Exemplification of the challenges associated with utilising fluorescence intensity based assays in discovery

Bibliography

• Ng R. Drugs: from discovery to approval, 2nd edition. Wiley-Blackwell, USA 2008
   Google Scholar
• Munos B. Lessons from 60 years of pharmaceutical innovation. Nat Rev Drug Discov 2009;8:959-68
   PubMed Web of Science ®Google Scholar
• Piantadosi S. Clinical trials: a methodologic perspective, 2nd edition. Wiley, USA 2005
   Google Scholar
• Martin R. Multiple sclerosis: closing in on an oral treatment. Nature 2010;464:360
   PubMed Web of Science ®Google Scholar
• David E, Tramontin T, Zemmel R. Pharmaceutical R&D: the road to positive returns. Nat Rev Drug Discov 2009;8:609-10
   PubMed Web of Science ®Google Scholar
• Overington JP, Al-Lazikani B, Hopkins AL. How many drug targets are there? Nat Rev Drug Discov 2006;5:993-6
   PubMed Web of Science ®Google Scholar
• Egan WJ, Walters WP, Murcko MA. Guiding molecules towards drug-likeness. Curr Opin Drug Discov Dev 2002;5:540-9
   PubMed Web of Science ®Google Scholar
• Lipinski C, Hopkins A. Navigating chemical space for biology and medicine. Nature 2004;432:855-61
   PubMed Web of Science ®Google Scholar
• Chen T, editors. A practical guide to assay development and high-throughput screening in drug discovery, CRC Press, USA 2009
   Google Scholar
• Bleicher KH, Bohm HJ, Muller K, Alanine AI. Hit and lead generation: beyond high-throughput screening. Nat Rev Drug Discov 2003;2:369-78
   PubMed Web of Science ®Google Scholar
• Paul SM, Mytelka DS, Dunwiddie CT, How to improve R&D productivity: the pharmaceutical industry's grand challenge. Nat Rev Drug Discov 2010;9:203-14
   PubMed Web of Science ®Google Scholar
• Gul S. Lab Overview of the gene-to-Lead phase in drug discovery. Eur Pharm Rev Digit 2009;6:3-6
   Google Scholar
• Available from: http://www.cerep.fr/cerep/users/pages/catalog/profiles/catalog.asp
   Google Scholar
• Eglen RM. High throughput screening, high content screening, primary and stem cells. Drug Discov World 2009;1:25-31
   Google Scholar
• Auld DS, Thorne N, Nguyen D-T, Inglese J. A specific mechanism for nonspecific activation in reporter-gene assays. ACS Chem Biol 2008;3:463-70
   PubMed Web of Science ®Google Scholar
• Dodgson K, Gedge L, Murray DC, Coldwell M. 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
   PubMed Web of Science ®Google Scholar
• Roddy TP, Horvath CR, Stout SJ, Mass spectrometric techniques for label-free high-throughput screening in drug discovery. Anal Chem 2007;79:8207-13
   PubMed Web of Science ®Google Scholar
• Gribbon P, Sewing A. Fluorescence readouts in HTS: no gain without pain? Drug Discov Today 2003;8:1035-43
   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;53:37-51
   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;50:2385-90
   PubMed Web of Science ®Google Scholar
• Lavis LD, Raines RT. Bright ideas for chemical biology. ACS Chem Biol 2008;3:142-55
   PubMed Web of Science ®Google Scholar
• Zaman MA, Oparil S, Calhoun DA. Drugs targeting the rennin-angiotensin-aldosterone system. Nat Rev Drug Discov 2002;1:621-36
   PubMed Web of Science ®Google Scholar
• la Porte CJ. Saquinavir, the pioneer antiretroviral protease inhibitor. Expert Opin Drug Metab Toxicol 2009;5:1313-22
   PubMed Web of Science ®Google Scholar
• Deacon CF, Ahren B, Holst JJ. Inhibitors of dipeptidyl peptidase IV: a novel approach for the prevention and treatment of type 2 diabetes? Exp Opin Investig Drugs 2004;13:1091-102
   PubMed Web of Science ®Google Scholar
• Augeri DJ, Robl JA, Betebenner DA, Discovery and preclinical profile of Saxagliptin (BMS-477118): a highly potent, long-acting, orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes. J Med Chem 2005;48:5025-37
   PubMed Web of Science ®Google Scholar
• Abbenante G, Fairlie DP. Protease inhibitors in the clinic. Med Chem 2005;1:71-104
   PubMed Web of Science ®Google Scholar
• Brocklehurst K, Gul S, Pickersgill RW. In: Hughes AB, editor, Substrate recognition in amino acids, peptides and proteins in organic chemistry. Volume 2. Wiley-VCH, Germany; 2009. p. 473-504
   Google Scholar
• Hsu MF, Kuo CJ, Chang KT, Mechanism of the maturation process of SARS-CoV 3CL protease. J Biol Chem 2005;280:31257-66
   PubMed Web of Science ®Google Scholar
• Knight CG. Fluorimetric assays of proteolytic enzymes. Methods Enzymol 1995;248:18-34
   PubMed Web of Science ®Google Scholar
• Schechter I, Berger A. On the active site of proteases. 3. Mapping the active site of papain: specific peptide inhibitors of papain. Biochem Biophys Res Commun 1968;32:898-902
   PubMed Web of Science ®Google Scholar
• Berger A, Schechter I. Mapping the active site of papain with the aid of peptide substrates and inhibitors. Philos Trans R Soc Lond B Biol Sci 1970;257:249-64
   PubMed Web of Science ®Google Scholar
• Schechter I, Berger A. On the size of the active site of proteinases. I. Papain. Biochem Biophys Res Commun 1967;27:157-62
   PubMed Web of Science ®Google Scholar
• Betzel C, Pal GP, Saenger W. Three-dimensional structure of proteinase K at 0.15-nm resolution. Eur J Biochem 1988;178:155-71
   PubMedGoogle Scholar
• Robertus JD, Alden RA, Birktoft JJ, An x-ray crystallographic study of the binding of peptide chloromethyl ketone inhibitors to subtilisin BPN. Biochemistry 1972;11:2439-49
   PubMed Web of Science ®Google Scholar
• Poulos TL, Alden RA, Freer ST, Polypeptide halomethyl ketones bind to serine proteases as analogs of the tetrahedral intermediate. X-ray crystallographic comparison of lysine- and phenylalanine-polypeptide chloromethyl ketone-inhibited subtilisin. J Biol Chem 1976;251:1097-103
   PubMed Web of Science ®Google Scholar
• Kowlessur D, Thomas EW, Topham CM, Dependence of the P2-S2 stereochemical selectivity of papain on the nature of the catalytic-site chemistry. Quantification of selectivity in the catalysed hydrolysis of the enantiomeric N-acetylphenylalanylglycine 4-nitroanilides. Biochem J 1990;266:653-60
   PubMed Web of Science ®Google Scholar
• Juric V, Chen CC, Lau LF. Fas-mediated apoptosis is regulated by the extracellular matrix protein CCN1 (CYR61) in vitro and in vivo. Mol Cell Biol 2009;29:3266-79
   PubMed Web of Science ®Google Scholar
• Lottenberg R, Christensen U, Jackson CM, Coleman PL. Assay of coagulation proteases using peptide chromogenic and fluorogenic substrates. Methods Enzymol 1981;80:341-61
   PubMed Web of Science ®Google Scholar
• Thomas DA, Francis P, Smith C, A broad-spectrum fluorescence-based peptide library for the rapid identification of protease substrates. Proteomics 2006;6:2112-20
   PubMed Web of Science ®Google Scholar
• Neefjes J, Dantuma NP. Fluorescent probes for proteolysis: tools for drug discovery. Nat Rev Drug Discov 2004;3:58-69
   PubMed Web of Science ®Google Scholar
• Harris JL, Backes BJ, Leonetti F, Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries. Proc Natl Acad Sci USA 2000;97:7754-9
   PubMed Web of Science ®Google Scholar
• Seidah NG, Mayer G, Zaid A, The activation and physiological functions of the proprotein convertases. Int J Biochem Cell Biol 2008;40:1111-25
   PubMed Web of Science ®Google Scholar
• Weir MR. Renin inhibitors: novel agents for renoprotection or a better angiotensin receptor blocker for blood pressure lowering? Curr Opin Nephrol Hypertens 2007;16:416-21
   PubMed Web of Science ®Google Scholar
• Abassi Z, Winaver J, Feuerstein GZ. The biochemical pharmacology of renin inhibitors: implications for translational medicine in hypertension, diabetic nephropathy and heart failure: expectations and reality. Biochem Pharmacol 2009;78:933-40
   PubMed Web of Science ®Google Scholar
• Kovac S, Shulkes A, Baldwin GS. Peptide processing and biology in human disease. Curr Opin Endocrinol Diabetes Obes 2009;16:79-85
   PubMed Web of Science ®Google Scholar
• Rholam M, Fahy C. Processing of peptide and hormone precursors at the dibasic cleavage sites. Cell Mol Life Sci 2009;66:2075-91
   PubMed Web of Science ®Google Scholar
• Geoghegan KF, Hoth LR, Varghese AH, Binding to the low-density lipoprotein receptor accelerates futile catalytic cycling in PCSK9 and raises the equilibrium level of intramolecular acylenzyme. Biochemistry 2009;48:2941-9
   PubMed Web of Science ®Google Scholar
• Naureckiene S, Ma L, Sreekumar K, Functional characterization of Narc 1, a novel proteinase related to proteinase K. Arch Biochem Biophys 2003;420:55-67
   PubMed Web of Science ®Google Scholar
• Duff CJ, Scott MJ, Kirby IT, Antibody-mediated disruption of the interaction between PCSK9 and the low-density lipoprotein receptor. Biochem J 2009;419:577-84
   PubMed Web of Science ®Google Scholar
• Cunningham D, Danley DE, Geoghegan KF, Structural and biophysical studies of PCSK9 and its mutants linked to familial hypercholesterolemia. Nat Struct Mol Biol 2007;14:413-9
   PubMed Web of Science ®Google Scholar
• Bottomley MJ, Cirillo A, Orsatti L, Structural and biochemical characterization of the wild type PCSK9-EGF(AB) complex and natural familial hypercholesterolemia mutants. J Biol Chem 2009;284:1313-23
   PubMed Web of Science ®Google Scholar
• Sauve AA, Schramm VL. SIR2: the biochemical mechanism of NAD+-dependent protein deacetylation and ADP-ribosyl enzyme intermediates. Curr Med Chem 2004;11:807-26
   PubMed Web of Science ®Google Scholar
• Smith BC, Hallows WC, Denu JM. Mechanisms and molecular probes of sirtuins. Chem Biol 2008;15:1002-13
   PubMed Web of Science ®Google Scholar
• Howitz KT, Bitterman KJ, Cohen HY, Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan. Nature 2003;425:191-6
   PubMed Web of Science ®Google Scholar
• Metoyer CF, Pruitt K. The role of sirtuin proteins in obesity. Pathophysiology 2008;15:103-8
   PubMedGoogle Scholar
• Milne JC, Lambert PD, Schenk S, Small molecule activators of SIRT1 as therapeutics for the treatment of type 2 diabetes. Nature 2007;450:712-6
   PubMed Web of Science ®Google Scholar
• Pacholec M, Bleasdale JE, Chrunyk B, SRT1720, SRT2183, SRT1460, and resveratrol are not direct activators of SIRT1. J Biol Chem 2010;285:8340-51
   PubMed Web of Science ®Google Scholar
• Beher D, Wu J, Cumine S, Resveratrol is not a direct activator of SIRT1 enzyme activity. Chem Biol Drug Des 2009;74:619-24
   PubMed Web of Science ®Google Scholar
• Haigis MC, Sinclair DA. Mammalian sirtuins: biological insights and disease relevance. Annu Rev Pathol 2010;5:253-95
   PubMed Web of Science ®Google Scholar
• Blume-Jensen P, Hunter T. Oncogenic kinase signalling. Nature 2001;411:355-65
   PubMed Web of Science ®Google Scholar
• Zhang J Adrian FJ, Jahnke W, Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors. Nature 2010;463:501-6
   PubMed Web of Science ®Google Scholar
• Smith DS, Eremin SA. Fluorescence polarization immunoassays and related methods for simple, high-throughput screening of small molecules. Anal Bioanal Chem 2008;391:1499-507
   PubMed Web of Science ®Google Scholar
• Degorce F, Card A, Soh S, HTRF: a technology tailored for drug discovery – a review of theoretical aspects and recent applications. Curr Chem Genomics 2009;28:22-32
   Google Scholar
• Lathia US, Ornatsky O, Baranov V, Nitz M. Development of inductively coupled plasma-mass spectrometry-based protease assays. Anal Biochem 2010;398:93-8
   PubMed Web of Science ®Google Scholar
• Meng QC, Oparil S. Purification and assay methods for angiotensin-converting enzyme. J Chromatogr A 1996;743:105-22
   PubMed Web of Science ®Google Scholar
• Todd MJ, Gomez J. Enzyme kinetics determined using calorimetry: a general assay for enzyme activity? Anal Biochem 2001;296:179-87
   PubMed Web of Science ®Google Scholar