Non-stoichiometric inhibition in biochemical high-throughput screening

Bibliography

• Kenny BA, Bushfield M, Parry-Smith DJ, The application of high-throughput screening to novel lead discovery. Prog Drug Res 1998;6:245-69
   Google Scholar
• Broach JR, Thorner J. High-throughput screening for drug discovery. Nature 1996;384:14-6
   PubMed Web of Science ®Google Scholar
• Mayr LM, Fuerst P. The future of high-throughput screening. J Biomol Screen 2008;13(6):443-8
   PubMed Web of Science ®Google Scholar
• Keseru G, Makara G. Hit discovery and hit-to-lead approaches. Drug Discov Today 2006;11:741-8
   PubMed Web of Science ®Google Scholar
• Simeonov A, Jadhav A, Thomas CJ, Fluorescence spectroscopic profiling of compound libraries. J Med Chem 2008;51(8):2363-71
   PubMed Web of Science ®Google Scholar
• Imbert PE, Unterreiner V, Siebert D, Recommendations for the reduction of compound artifacts in time-resolved fluorescence resonance energy transfer assays. Assay Drug Dev Technol 2007;5(3):363-72
   PubMed Web of Science ®Google Scholar
• Mayr LM, Bojanic D. Novel trends in high-throughput screening. Curr Opin Pharmacol 2009;9(5):580-8
   PubMed Web of Science ®Google Scholar
• Lipinski CA, Lombardo F, Dominy BW, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 1997;23:3-25
   Web of Science ®Google Scholar
• Kennedy T. Managing the drug discovery/development interface. Drug Discov Today 1997;2:436-44
   Web of Science ®Google Scholar
• Walters WP, Ajay AA, Murcko MA. Recognizing molecules with drug-like properties. Curr Opin Chem Biol 1999;3(4):384-7
   PubMed Web of Science ®Google Scholar
• Huth JR, Mendoza R, Olejniczak ET, ALARM NMR: a rapid and robust experimental method to detect reactive false positives in biochemical screens. J Am Chem Soc 2005;127(1):217-24
   PubMed Web of Science ®Google Scholar
• Rishton GM. Reactive compounds and in vitro false positives in HTS. DDT 1997;2(9):382-4
   Web of Science ®Google Scholar
• Thorne N, Auld DS, Inglese J. Apparent activity in high-throughput screening: origins of compound-dependent assay interference. Curr Opin Chem Biol 2010;14(3):315-24
   PubMed Web of Science ®Google Scholar
• Jager S, Brand L, Eggeling C. New fluorescence techniques for high-throughput drug discovery. Curr Pharm Biotechnol 2003;4(6):463-76
   PubMedGoogle Scholar
• Habig M, Blechschmidt A, Dressler S, Efficient elimination of nonstoichiometric enzyme inhibitors from HTS hit lists. J Biomol Screen 2009;14(6):679
   PubMed Web of Science ®Google Scholar
• Malo N, Hanley JA, Cerquozzi S, Statistical practice in high-throughput screening data analysis. Nat Biotechnol 2006;24(2):167
   PubMed Web of Science ®Google Scholar
• Babaoglu K, Simeonov A, Irwin JJ, Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. J Med Chem 2008;51(8):2502-11
   PubMed Web of Science ®Google Scholar
• Johnston PA. Redox cycling compounds generate H2O2 in HTS buffers containing strong reducing reagents - real hits or promiscuous artifacts? Curr Opin Chem Biol 2010. [Epub ahead of print]
   Google Scholar
• Soares KM, Blackmon N, Shun TY, Profiling the NIH Small Molecule Repository for compounds that generate H2O2 by redox cycling in reducing environments. Assay Drug Dev Technol 2010;8(2):152-74
   PubMed Web of Science ®Google Scholar
• Cimmperman P, Baranauskiene L, Jachimoviciute S, A quantitative model of thermal stabilization and destabilization of proteins by ligands. Biophysics J 2008;95(7):3222-31
   PubMed Web of Science ®Google Scholar
• Bista M, Kowalska K, Janczyk W, Robust NMR screening for lead compounds using tryptophan-containing proteins. JACS 2009;131(22):7500-1
   PubMed Web of Science ®Google Scholar
• Rix U, Superti-Furga G. Target profiling of small molecules by chemical proteomics. Nat Chem Biol 2009;5(9):616
   PubMed Web of Science ®Google Scholar
• Tanramluk D, Schreyer A, Pitt WR, On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine. Chem Biol Drug Des 2009;74(1):16
   PubMed Web of Science ®Google Scholar
• Zhang X, Crespo A, Fernandez A. Turning promiscuous kinase inhibitors into safer drugs. Trends Biotechnol 2008;26(6):295-301
   PubMed Web of Science ®Google Scholar
• Steuer C, Heinonen KH, Kattner L, Optimization of assay conditions for Dengue Virus Protease: effect of various polyols and nonionic detergents. J Biomol Screen 2009;14(9):1102
   PubMed Web of Science ®Google Scholar
• Giannetti AM, Koch BD, Browner MF. Surface plasmon resonance based assay for the detection and characterization of promiscuous inhibitors. J Med Chem 2008;51(3):574-80
   PubMed Web of Science ®Google Scholar
• McGovern SL, Caselli E, Grigorieff N, A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J Med Chem 2002;45(8):1712-22
   PubMed Web of Science ®Google Scholar
• Baell JB, Holloway GA. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem 2010;53(7):2719-40
   PubMed Web of Science ®Google Scholar
• Crisman TJ, Parker CN, Jenkins JL, Understanding false positives in reporter gene assays: in silico chemogenomics approaches to prioritize cell-based HTS data. J Chem Inf Model 2007;47(4):1319
   PubMed Web of Science ®Google Scholar
• Roche O, Schneider P, Zuegge J, Development of a virtual screening method for identification of “Frequent Hitters” in compound libraries. J Med Chem 2002;45:137-42
   PubMed Web of Science ®Google Scholar
• Nakano H, Omura S. Chemical biology of natural indolocarbazole products: 30 years since the discovery of staurosporine. J Antibiot 2009;62(1):17-26
   PubMed Web of Science ®Google Scholar
• Bantscheff M, Scholten A, Heck AJR. Revealing promiscuous drug-target interactions by chemical proteomics. Drug Discov Today 2009;14(21):1021
   PubMed Web of Science ®Google Scholar
• Hopkins AL, Mason JS, Overington JP. Can we rationally design promiscuous drugs? Curr Opin Struct Biol 2006;16:127
   PubMed Web of Science ®Google Scholar
• Evans BE, Rittle KE, Bock MG, Methods for drug discovery - Development of potent, selective, orally effective cholecystokinin antagonists. J Med Chem 1988;31(12):2235-46
   PubMed Web of Science ®Google Scholar
• Costantino L, Barlocco D. Priviledged structures as leads in medicinal chemistry. Curr Med Chem 2006;13(1):65-86
   PubMed Web of Science ®Google Scholar
• Di L, Kerns EH. Biological assay challenges from compound solubility: strategies for bioassay optimization. Drug Discov Today 2006;11(9-10):446-51
   PubMed Web of Science ®Google Scholar
• Liu HY, Wang Z, Regni C, Detailed kinetic studies of an aggregating inhibitor; Inhibition of phosphomannomutase/phosphoglucomutase by Disperse Blue 56. Biochemistry 2004;27:8662-9
   Google Scholar
• Reddie K, Roberts D, Dore T. Inhibition of kinesin motor proteins by adociasulfate-2. J Med Chem 2006;49:4857-60
   PubMed Web of Science ®Google Scholar
• Frenkel YV, Clark ADJ, Das K, Concentration and pH dependent aggregation of hydrophobic drug molecules and relevance to oral bioavailability. J Med Chem 2005;48:1974-83
   PubMed Web of Science ®Google Scholar
• Johnson TO, Ermolieff J, Jirousek MR. Protein tyrosine phosphatase 1B inhibitors for diabetes. Nat Rev Drug Discov 2002;1(9):696-709
   PubMed Web of Science ®Google Scholar
• Jenkins JL, Kao RYT, Shapiro R. Virtual screening to enrich hit lists from high-throughput screening: a case study on small-molecule inhibitors of angiogenin. Proteins Structure Funct Genet 2003;50(1):81-93
   PubMed Web of Science ®Google Scholar
• Nicholas GM, Eckman LL, Newton GL, Inhibition and kinetics of Mycobacterium tuberculosis and Mycobacterium smegmatis mycothiol-S-conjugate amidase by natural product inhibitors. Bioorg Med Chem 2003;11(4):601-8
   PubMed Web of Science ®Google Scholar
• Collins I, Workman P. New approaches to molecular cancer therapeutics. Nat Chem Biol 2006;2(12):689-700
   PubMed Web of Science ®Google Scholar
• McGovern SL, Helfand BT, Feng BY, A specific mechanism of nonspecific inhibition. J Med Chem 2003;46(20):4265-72
   PubMed Web of Science ®Google Scholar
• Ryan AJ, Gray NM, Lowe PN, Effect of detergent on “promiscuous” inhibitors. J Med Chem 2003;46(16):3448-51
   PubMed Web of Science ®Google Scholar
• Coan KED, Maltby DA, Burlingame AL, Promicuous aggregate-based inhibitors promote enzyme unfolding. J Med Chem 2009;52(7):2067
   PubMed Web of Science ®Google Scholar
• Coan KED, Shoichet BK. Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors. J Am Chem Soc 2008;130(29):9606-12
   PubMed Web of Science ®Google Scholar
• Goodwin JJ. Inventor Flow cell system for solubility testing. 2003
   Google Scholar
• Shoichet BK. Interpreting steep dose-response curves in early inhibitor discovery. J Med Chem 2006;49(25):7274-7
   PubMed Web of Science ®Google Scholar
• McGovern SL, Shoichet BK. Kinase inhibitors: not just for kinases anymore. J Med Chem 2003;46:1478-83
   PubMed Web of Science ®Google Scholar
• Lendel C, Bertoncini CW, Cremades N, On the mechanism of nonspecific inhibitors of protein aggregation: dissecting the interactions of alpha-synuclein with congo red and lacmoid. Biochemistry 2009;48(35):8322-34
   PubMed Web of Science ®Google Scholar
• Rishton G. Aggregator compounds confound amyloid fibrillization assay. Nat Chem Biol 2008;4(3):159-60
   PubMed Web of Science ®Google Scholar
• Feng BY, Shoichet BK. Small-molecule aggregates inhibit amyloid polymerization. Nat Chem Biol 2008;4:197-9
   PubMed Web of Science ®Google Scholar
• Seidler J, McGovern SL, Doman TN, Identification and prediction of promiscuous aggregating inhibitors among known drugs. J Med Chem 2003;46(21):4477-86
   PubMed Web of Science ®Google Scholar
• Coan KED, Shoichet BK. Stability and equilibria of promiscuous aggregates in high protein milieus. Mol Biosyst 2007;3(3):208-13
   PubMed Web of Science ®Google Scholar
• Doak AK, Wille H, Prusiner SB, Colloid formation by drugs in simulated intestical fluid. J Med Chem 2010;53(10):4259
   PubMed Web of Science ®Google Scholar
• Frenkel YV, Gallicchio E, Das K, Molecular dynamics study of non-nucleoside reverse transcriptase inhibitor 4-[[4-[[4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/Rilpivirine) aggregates: correlation between amphiphilic properties of the drug and oral bioavailability. J Med Chem 2009;52(19):5896
   PubMed Web of Science ®Google Scholar
• Feng BY, Shelat A, Doman TN, High-throughput assays for promiscuous inhibitors. Nat Chem Biol 2005;1(3):146-8
   PubMed Web of Science ®Google Scholar
• Feng BY, Shoichet BK. A detergent-based assay for the detection of promiscuous inhibitors. Nat Protocols 2006;1(2):550-3
   PubMed Web of Science ®Google Scholar
• Feng BY, Simeonov A, Jadhav A, A high-throughput screen for aggregation-based inhibition in a large compound library. J Med Chem 2007;50(10):2385-90
   PubMed Web of Science ®Google Scholar
• Feng BY, Shoichet BK. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J Med Chem 2006;49(7):2151-4
   PubMed Web of Science ®Google Scholar
• Jadhav A, Ferreira RS, Klumpp C, Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease. J Med Chem 2010;53(1):37
   PubMed Web of Science ®Google Scholar
• Ferreira RS, Simeonov A, Jadhav A, Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem 2010;53(13):4891
   PubMed Web of Science ®Google Scholar
• Cai L, Gochin M. Colloidal aggregate detection by rapid fluorescence measurement of liquid surface curvature changes in multiwell plates. J Biomol Screen 2007;12(7):966-71
   PubMed Web of Science ®Google Scholar
• Wei M, Wynn R, Hollis G, High-throughput determination of mode of inhibition in lead identification and optimization. J Biomol Screen 2007;12(2):220-8
   PubMed Web of Science ®Google Scholar
• Bergsdorf C, Ottl J. Affinity-based screening techniques: their impact and benefit to increase the number of high quality leads. Expert Opin Drug Discov 2010; Early online release
   Google Scholar
• Alsenz J, Kansy M. High throughput solubility measurement in drug discovery and development. Adv Drug Deliv Rev 2007;59(7):546-67
   PubMed Web of Science ®Google Scholar
• Chan LL, Lidstone EA, Finch KE, A method for identifying small-molecule aggregators using photonic crystal biosensor microplates. Jala 2009;14(6):348-59
   PubMed Web of Science ®Google Scholar
• Parker CN, Bajorath J. Towards unified compound screening strategies: a critical evaluation of error sources in experimental and virtual high-throughput screening. QSAR Comb Sci 2006;25(12):1153-61
   Google Scholar
• Zhu Z, Cuozzo J. High-throughput affinity-based technologies for small-molecule drug discovery. J Biomol Screen 2009;14(10):1157
   PubMed Web of Science ®Google Scholar
• Shoichet BK. Interpreting steep dose-response curves in early inhibitor discovery. J Med Chem 2006;49(25):7274-7
   PubMed Web of Science ®Google Scholar
• Fomenko I, Durst M, Balaban D. Robust regression for high throughput drug screening. Comput Methods Prog Biomed 2006;82(1):31-7
   PubMed Web of Science ®Google Scholar
• Lundqvist T. The devil is still in the details - driving early drug discovery forward with biophysical experimental methods. Curr Opin Drug Disc Dev 2005;8(4):513-19
   PubMed Web of Science ®Google Scholar
• Cummings MD, Farnum MA, Nelen MI. Universal screening methods and applications of ThermoFluor (R). J Biomol Screen 2006;11(7):854-63
   PubMed Web of Science ®Google Scholar
• Senisterra GA, Finerty PJ Jr. High throughput methods of assessing protein stability and aggregation. Mol Biosyst 2009;5(3):217-23
   PubMed Web of Science ®Google Scholar
• Senisterra GA, Markin E, Yamazaki K, Screening for ligands using a generic and high-throughput light-scattering-based assay. J Biomol Screen 2006;11(8):940-8
   PubMed Web of Science ®Google Scholar
• Zhang R, Monsma F. Fluorescence-based thermal shift assays. Curr Opin Drug Discov Devel 2010;13(4):389-402
   PubMed Web of Science ®Google Scholar
• Ladbury JE, Klebe G, Freire E. INNOVATION Adding calorimetric data to decision making in lead discovery: a hot tip. Nat Rev Drug Discov 2010;9(1):23-7
   PubMed Web of Science ®Google Scholar
• Freire E. Do enthalpy and entropy distinguish first in class from best in class? Drug Discov Today 2008;13(19-20):869-74
   PubMed Web of Science ®Google Scholar
• SBS/IUPAC Current draft recommendations for a glossary of terms used in biomolecular screening. Available from: http://www.slas.org/education/glossary.cfm
   Google Scholar
• Shoichet BK. Screening in a spirit haunted world. Drug Discov Today 2006;11(13-14):607-15
   PubMed Web of Science ®Google Scholar