. Elsevier Academic, San DiegoGoogle Scholar
  54. Inglese J, Johnson RL, Simeonov A, Xia M, Zheng W, Austin CP, Auld DS (2007) High-throughput screening assays for the identification of chemical probes. Nat Chem Biol 3:466–479PubMedCrossRefGoogle Scholar
  55. Iversen PW, Eastwood BJ, Sittampalam GS, Cox KL (2006) A comparison of assay performance measures in screening assays: signal window, Z′ factor, and assay variability ratio. J Biomol Screen 11:247–252PubMedCrossRefGoogle Scholar
  56. Jacoby E, Bouhelal R, Gerspacher M, Seuwen K (2006) The 7 TM G-protein-coupled receptor target family. Chem Med Chem 1:761–782PubMedCrossRefGoogle Scholar
  57. Jain AN (2003) Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem 46:499–511PubMedCrossRefGoogle Scholar
  58. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727–748PubMedCrossRefGoogle Scholar
  59. Karvinen J, Elomaa A, Mäkinen ML, Hakala H, Mukkala VM, Peuralahti J, Hurskainen P, Hovinen J, Hemmilä I (2004) Caspase multiplexing: simultaneous homogeneous time-resolved quenching assay (TruPoint) for caspases 1, 3, and 6. Anal Biochem 325:317–325PubMedCrossRefGoogle Scholar
  60. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3:935–949PubMedCrossRefGoogle Scholar
  61. Kon T, Tanigawa T, Hayamizu K, Shen M, Tsuji T, Naito Y, Yoshikawa T (2004) Singlet oxygen quenching activity of human serum. Redox Rep 9:325–330PubMedCrossRefGoogle Scholar
  62. Koresawa M, Okabe T (2004) High-throughput screening with quantitation of ATP consumption: a universal non-radioisotope, homogeneous assay for protein kinase. Assay Drug Dev Technol 2:153–160PubMedCrossRefGoogle Scholar
  63. Krivov GG, Shapovalov MV, Dunbrack RL (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins: Struct, Funct, Bioinf 77:778–795CrossRefGoogle Scholar
  64. Kumar S, Wittmann C, Heinzle E (2004) Minibioreactors. Biotechnol Lett 26:1–10PubMedCrossRefGoogle Scholar
  65. Kunapuli P, Lee S, Zheng W, Alberts M, Kornienko O, Mull R, Kreamer A, Hwang JI, Simon MI, Strulovici B (2006) Identification of small molecule antagonists of the human mas-related gene-X1 receptor. Anal Biochem 351:50–61PubMedCrossRefGoogle Scholar
  66. Lakowicz JR (2006) Principles of fluorescence spectroscopy. Springer, HeidelbergCrossRefGoogle Scholar
  67. Leung D, Abbenante G, Fairlie DP (2000) Protease inhibitors: current status and future prospects. J Med Chem 43:305–341PubMedCrossRefGoogle Scholar
  68. Li H, Sutter J, Hoffman R (2000) HypoGen: an automated system for generating 3D predictive pharmacophore models. In: Guner OF (ed) Pharmacophore perception, development, and use in drug design. International University Line, San Diego, pp 171–189Google Scholar
  69. Lipinski CA (2000) Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Toxicol Methods 44:235–249PubMedCrossRefGoogle Scholar
  70. Lowery RG, Kleman-Leyer K (2006) Transcreener: screening enzymes involved in covalent regulation. Expert Opin Ther Targets 10:179–190PubMedCrossRefGoogle Scholar
  71. Macarrón R, Hertzberg RP (2011) Design and implementation of high throughput screening assays. Mol Biotechnol 47:270–285PubMedCrossRefGoogle Scholar
  72. Mahajan NP, Harrison-Shostak DC, Michaux J, Herman B (1999) Novel mutant green fluorescent protein protease substrates reveal the activation of specific caspases during apoptosis. Chem Biol 6:401–409PubMedCrossRefGoogle Scholar
  73. Martin YC (2000) DISCO: what we did right and what we missed. In: Guner OF (ed) Pharmacophore perception, development, and use in drug design. International University Line, San Diego, pp 49–68Google Scholar
  74. Martí-Renom M a, Stuart a C, Fiser a et al (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291–325Google Scholar
  75. Mathis G (1993) Rare earth cryptates and homogeneous fluoroimmunoassays with human sera. Clin Chem 39:1953–1959PubMedGoogle Scholar
  76. May KML, Wang Y, Bachas LG, Anderson KW (2004) Development of a whole-cell-based biosensor for detecting histamine as a model toxin. Anal Chem 76:4156–4161PubMedCrossRefGoogle Scholar
  77. McDonald OB, Chen WJ, Ellis B, Hoffman C, Overton L, Rink M, Smith A, Marshall CJ, Wood ER (1999) A scintillation proximity assay for the Raf/MEK/ERK kinase cascade: high-throughput screening and identification of selective enzyme inhibitors. Anal Biochem 268:318–329PubMedCrossRefGoogle Scholar
  78. Miller MD, Kearsley SK, Underwood DJ, Sheridan RP (1994) FLOG: a system to select “quasi-flexible” ligands complementary to a receptor of known three-dimensional structure. J Comput Aided Mol Des 8:153–174PubMedCrossRefGoogle Scholar
  79. Misura KMS, Baker D (2005) Progress and challenges in high-resolution refinement of protein structure models. Proteins 59:15–29PubMedCrossRefGoogle Scholar
  80. Mitchell J, Laskowski R, Alex A, Thornton J (1999) BLEEP – potential of mean force describing protein-ligand interactions: I. Generating potential. J Comput Chem 20:1165–1176CrossRefGoogle Scholar
  81. Moore KJ (1999) Single molecule detection technologies in miniaturized high throughput screening: fluorescence correlation spectroscopy. J Biomol Screen 4:335–353PubMedCrossRefGoogle Scholar
  82. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639–1662CrossRefGoogle Scholar
  83. Nagy L, Schwabe JWR (2004) Mechanism of the nuclear receptor molecular switch. Trends Biochem Sci 29:317–324PubMedCrossRefGoogle Scholar
  84. Nonner W, Eisenberg B (2000) Electrodiffusion in ionic channels of biological membranes. J Mol Liq 87:149–162CrossRefGoogle Scholar
  85. O’Boyle DR, Nower PT, Lemm JA, Valera L, Sun JH, Rigat K, Colonno R, Gao M (2005) Development of a cell-based high-throughput specificityscreen using a hepatitis C virus-bovine viral diarrhea virus dual replicon assay. Antimicrob Agents Chemother 49:1346–1353Google Scholar
  86. Olefsky JM (1999) Insulin-stimulated glucose transport mini review series. J Biol Chem 274:1863PubMedCrossRefGoogle Scholar
  87. Ortuso F, Langer T, Alcaro S (2006) GBPM: GRID-based pharmacophore model: concept and application studies to protein-protein recognition. Bioinformatics 22:1449–1455PubMedCrossRefGoogle Scholar
  88. Pandit D, So S-S, Sun H (2006) Enhancing specificity and sensitivity of pharmacophore-based virtual screening by incorporating chemical and shape features–a case study of HIV protease inhibitors. J Chem Inf Comput Sci 46:1236–1244CrossRefGoogle Scholar
  89. Pfleger KDG, Eidne KA (2006) Illuminating insights into protein-protein interactions using bioluminescence resonance energy transfer (BRET). Nat Methods 3:165–174PubMedCrossRefGoogle Scholar
  90. Pope A, Haupts U, Moore K (1999) Homogeneous fluorescence readouts for miniaturized high-throughput screening: theory and practice. Drug Discov Today 4:350–362PubMedCrossRefGoogle Scholar
  91. Poptodorov K, Luu T, Hoffmann RD (2006) Pharmacophore model generation software tools. In: Langer T, Hoffmann WD (eds) Pharmacophores and pharmacophore searches. Wiley-VCH Verlag GmbH & Co. KGaA, pp 15–47Google Scholar
  92. Pui TS, Sudibya HG, Luan X, Zhang Q, Ye F, Huang Y, Chen P (2010) Non-invasive detection of cellular bioelectricity based on carbon nanotube devices for high-throughput drug screening. Adv Mater 22:3199–3203PubMedCrossRefGoogle Scholar
  93. Qureshi SA (2007) Lactamase: an ideal reporter system for monitoring gene expression in live eukaryotic cells. BioTechniques 42:91–95PubMedCrossRefGoogle Scholar
  94. Rabinowitz JD, Rigler P, Carswell-Crumpton C, Beeson C, McConnell HM (1997) Screening for novel drug effects with a microphysiometer: a potent effect of clofilium unrelated to potassium channel blockade. Life Sci 61:PL87–PL94PubMedCrossRefGoogle Scholar
  95. Ramm P (1999) Imaging systems in assay screening. Drug Discov Today 4:401–410PubMedCrossRefGoogle Scholar
  96. Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470–489PubMedCrossRefGoogle Scholar
  97. Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE (2012) Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins: Struct, Funct, Bioinf 82:2071–2079Google Scholar
  98. Rohl CA, Strauss CEM, Misura KM, Baker D (2004) Protein structure prediction using Rosetta. Methods Enzymol 383:66–93PubMedCrossRefGoogle Scholar
  99. Sabisz M, Skladanowski A (2009) Cancer stem cells and escape from drug-induced premature senescence in human lung tumor cells: implications for drug resistance and in vitro drug screening models. Cell Cycle 8:3208–3217PubMedCrossRefGoogle Scholar
  100. Sato M, Ozawa T, Inukai K, Asano T,Umezawa Y (2002) Fluorescent indicators for imaging protein phosphorylation in single living cells. Nature Biotechnol 20:287–94Google Scholar
  101. Schroeder KS (1996) FLIPR: a new instrument for accurate, high throughput optical screening. J Biomol Screen 1:75–80CrossRefGoogle Scholar
  102. Scott JE, Williams KP (2004) Validating identity, mass purity and enzymatic purity of enzyme preparationsGoogle Scholar
  103. Seethala R, Prabhavathi F (2001) Handbook of drug screening. CRC Press, Hoboken, p 106CrossRefGoogle Scholar
  104. Sever JL (1962) Application of a microtechnique to viral serological investigations. J Immunol 88:320–329PubMedGoogle Scholar
  105. Seville M, West AB, Cull MG, McHenry CS (1996) Fluorometric assay for DNA polymerases and reverse transcriptase. BioTechniques 21:664–672PubMedGoogle Scholar
  106. Sharma SV, Da H, Settleman J (2010) Cell line-based platforms to evaluate the therapeutic efficacy of candidate anticancer agents. Nat Rev Cancer 10:241–253PubMedCrossRefGoogle Scholar
  107. Shoichet BK (2006) Screening in a spirit haunted world. Drug Discov Today 11:607–615PubMedPubMedCentralCrossRefGoogle Scholar
  108. Singh P, Harden BJ, Lillywhite BJ, Broad PM (2004) Identification of kinase inhibitors by an ATP depletion method. Assay Drug Dev Technol 2:161–169PubMedCrossRefGoogle Scholar
  109. Sliwoski G, Kothiwale S, Meiler J, Lowe EW (2014) Computational methods in drug discovery. Pharmacol Rev 66:334–395PubMedPubMedCentralCrossRefGoogle Scholar
  110. Sportsman JR, Gaudet EA, Boge A (2004) Immobilized metal ion affinity-based fluorescence polarization (IMAP): advances in kinase screening. Assay Drug Dev Technol 22:205–214CrossRefGoogle Scholar
  111. Sundberg S (2000) High-throughput and ultra-high-throughput screening: solution- and cell-based approaches. Curr Opin Biotechnol 11:47–53PubMedCrossRefGoogle Scholar
  112. Taylor DL (2006) In: Taylor D, Haskins JR, Giuliano KA (eds) High content screening. Humana, TotowaGoogle Scholar
  113. Terpetschnig E, Szmacinski H, Malak H, Lakowicz JR (1995) Metal-ligand complexes as a new class of long-lived fluorophores for protein hydrodynamics. Biophys J 68:342–350PubMedPubMedCentralCrossRefGoogle Scholar
  114. Toba S, Srinivasan J, Maynard AJ, Sutter J (2006) Using pharmacophore models to gain insight into structural binding and virtual screening: an application study with CDK2 and human DHFR. J Chem Inf Model 46:728–735PubMedCrossRefGoogle Scholar
  115. Trinquet E, Mathis G (2006) Fluorescence technologies for the investigation of chemical libraries. Mol BioSyst 2:380–387PubMedCrossRefGoogle Scholar
  116. Trinquet E, Fink M, Bazin H, Fink M, Bazin H, Grillet F, Maurin F, Bourrier E, Ansanay H, Leroy C, Michaud A, Durroux T, Maurel D, Malhaire F, Goudet C, Pin JP, Naval M, Hernout O, Chrétien F, Fink M, Bazin H, Grillet F, Maurin F, Bourrier E, Ansanay H, Leroy C, Michaud A, Durroux T, Maurel D, Malhaire F, Goudet C, Pin JP, Naval M, Hernout O, Chrétien F, Chapleur Y, Mathis G (2006) 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 358:126–135PubMedCrossRefGoogle Scholar
  117. Velec HFG, Gohlke H, Klebe G (2005) Drug Score CSD-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem 48:6296–6303PubMedCrossRefGoogle Scholar
  118. Verma R, Peters NR, D’Onofrio M, Tochtrop GP, Sakamoto KM, Varadan R, Zhang M, Coffino P, Fushman D, Deshaies RJ, King RW (2004) Ubistatins inhibit proteasome-dependent degradation by binding the ubiquitin chain. Science 306:117–120PubMedCrossRefGoogle Scholar
  119. Williams C (2004) cAMP detection methods in HTS: selecting the best from the rest. Nat Rev Drug Discov 3:125–135PubMedCrossRefGoogle Scholar
  120. Wolber G, Langer T (2005) Ligand Scout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J Chem Inf Model 45:160–169PubMedCrossRefGoogle Scholar
  121. Wolber G, Seidel T, Bendix F, Langer T (2008) Molecule-pharmacophore super positioning and pattern matching in computational drug design. Drug Discov Today 13:23–29PubMedCrossRefGoogle Scholar
  122. Wölcke J, Ullmann D (2001) Miniaturized HTS technologies – uHTS. Drug Discov Today 6:637–646CrossRefPubMedGoogle Scholar
  123. Xiang Z (2006) Advances in homology protein structure modeling. Curr Protein Pept Sci 7:217–227PubMedPubMedCentralCrossRefGoogle Scholar
  124. Xu X, Gerard AL, Huang BC, Anderson DC, Payan DG, Luo Y (1998) Detection of programmed cell death using fluorescence energy transfer. Nucleic Acids Res 26:2034–2035PubMedPubMedCentralCrossRefGoogle Scholar
  125. Yang S-Y (2010) Pharmacophore modeling and applications in drug discovery: challenges and recent advances. Drug Discov Today 15:444–450PubMedCrossRefGoogle Scholar
  126. Yang S-T, Zhang X, Wen Y (2008) Microbioreactors for high-throughput cytotoxicity assays. Curr Opin Drug Discov Dev 11:111–127Google Scholar
  127. Yang J, Copeland RA, Lai Z (2009) Defining balanced conditions for inhibitor screening assays that target bisubstrate enzymes. J Biomol Screen 14:111–120PubMedCrossRefGoogle Scholar
  128. Zang R, Li D, Tang I-C, Wang J, Yang S-T (2012) Cell-based assays in high-throughput screening for drug discovery. Int J Biotechnol Wellness Ind 1:31–51Google Scholar
  129. Zhang JH, Chung TD, Oldenburg KR (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 4:67–73PubMedCrossRefGoogle Scholar
  130. Zheng W, Spencer RH, Kiss L (2004) High throughput assay technologies for ion channel drug discovery. Assay Drug Dev Technol 2:543–552PubMedCrossRefGoogle Scholar
  131. Zheng CJ, Han LY, Yap CW, Ji ZL, Cao ZW, Chen YZ (2006) Therapeutic targets: progress of their exploration and investigation of their characteristics. Pharmacol Rev 58:259–279PubMedCrossRefGoogle Scholar
  132. Zlokarnik G, Negulescu PA, Knapp TE, Mere L, Burres N, Feng L, Whitney M, Roemer K, Tsien RY (1998) Quantitation of transcription and clonal selection of single living cells with beta-lactamase as reporter. Science 279:84–88PubMedCrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Nandu Thrithamarassery Gangadharan
    • 1
  • Ananda Baskaran Venkatachalam
    • 2
  • Shiburaj Sugathan
    • 1
    Email author
  1. 1.Division of MicrobiologyJawaharlal Nehru Tropical Botanic Garden and Research InstituteThiruvananthapuramIndia
  2. 2.Atlantic Centre for Transplantation ResearchDalhousie UniversityHalifaxCanada

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