Translation of new technologies: From basic research to drug discovery and development

Current Drug Discovery Technologies

Volumn 5, Issue 3, 2008, Pages 250-262

  Bhogal, Nirmala ^a   Balls, Michael ^a  

^a RUSSELL AND BURCH HOUSE   (United Kingdom)

Author keywords

Biomarkers; Culture models; In silico; Nanotechnology; Systems biology

Indexed keywords

ALOSETRON; ASTEMIZOLE; BENOXAPROFEN; BROMFENAC; CERIVASTATIN; CHLORMEZANONE; CISAPRIDE; CYCLOOXYGENASE 2 INHIBITOR; DEXFENFLURAMINE; ENCAID; ENCAINIDE; ETRETINATE; FANOLESOMAB TC 99M; FENFLURAMINE; FENTANYL; FLOSEQUINAN; GREPAFLOXACIN; HYDROMORPHONE; LEVACETYLMETHADOL; METHAQUALONE; MIBEFRADIL; MORPHINE; NARCOTIC AGENT; NATALIZUMAB; NOMIFENSINE MALEATE; OMINIFLOX; PAREST; PEMOLINE MAGNESIUM; PERGOLIDE MESILATE; PHENACETIN; PHENFORMIN; PHENOLPHTHALEIN; ROFECOXIB; SELDANE D; SUPROFEN; TEMAFLOXACIN; TERFENADINE; TIENILIC ACID; TROGLITAZONE; UNCLASSIFIED DRUG; UNINDEXED DRUG; VALDECOXIB; ZIMELDINE; ZOMEPIRAC;

ANAPHYLAXIS; ARTICLE; BIOMEDICAL ENGINEERING; BIRTH DEFECT; CLINICAL TRIAL; DRUG APPROVAL; DRUG DEPENDENCE; DRUG DESIGN; DRUG DEVELOPMENT; DRUG EFFICACY; DRUG FATALITY; DRUG INDUSTRY; DRUG OVERDOSE; DRUG RESEARCH; DRUG SAFETY; DRUG SCREENING; DRUG SURVEILLANCE PROGRAM; DRUG SYNTHESIS; FLANK PAIN; GENE TECHNOLOGY; GENOMICS; GUILLAIN BARRE SYNDROME; HEART ARRHYTHMIA; HEMOLYTIC ANEMIA; HIGH THROUGHPUT SCREENING; HUMAN; KIDNEY INJURY; LACTIC ACIDOSIS; LIVER TOXICITY; MEDICAL TECHNOLOGY; METHODOLOGY; MICROFLUIDICS; NANOTECHNOLOGY; NONHUMAN; PHARMACOKINETICS; PRIORITY JOURNAL; TECHNIQUE; TORSADE DES POINTES; TOXIC EPIDERMAL NECROLYSIS; TOXICITY TESTING; UNSPECIFIED SIDE EFFECT; VALVULAR HEART DISEASE;

ANIMALS; BIOTECHNOLOGY; DRUG DISCOVERY; DRUG EVALUATION, PRECLINICAL; GENOMICS; HUMANS; NANOTECHNOLOGY; RESEARCH DESIGN; SYSTEMS BIOLOGY; TECHNOLOGY, PHARMACEUTICAL;

EID: 51349112312     PISSN: 15701638     EISSN: None     Source Type: Journal    
DOI: 10.2174/157016308785739839     Document Type: Article

References (95)

1. Thomas J., Moore A.B., Michael R., Cohen R., Curt D., Furberg, M.D.: Serious Adverse Drug Events Reported to the Food and Drug Administration, 1998-2005. Arch. Intern. Med. 167, 1752-1759, (2007).
2. Kola I., Landis J.: Can the pharmaceutical industry reduce attrìtìon rates? Nat. Rev. Drug Discov. 3, 711-715, (2004).
3. Overington J.P., Al-Lazikani B., Hopkins A.L.: How many drug targets are there? Nat. Rev. Drug Discov. 5, 993-996, (2006).
4. Lawrence S.: Biotech drug market steadily expands. Nat. Biotechnol. 23, 1466, (2005).
5. Anons.: Tufts CSDD Impact Report Sept/Oct 2005. Available from: csdd.tufts.edu/InfoServices/ImpactReportPDFs/impactReportSeptemberOctober2005. pdf (accessed 1/10/07).
6. Fung M. Evaluation of the characteristics of safety withdrawal of prescription drugs from worldwide pharmaceutical markets - 1960 to 1999. Drug Information J. 35, 293-317, (2001).
7. Han J., Zhu Z., Hsu C.C., Finley W.H.: Selection of antisense oligonucleotides on the basis of genomic frequency of the target sequence. Antisense Res. Dev. 4, 53-65, (1994).
8. Serruto D., Rappuoli R.: Post-genomic vaccine development. FEBS Lett. 580, 2985-2992, Sp. Iss. SI, (2006).
9. Tapolczay D., Chorlton A., McCubbin Q.: Probing drug structure improves the odds. Drug Discov. Devel. 30-33, 2000.
10. Schreiber S.L.: Target-oriented and diversity-oriented organic synthesis in drug discovery. Science 287, 1964-1969, (2000).
11. Villar H.O., Yan J., Hansen M.R.: Using NMR for ligand discovery and optimization. Curr. Opin. Chem. Biol. 8, 387-391, (2004).
12. Swayze E.E., Jefferson E.A., Sannes-Lowery K.A., Blyn L.B., Risen L.M., Arakawa S., Osgood S.A., Hofstadler S.A., et al.: SAR by MS: A ligand-based technique for drug lead discovery against RNA targets. J. Med. Chem. 45, 3816-3819, (2002).
13. Hartshorn M.J., Murray C.W., Cleasby A., Frederickson M., Tickle I.J., Jhoti H.: Fragment-based lead discovery using X-Ray crystallography. J. Med. Chem. 48, 403-413, (2005).
14. Lofas S.: Optimizing the hit-to-lead process using SPR analysis. Assay Drug Dev. Technol. 4, 407-415, (2004).
15. Rees D.C., Congreve M., Murray C.W., Carr R.: Fragment-based lead discovery. Nat. Rev. Drug Discov. 3, 660-672, (2004).
16. Scheuermann J., Dumelin C.E., Melkko S., Neri D.: DNA-encoded chemical libraries. J. Biotechnol. 126, 568-581, (2006).
17. Rees D.C.: Nonpeptide ligands for neuropeptide receptors. Annu. Rep. Med. Chem. 28, 59-68, (1993).
18. Galan-Caridad J., Harel S., Arenzana T., Hou Z., Doetsch F., Mirny L., Reizis B.: Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell 129, 345-357, (2007).
19. Mascini M., Bagni G., Di Pietro M.L., Ravera M., Baracco S., Osella D.: Electrochemical biosensor evaluation of the interaction between DNA and metallo-drugs. Biometals 19,409-418, (2006).
20. Vogelstein B., Kinzler K.W.: Cancer genes and the pathways they control. Nat. Med. 10, 789-799, (2004).
21. Craig R., Li S.L.: Function and molecular mechanism of tumor-targeted peptides for delivering therapeutic genes and chemical drugs. Mini-Reviews Med. Chem. 6, 757-764, (2006).
22. Hoogenboom H.R.: Selecting and screening recombinant antibody libraries. Nat. Biotechnol. 23, 1105-1116, (2005).
23. Fraser A.G., Kamath R.S., Zipperlen P., Martinez-Campos M., Sohrmann M., Ahringer J.: Functional genomic analysis of C. elegans chromosome 1 by systematic TNA interference. Nature 408, 325-330, (2002).
24. Mousses S., Caplen N.J., Cornelison R., Weaver D., Basik M., Hautaniemi S., Elkahloun A.G., Lotufo R.A. et al.: RNAi Microarray Analysis in Cultured Mammalian Cells. Genome Res. 13, 2341-2347, (2003).
25. Borrebaeck CAK. Wingren C: High-throughput proteomics using antibody microarrays: an update. Expert Rev. Mol. Diag. 7, 673-686, (2007).
26. Langezaal I., Hoffmann S., Hartung T., Coecke S.: Evaluation and prevalidation of an immunotoxicity toxicity test based on human whole-blood cytokine release. Altern. Lab. Anim. 30, 581-595, (2002).
27. Bollard M.E., Murray A.J., Clarke K., Nicholson J.K., Griffin J.L.: A study of metabolic compartmentation in the rat heart and cardiac mitochondria using high resolution magic angle spinning 1H NMR spectroscopy. FEBS Lett. 553, 73-78, (2003).
28. Bollard M.E., Stanley E.G., Lindon J.C., Nicholson J.K., Holmes E.: NMR-based metabonomic approaches for evaluating physiological influences on biofluid composition. NMR Biomed. 18, 143-162, (2005).
29. Wishart D.S., Tzur D., Knox C., Eisner R., Guo A.C., Young N., Cheng D., Jewell K., et al: , HMDB: the Human Metabolome Database. Nucleic Acids Res. 35, D521-D526, (2007).
30. Acute-Tox project: www.acutetox.org (accessed 1/10/07).
31. Metacyte initiative: http://metacyt.indiana.edu/ (accessed 1/10/07).
32. Kriete A.: Bridging biological scales by state-space analysis and modeling using molecular, tissue cytometric and physiological data. Cytometry 69A, 113-116, (2006).
33. 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).
34. Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., et al.: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627, (2000).
35. Piganeau N., Schauer U.E., Schroeder R.: A yeast RNA-hybrid system for the detection ofRNA-RNA interactions in vivo. RNA 12, 177-184, (2006).
36. Giot L., Bader J.S., Brouwer C., Chaudhuri A., Kuang B., Li Y., Hao Y.L., Ooi C.E., et al.: A protein interaction map of drosophila melangaster. Science 302, 1727-1736, (2003).
37. Gong S., Yoon G., Jang I., Bolser D., Dafas P., Schroeder M., Choi H., Cho Y., et al.: PSIbase: a database of Protein Structural Interactome map (PSI-MAP). Bioiuformatics 21, 2541-2543, (2005).
38. Salwinski L., Miller C.S., Smith A.J., Pettit F.K., Bowie J.U., Eisenberg D.: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 32, D449-D451, (2000).
39. Bader G.D., Betel D., Hogue C.W.: BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31, 48-50, (2003).
40. Zanzoni A., Montecchi-Palazzi L., Quondam M., Ausiello G., Helmer-Citterich M., Cesareni G.:http://www.ingentaconnect.com/content/els/ 00145793/2002/00000513/00000001/art03293 - aff_l MINT: a Molecular INTeraction database. FEBS Lett. 513, 135-140, (2002).
41. GeneQuest: http://bioinformatics.org/textknowledge/search.php (accessed 1/10/07).
42. Human Interactome Map: http://www.himap.org/main/index.jsp (accessed 1/10/07).
43. Cytoscape: http://www.cytoscape.org/ (accessed 1/10/07).
44. Aoki-Kinoshita K.F.: Overview of KEGG applications to omics-related research. J. Pestic. Sci. 31, 296-299, (2006).
45. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., et al.: Minimum infonnation about a microarray experiment (MIAME)- towards standards for microarray data. Nat. Genet. 29, 365-371, (2001).
46. NIH road map: http://nihroadmap.nih.gov/initiatives.asp (accessed 1/10/07).
47. De Moor B.: Generalizations of the singular value and the QR decomposition. Signal Processing 25, 135-146, (1991).
48. Arigon A.M., Perrière G., Gouy M.: HoSeql: automated homologous sequence identification in gene family databases. Bio informatics 22, 1786-1787, (2006).
49. Pubchem.: http://pubchem.ncbi.nlm.nih.gov/ (accessed 1/10/07).
50. The Binding DB.: http://www.bindingdb.org/bind/index.jsp (accessed 1/10/07).
51. Therapeutic Target database: http://xin.cz3.nus.edu.sg/group/cjttd/ttd. asp (accessed 1/10/07).
52. Villoutreix B.O., Renault N., Lagorce D., Sperandio O., Montes M., Miteva M.A.: Free resources to assist structure-based virtual ligand screening experiments. Curr. Prot. Pep. Sci. 8, 381-411, (2007).
53. Drugs.com: http://www.drugs.com/alpha/al.html (accessed 1/10/07).
54. Human membrane transporter database: http://lab.digibench.net/ transporter/ (accessed 1/10/07).
55. Transport DB: http://www.membranetransport.org/ (accessed 1/10/07).
56. ADME DB: http://www.fqs.pl/life_science/adme_db (accessed 1/10/07).
57. Leadscope: http://www.leadscope.com/fdadb_cat.php (accessed 1/10/07).
58. Drug-induced toxicity related proteins database: http://bioinf.xmu.edu. cn/databases/ADR/index.html (accessed 1/10/07).
59. Fang N., Lee H., Sun C., Zhang X.: Sub-diffraction-limited optical imaging with a silver superlens. Science 308, 534-537, (2005).
60. Berquand A., Mingeot-Leclercq M.P., Dufrene Y.F.: Real-time imaging of drug-membrane interactions by atomic force microscopy. Biochim. Biophys. Acta Biomemb. 1664, 198-205, (2004).
61. Pereira R.D., da Silva M.I.N., Cotta M.A.: Adhesion forces measured between a calcium blocker drug and its receptor in living cells using atomic force microscope. FEBS Lett. 552, 155-159, (2003).
62. Edwardson J.M., Henderson R.M.: Atomic force microscopy and drug discovery. Drug Discov. Today 9, 64-71, (2004).
63. Patterson G.H., Lippincott-Schwartz J.: A photoactivatable GFP for selective photolabeling of proteins and cells. Science 297, 1873-1877, (2002).
64. Matz M.V., Fradkov A.F., Labas Y.A., Savitsky A.P., Zaraisky A.G., Markelov M.L., Lukyanov S.A.: Fluorescent proteins from nonbiolumines-cent Anthozoa species. Nat. Biotechnol. 17, 969-973, (1999).
65. Leatherdale C.A., Woo W.K., Mikulec F.V., Bawendi M.G.: On the Absorption Cross Section of CdSe Nanocrystal Quantum Dots. Phys. Chem. B 106, 7619-7622 (2002).
66. So M.K., Xu C., Loening A.M., Gambhir S.S., Rao J.: Self-Illuminating Quantum Dot Conjugates for in vivo imaging. Nat. Biotechnol. 24, 339-343, (2006).
67. Janasek D., Franzke J., Manz A.: Scaling and the design of miniaturized chemical-analysis systems. Nature 442, 374-380, (2006).
68. Viravaidya K., Sin A., Shuler M.L.: Development of a microscale cell culture analog to probe naphthalene toxicity. Biotechnol. Prog. 20, 316-323, (2004).
69. Khetani S.R., Bhatia S.N.: Engineering tissues for in vitro applications. Curr. Opin. Biotechnol. 17, 524-531, (2006).
70. Tabuchi M., Ueda M., Kaji N., Yamasaki Y., Nagasaki Y., Yoshikawa K., Kataoka K., Baba Y.: Nanospheres for DNA separation chips. Nat. Biotechnol. 22, 337-340, (2004).
71. Zou Z.W., Kai J.H., Rust M.J., Han J., Ahn C.H.: Functionalized nano interdigitated electrodes arrays on polymer with integrated microfluidics for direct bio-affinity sensing using impedimetric measurement. Sensors and actuators A- Physical. 136, 518-526, Sp. Iss. SI, (2007).
72. Reichl S., Döhring S., Bednarz, J., Müller-Goymann, C.C.: Human cornea construct HCC-an alternative for in vitro permeation studies? A comparison with human donor corneas. Eur. J. Pharm. Biopharm. 60, 305-308, (2005).
73. Roguet R.: Reconstructed human epidermis equivalents. Characterisation and Applications in cutaneous pharmacotoxicity. Skin Pharmacol. Appl. Skin Physiol. 15(suppl 1), 1-3, (2002).
74. Atterwill C.K., Purcell W.M.: In Neurotoxicology in vitro; VW Penreath Ed., Taylor and Francis, London, pp. 213-238, (1999).
75. Lengauer T., Lemmen C., Rarey M., Zimmermann M.: Novel technologies for virtual screening. Drug Discov. Today 9, 27-34, (2004).
76. Dror O., Shulman-Peleg A., Nussinobv R., Wolfson H.J.: Predicting molecular interactions in silico: 1. A guide to pharmcophore identification and its applications to drug design. Curr. Med. Chem. 11. 71-90, (2004).
77. Martin Y.C.: 3D database searching in drug design. J. Med. Chem. 35, 2145-2154, (1992).
78. Zinke S., Gerner I., Schlede E.: Evaluation of a rule base for identifying contact allergens by using a regulatory database: Comparison of data on chemicals notified in the European Union with "structured alerts" used in the DEREK expert system. Altera. Lab Anim. 30, 285-298, (2002).
79. Matthews E.J., Contrera J.F.: A new highly specific method for predicting the carcinogenic potential of phannaceuticals in rodents using enhanced MCASE QSAR-ES software. Regul. Toxicol. Pharmacol. 28, 242, (1998).
80. Health Safety Laboratories, UK: Megan software: http://www.hsl.gov.uk/ capabilities/pbpk-jip.htm (accessed 1/10/07).
81. US EPA biokinetic modeling: http://cfpub.epa.gov/ncea/cfm/recordisplay. cfm?deid=135427 (accessed 1/10/07).
82. Liu B.-F., Zhang G., Luo Q.: Micro-separation towards systems biology. J. Chromatography A 1106, 19-28, (2005).
83. McLean M.A., Tarn C.Y.J., Baratta M.T., Holliman C.L., Ings R.M., Galluppi G.R.: Accelerating drug development: Methodology to support first-in-man pharmacokinetic studies by the use of drug candidate microdosing. Drag Dev. Res. 68. 14-22, (2007).
84. Daly A.K.: Nomenclature for human CYP2D6 alleles. Pharmacogenetics 6, 193-201, (1996).
85. Anglicheau D., Legendre C., Beaune P., Thervet E.: Cytochrome P450 3A polymorphisms and immunosuppressive drugs: an update. Pharmacogenomics 8, 835-849, (2007).
86. Paoluzzi L., Singh A.S., Price D.K., Danesi R., Mathijssen R.H.J., Verweij J., Figg W.D., Sparreboom A.: Influence of genetic variants in UGTIAI and UGT1A9 on the in vivo glucuronidation of SN 38. J. Clin. Pharm. 44, 854-860, (2004).
87. Niemi M.: Role of OATP transporters in the disposition of drugs. Pharmacogenomics 8, 787-802, (2007).
88. Mank-Seymour A.R., Richmond J.L., Wood L.S., Reynolds J.M., Fan Y.T., Warnes G.R., Milos P.M., Thompson J.F.: Association of torsades de pointes with novel and known single nucleotide polymorphisms in long QT syndrome genes. Am. Heart J. 152 ,1116-1122, (2006).
89. Pharmacogenetics and Pharmacogenomics Knowledge Base: http://www.pharmgkb.org/index.jsp (accessed 1/10/07).
90. Anons: Guidance for Industry: Pharmacogenomic Data Submissions. U.S. Department of Health and Human Services, Food and Drug Administration, CDER, CBER, CDRH (2003). http://www.fda.gov/cder/guidance/5900dft.pdf (accessed 1/10/07).
91. Belli F., Testori A., Rivoltini L., Maio M., Andreola G., Sertoli M.R., Gallino G., Piris A., et al.: Vaccination of metastatic melanoma patients with autologous tumor-derived heat shock protein gp96-peptide complexes: clinical and immunologic findings. J. Clin. Oncol. 20, 4169-4180, (2002).
92. Exner D.V., Dries D.L., Domanski M.J., Cohn J.N.: Lesser response to angiotensin-converting-enzyme inhibitor therapy in black as compared with white patients with left ventricular dysfunction. N. Engl. J. Med. 344, 1351-1357, (2001).
93. Sobels F.H.: Evaluating the mutagenic potential of chemicals: the minimal battery and extrapolation problems. Archiv. Toxicol 46, 21-30, (1980).
94. Sutter T.R.: Molecular and cellular approaches to extrapolation for risk assessment. Environmental Health Perspectives 103, 386-389, (1995).
95. Predictomics: http://www.predictomics.com/principal.htm (accessed 1/10/07).