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Review

Combining label-free cell phenotypic profiling with computational approaches for novel drug discovery

Bibliography

  • Hart CP. Finding the target after screening the phenotype. Drug Discov Today 2005;10:513-19
  • Swinney DC, Anthony J. How were new medicines discovered? Nat Rev Drug Discov 2011;10:507-19
  • Lee JA, Uhlik MT, Moxham CM, et al. Modern phenotypic drug discovery is a viable, neoclassic pharma strategy. J Med Chem 2012;55:4527-38
  • Eggert US. The why and how of phenotypic small-molecule screens. Nat Chem Biol 2013;9:206-9
  • Fang Y. Troubleshooting and deconvoluting label-free cell phenotypic assays in drug discovery. J Pharmacol Toxicol Methods 2013;67:69-81
  • Fang Y. Label-free cell phenotypic drug discovery. Comb Chem High Throughput Screen 2014;17:566-78
  • Fang Y. Label-free drug discovery. Front Pharmacol 2014;5:52
  • Paolini GV, Shapland RH, van Hoorn WP, et al. Global mapping of pharmacological space. Nat Biotechnol 2006;24:805-15
  • Yildirim MA, Goh KI, Cusick ME, et al. Drug-target network. Nat Biotechnol 2007;25:1119-26
  • Kolb P, Ferreira RS, Irwin JJ, et al. Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol 2009;20:429-36
  • Keiser MJ, Roth BL, Armbruster BN, et al. Relating protein pharmacology by ligand chemistry. Nat Biotechnol 2007;25:197-206
  • Keiser MJ, Setola V, Irwin JJ, et al. Predicting new molecular targets for known drugs. Nature 2009;462:175-81
  • Lounkine E, Keiser MJ, Whitebread S, et al. Large-scale prediction and testing of drug activity on side-effect targets. Nature 2012;486:361-7
  • McGregor MJ, Muskal SM. Pharmacophore fingerprinting 1. application to QSAR and focused library design. J Chem Inf Comput Sci 1999;39:569-74
  • McGregor MJ, Muskal SM. Pharmacophore fingerprinting 2. application to primary library design. J Chem Inf Comput Sci 2000;40:117-25
  • Lyne PD. Structure-based virtual screening: an overview. Drug Discov Today 2002;7:1047-55
  • Blundell TL, Jhoti H, Abell C. High-throughput crystallography for lead discovery in drug design. Nat Rev Drug Discov 2002;1:45-54
  • Shoichet BK. Virtual screening of chemical libraries. Nature 2004;432:862-5
  • Klebe G. Virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 2006;11:580-94
  • Koutsoukas A, Simms B, Kirchmair J, et al. From in silico target prediction to multi-target drug design: current databases, methods and applications. J Proteomics 2011;74:2554-74
  • Villoutreix BO, Eudes R, Miteva MA. Structure-based virtual ligand screening: recent success stories. Comb Chem High Throughput Screen 2009;12:1000-17
  • Shoichet BK, Kobilka BK. Structure-based drug screening for G-protein-coupled receptors. Trends Pharmacol Sci 2012;33:268-72
  • Ananiadou S, Kell DB, Tsujii J. Text mining and its potential applications in systems biology. Trends Biotechnol 2006;24:571-9
  • Campillos M, Kuhn M, Gavin AC, et al. Drug target identification using side-effect similarity. Science 2008;321:263-6
  • Fang Y. The development of label-free cellular assays for drug discovery. Expert Opin Drug Discov 2011;6:1285-98
  • Kenakin T. Cellular assays as portals to seven-transmembrane receptor-based drug discovery. Nat Rev Drug Discov 2009;8:617-26
  • Rocheville M, Martin J, Jerman J, et al. Mining the potential of label-free biosensors for seven-transmembrane receptor drug discovery. Prog Mol Biol Transl Sci 2013;115:123-42
  • Fang Y. Ligand-receptor interaction platforms and their applications for drug discovery. Expert Opin Drug Discov 2012;7:969-88
  • Fang Y, Ferrie AM, Fontaine NH, et al. Resonant waveguide grating biosensor for living cell sensing. Biophys J 2006;91:1925-40
  • Chen JY, Shahid A, Garcia MP, et al. Dissipation monitoring for assessing EGF-induced changes of cell adhesion. Biosens Bioelectron 2012;38:375-81
  • Wong S-H, Gao A, Ward S, et al. Development of a label-free assay for sodium-dependent phosphate transporter NaPi-IIb. J Biomol Screen 2012;17:829-34
  • Sun H, Wei Y, Xiong Q, et al. Label-free cell phenotypic profiling decodes the composition and signaling of an endogenous ATP-sensitive potassium channel. Sci Rep 2014;4:4934
  • Hennen S, Wang H, Peters L, et al. Decoding signaling and function of the orphan G protein-coupled receptor GPR17 with a small-molecule agonist. Sci Signal 2013;6:ra93
  • Carter RL, Grisanti LA, Yu JE, et al. Dynamic mass redistribution analysis of endogenous beta-adrenergic receptor signaling in neonatal rat cardiac fibroblasts. Pharmacol Res Perspect 2014;2:24
  • Bagnaninchi PO, Drummond N. Real-time label-free monitoring of adipose-derived stem cell differentiation with electric cell-substrate impedance sensing. Proc Natl Acad Sci USA 2011;108:6462-7
  • Pai S, Verrier F, Sun H, et al. Dynamic mass redistribution assay decodes differentiation of a neural progenitor stem cell. J Biomol Screen 2012;17:1180-91
  • Deng H, Sun H, Fang Y. Label-free cell phenotypic assessment of the biased agonism and efficacy of agonists at the endogenous muscarinic M3 receptors. J Pharmacol Toxicol Methods 2013;68:323-33
  • Ferrie AM, Deichmann OD, Wu Q, et al. High resolution resonant waveguide grating imager for cell cluster analysis under physiological condition. Appl Phys Lett 2012;100:223701
  • Zhang X, Deng H, Xiao Y, et al. Label-free cell phenotypic profiling identifies pharmacologically active compounds in two Traditional Chinese Medicinal plants. RSC Adv 2014;4:26368-77
  • Shoemaker RH. The NCI60 human tumour cell line anticancer drug screen. Nat Rev Cancer 2006;6:813-23
  • Garnett MJ, Edelman EJ, Heidorn SJ, et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 2012;483:570-5
  • Barretina J, Caponigro G, Stransky N, et al. The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012;483:603-7
  • Fang Y. Label-free biosensors for cell biology. Int J Electrochem 2011;2011:e460850
  • Febles NK, Ferrie AM, Fang Y. Label-free single cell quantification of the invasion of spheroidal colon cancer cells through 3D Matrigel. Anal Chem 2014;86:8842-9
  • Justice BA, Badr NA, Felder RA. 3D cell culture opens new dimensions in cell-based assays. Drug Discov Today 2009;14:102-7
  • Guan N, Deng J, Li T, et al. Label-free monitoring of T cell activation by the impedance-based xCELLigence system. Mol Biosyst 2013;9:1035-43
  • Yanase Y, Hiragun T, Yanase T, et al. Application of SPR imaging sensor for detection of individual living cell reactions and clinical diagnosis of type I allergy. Allergol Int 2013;62:163-9
  • Yashunsky V, Kharilker L, Zlotkin-Rivkin E, et al. Real-time sensing of enteropathogenic E. coli-induced effects on epithelial host cell height, cell-substrate interactions, and endocytic processes by infrared surface plasmon spectroscopy. PLoS One 2013;8:e78431
  • Abassi YA, Xi B, Li N, et al. Dynamic monitoring of beating periodicity of stem cell-derived cardiomyocytes as a predictive tool for preclinical safety assessment. Br J Pharmacol 2012;165:1424-41
  • Ferrie AM, Wu Q, Deichmann O, et al. High frequency resonant waveguide grating imager for assessing drug-induced cardiotoxicity. Appl Phys Lett 2014;104:183702
  • Ramsden JJ, Li S-Y, Prenosil JE, et al. Optical method for measurement of number and shape of attached cells in real time. Cytometry 1995;19:97-102
  • Fang Y, Ferrie AM, Fontaine NH, et al. Characteristics of dynamic mass redistribution of EGF receptor signaling in living cells measured with label free optical biosensors. Anal Chem 2005;77:5720-5
  • Ferrie AM, Wang C, Deng H, et al. Label-free optical biosensor with microfluidics identifies an intracellular signalling wave mediated through the beta2-adrerengic receptor. Integr Biol 2013;5:1253-61
  • Copeland RA, Pompliano DL, Meek TD. Drug-target residence time and its implications for lead optimization. Nat Rev Drug Discov 2006;5:730-9
  • Deng H, Wang C, Su M, et al. Probing biochemical mechanisms of action of muscarinic M3 receptor antagonists with label-free whole-cell assays. Anal Chem 2012;84:8232-9
  • Guo D, Mulder-Krieger T, Ijzerman AP, et al. Functional efficacy of adenosine A2A receptor agonists is positively correlated to their receptor residence time. Br J Pharmacol 2012;166:1846-959
  • Ferrie AM, Sun H, Fang Y. Label-free integrative pharmacology on-target of drugs at the beta2-adrenergic receptor. Sci Rep 2011;1:33
  • Morse M, Tran E, Levension RL, et al. Ligand-directed functional selectivity at the mu opioid receptor revealed by label-free on-target pharmacology. PLoS One 2011;6:e25643
  • Morse M, Sun H, Tran E, et al. Label-free integrative pharmacology on target of opioid ligands at the opioid receptor family. BMC Pharmacol Toxicol 2013;14:17
  • Ferrie AM, Sun H, Zaytseva N, et al. Divergent label-free cell phenotypic pharmacology of ligands at the overexpressed beta2-adrenergic receptors. Sci Rep 2014;4:3828
  • Eisen MB, Spellman PT, Brown PO, et al. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998;95:14863-8
  • Orgovan N, Peter B, Bősze S, et al. Dependence of cancer cell adhesion kinetics on integrin ligand surface density measured by a high-throughput label-free resonant waveguide grating biosensor. Sci Rep 2014;4:4034
  • Abassi YA, Xi B, Zhang W, et al. Kinetic cell-based morphological screening: prediction of mechanism of compound action and off-target effects. Chem Biol 2009;16:712-23
  • Fu H, Fu W, Sun M, et al. Kinetic cellular phenotypic profiling: prediction, identification, and analysis of bioactive natural products. Anal Chem 2011;83:6518-26
  • Owens RM, Wang C, You JA, et al. Real-time quantitation of viral replication and inhibitor potency using a label-free optical biosensor. J Recept Signal Transduct Res 2009;29:195-201
  • Kang L, Chung BG, Langer R, et al. Microfluidics for drug discovery and development: from target selection to product lifecycle management. Drug Discov Today 2008;13:1-13
  • Zaytseva N, Miller W, Goral V, et al. Microfluidic resonant waveguide grating biosensor system for whole cell sensing. Appl Phys Lett 2011;96:163703
  • Goral V, Jin Y, Sun H, et al. Agonist-directed desensitization of the beta2-adrenergic receptor. PLoS One 2011;6:e19282
  • Goral V, Wu Q, Sun H, et al. Label-free optical biosensor with microfluidics for sensing ligand-directed functional selectivity on trafficking of thrombin receptor. FEBS Lett 2011;585:1054-60
  • Deng H, Wang C, Fang Y. Label-free cell phenotypic assessment of the molecular mechanism of action of epidermal growth factor receptor inhibitors. RSC Adv 2013;3:10370-8
  • Dodgson K, Gedge L, Murray DC, et al. A 100K well screen for a muscarinic receptor using the Epic label-free system – a reflection on the benefits of the label-free approach to screening seven-transmembrane receptors. J Recept Signal Transduct Res 2009;29:163-72
  • Bajorath J. Integration of virtual and high-throughput screening. Nat Rev Drug Discov 2002;1:882-94
  • Gregori-Puigjané E, Setola V, Hert J, et al. Identifying mechanism-of-action targets for drugs and probes. Proc Natl Acad Sci USA 2012;109:11178-83
  • Martin YC, Kofron JL, Traphagen LM. Do structurally similar molecules have similar biological activity? J Med Chem 2002;45:4350-8
  • Boström J, Hogner A, Schmitt S. Do structurally similar ligands bind in a similar fashion? J Med Chem 2006;49:6716-25
  • Strebhardt K, Ullrich A. Paul Ehrlich’s magic bullet concept: 100 years of progress. Nat Rev Cancer 2008;8:473-80
  • Schueler FW. Chemobiodynamics and drug design. McGraw-Hill; New York: 1960
  • Maggiora G, Vogt M, Stumpfe D, et al. Molecular similarity in medicinal chemistry. J Med Chem 2014;57:3186-204
  • Willett P. Similarity-based virtual screening using 2D fingerprints. Drug Discov Today 2006;11:1046-53
  • Keiser MJ, Irwin JJ, Shoichet BK. The chemical basis of pharmacology. Biochemistry 2010;49:10267-76
  • Willett P, Barnard JM, Downs GM. Chemical similarity searching. J Chem Inf Model 1998;38:983-6
  • Vieth M, Higgs RE, Robertson DH, et al. Kinomics-structural biology and chemogenomics of kinase inhibitors and targets. Biochim Biophys Acta 2004;1697:243-57
  • Izrailev S, Farnum MA. Enzyme classification by ligand binding. Proteins 2004;57:711-24
  • Rask-Andersen M, Almén MS, Schiöth HB. Trends in the exploitation of novel drug targets. Nat Rev Drug Discov 2011;10:579-90
  • Roth BL, Sheffler DJ, Kroeze WK. Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia. Nat Rev Drug Discov 2004;3:353-9
  • Oshiro C, Bradley EK, Eksterowicz J, et al. Performance of 3D-database molecular docking studies into homology models. J Med Chem 2004;47:764-7
  • Polgar T, Baki A, Szendrei GI, et al. Comparative virtual and experimental high-throughput screening for glycogen synthase kinase-3b inhibitors. J Med Chem 2005;48:7946-59
  • Feng BY, Simeonov A, Jadhav A, et al. A high-throughput screen for aggregation-based inhibition in a large compound library. J Med Chem 2007;50:2385-90
  • Babaoglu K, Simeonov A, Irwin J, et al. Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. J Med Chem 2008;51:2502-11
  • Kolb P, Rosenbaum DM, Irwin JJ, et al. Structure-based discovery of beta2-adrenergic receptor ligands. Proc Natl Acad Sci USA 2009;106:6843-8
  • Audet M, Bouvier M. Insights into signaling from the beta2-adrenergic receptor structure. Nat Chem Biol 2008;4:397-403
  • Venkatakrishnan AJ, Deupi X, Lebon G, et al. Molecular signatures of G-protein-coupled receptors. Nature 2013;494:185-94
  • Congreve M, Langmead CJ, Mason JS, et al. Progress in structure based drug design for G protein-coupled receptors. J Med Chem 2011;54:4283-311
  • Overington JP, Al-Lazikani B, Hopkins AL. How many drug targets are there? Nat Rev Drug Discov 2006;5:993-6
  • Carlsson J, Yoo L, Gao ZG, et al. Structure-based discovery of A2A adenosine receptor ligands. J Med Chem 2010;53:3748-55
  • Carlsson J, Coleman RG, Setola V, et al. Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol 2011;7:769-78
  • Mysinger MM, Weiss DR, Ziarek JJ, et al. Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4. Proc Natl Acad Sci USA 2012;109:5517-22
  • Villar HO, Hansen MR. Mining and visualizing the chemical content of large databases. Curr Opin Drug Discov Devel 2009;12:367-75
  • Banville DL. Mining chemical and biological information from the drug literature. Curr Opin Drug Discov Devel 2009;12:376-87
  • Yang Y, Adelstein SJ, Kassis AI. Target discovery from data mining approaches. Drug Discov Today 2009;14:147-54
  • Fliri AF, Loging WT, Thadeio PF, et al. Analysis of drug-induced effect patterns to link structure and side effects of medicines. Nat Chem Biol 2005;1:389-97
  • Malo N, Hanley JA, Cerquozzi S, et al. Statistical practice in high-throughput screening data analysis. Nat Biotechnol 2006;24:167-75
  • Scott JD, Pawson T. Cell signaling in space and time: where proteins come together and when they’re apart. Science 2009;326:1220-4
  • Kenakin T, Christopoulos A. Signalling bias in new drug discovery: detection, quantification and therapeutic impact. Nat Rev Drug Discov 2013;12:205-16
  • Srinivasan S, Nwachukwu JC, Parent AA, et al. Ligand-binding dynamics rewire cellular signaling via estrogen receptor-alpha. Nat Chem Biol 2013;9:326-32
  • Beher D, Wu J, Cumine S, et al. Resveratrol is not a direct activator of SIRT1 enzyme activity. Chem Biol Drug Des 2009;74:619-24
  • Hu H, Deng H, Fang Y. Label-free phenotypic profiling identified D-luciferin as a GPR35 agonist. PLoS One 2012;7:e34934
  • Kenakin T. A holistic view of GPCR signaling. Nat Biotechnol 2010;28:928-9
  • Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009;5:789-96
  • Rosenbaum DM, Rasmussen SG, Kobilka BK. The structure and function of G-protein-coupled receptors. Nature 2009;459:356-63
  • Dror RO, Pan AC, Arlow DH, et al. Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc Natl Acad Sci USA 2011;108:13118-23
  • Tanrikulu Y, Krüger B, Proschak E. The holistic integration of virtual screening in drug discovery. Drug Discov Today 2013;18:358-64
  • Deng H, Hu H, He M, et al. Discovery of 2-(4-methylfuran-2(5H)-ylidene)malononitrile and thieno[3,2-b]thiophene-2-carboxylic acid derivatives as G protein-coupled receptor-35 (GPR35) agonists. J Med Chem 2011;54:7385-96
  • Levitzki A, Mishani E. Tyrphostins and other tyrosine kinase inhibitors. Annu Rev Biochem 2006;75:93-109
  • Deng H, Hu H, Fang Y. Tyrphostin analogs are GPR35 agonists. FEBS Lett 2011;585:1957-62
  • Deng H, Hu H, Fang Y. Multiple tyrosine metabolites are GPR35 agonists. Sci Rep 2012;2:373
  • Deng H, Fang Y. Discovery of nitrophenols as GPR35 agonists. MedChemComm 2012;3:1270-4
  • Yang Y, Lu JY, Wu X, et al. G-protein-coupled receptor 35 is a target of the asthma drugs cromolyn disodium and nedocromil sodium. Pharmacology 2010;86:1-5
  • Deng H, Fang Y. Anti-inflammatory gallic acid and wedelolactone are G protein-coupled receptor-35 agonists. Pharmacology 2012;89:211-19
  • Tognolini M, Incerti M, Pala D, et al. Target hopping as a useful tool for the identification of novel EphA2 protein-protein antagonists. ChemMedChem 2014;9:67-72
  • Leeson PD, Springthorpe B. The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discov 2007;6:881-90
  • Hopkins AL, Groom CR, Alex A. Ligand efficiency: a useful metric for lead selection. Drug Discov Today 2004;9:430-1
  • Abad-Zapatero C. Ligand efficiency indices for effective drug discovery. Expert Opin Drug Discov 2007;2:469-88
  • Abad-Zapatero C, Perisic O, Wass J, et al. Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation. Drug Discov Today 2010;15:804-11
  • Gaulton A, Bellis LJ, Bento AP, et al. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 2012;40:d1100-7
  • Li Q, Cheng T, Wang Y, et al. PubChem as a public resource for drug discovery. Drug Discov Today 2010;15:1052-7
  • Law V, Knox C, Djoumbou Y, et al. DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res 2014;42:D1091-7
  • Besnard J, Ruda GF, Setola V, et al. Automated design of ligands to polypharmacological profiles. Nature 2012;492:215-20
  • Irwin JJ, Shoichet BK. ZINC - a free database of commercially available compounds for virtual screening. J Chem Inf Model 2005;45:177-82

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