Genomics and the discovery of new drug targets

Current Opinion in Chemical Biology

Volumn 3, Issue 1, 1999, Pages 71-76

  Jones, David A ^a   Fitzpatrick, Frank A ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; COMPLEMENTARY DNA; MESSENGER RNA; PROTEIN; RIBOZYME;

DATA BASE; DRUG TARGETING; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE FUNCTION; GENE TECHNOLOGY; GENOME; MOLECULAR BIOLOGY; MULTIGENE FAMILY; REVIEW; SEQUENCE HOMOLOGY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

EID: 0033023420     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(99)80013-1     Document Type: Article

References (44)

1. Dykes CW Genes, disease and medicine. Br J Clin Pharmacol. 42:1996;683-695.
2. Zweiger G, Scott RW From expressed sequence tags to 'epigenomics': an understanding of disease processes. Curr Opin Biotechnol. 8:1997;684-687.
3. Wiley SR, Schooley K, Smolak PJ, Din WS, Huang CP, Nicholl JK, Sutherland GR, Smith TD, Rauch C, Smith CAet al. Identification and characterization of a new member of the TNF family that induces apoptosis. Immunity. 3:1995;673-682.
4. Hahne M, Kataoka T, Schroter M, Hofmann K, Irmler M, Bodmer JL, Schneider P, Bornand T, Holler N, French LEet al. APRIL, a new ligand of the tumor necrosis factor family, stimulates tumor cell growth. J Exp Med. 188:1998;1185-1190.
5. Tan KB, Harrop J, Reddy M, Young P, Terrett J, Emery J, Moore G, Truneh A Characterization of a novel TNF-like ligand and recently described TNF ligand and TNF receptor superfamily genes and their constitutive and inducible expression in hematopoietic and non-hematopoietic cells. Gene. 204:1997;35-46.
6. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ Basic local alignment search tool. J Mol Biol. 215:1990;403-410.
7. Chinnaiyan AM, O'Rourke K, Yu GL, Lyons RH, Garg M, Duan DR, Xing L, Gentz R, Ni J, Dixit VM Signal transduction by DR3, a death domain-containing receptor related to TNFR-1 and CD95. Science. 274:1996;990-992.
8. Pan G, O'Rourke K, Chinnaiyan AM, Gentz R, Ebner R, Ni J, Dixit VM The receptor for the cytotoxic ligand TRAIL. Science. 276:1997;111-113. This work identified a potential receptor for tumor necrosis factor related apoptosis-inducing ligand by searching expressed sequence tag databases for genes in the tumor necrosis factor receptor family.
9. Kwon BS, Tan KB, Ni J, Oh KO, Lee ZH, Kim KK, Kim YJ, Wang S, Gentz R, Yu GLet al. A newly identified member of the tumor necrosis factor receptor superfamily with a wide tissue distribution and involvement in lymphocyte activation. J Biol Chem. 272:1997;14272-14276.
10. Pan G, Ni J, Wei YF, Yu G, Gentz R, Dixit VM An antagonist decoy receptor and a death domain-containing receptor for TRAIL. Science. 277:1997;815-818. This paper identified two new additional receptors for TNF-related apoptosis-inducing ligand (TRAIL). One of these retained an active ligand binding site, but lacked the intracellular death domain. The authors postulated that this apoptosis-inactive receptor is a TRAIL antagonist.
11. ••], these authors conclude that tumor necrosis factor related apoptosis-inducing ligand induced apoptosis was regulated by a receptors lacking functional intracellar signaling capabilities.
12. Drake FH, Dodds RA, James IE, Connor JR, Debouck C, Richardson S, Lee-Rykaczewski E, Coleman L, Rieman D, Barthlow Ret al. Cathepsin K, but not cathepsins B, L, or S, is abundantly expressed in human osteoclasts. J Biol Chem. 271:1996;12511-12516.
13. Votta BJ, Levy MA, Badger A, Bradbeer J, Dodds RA, James IE, Thompson S, Bossard MJ, Carr T, Connor JRet al. Peptide aldehyde inhibitors of cathepsin K inhibit bone resorption both in vitro and in vivo. J Bone Miner Res. 12:1997;1396-1406.
14. McGrath ME, Klaus JL, Barnes MG, Bromme D Crystal structure of human cathepsin K complexed with a potent inhibitor. Nat Struct Biol. 4:1997;105-109.
15. Zhao B, Janson CA, Amegadzie BY, D'Alessio K, Griffin C, Hanning CR, Jones C, Kurdyla J, McQueney M, Qiu Xet al. Crystal structure of human osteoclast cathepsin K complex with E-64. Nat Struct Biol. 4:1997;109-111.
16. Gelb BD, Shi GP, Chapman HA, Desnick RJ Pycnodysostosis, a lysosomal disease caused by cathepsin K deficiency. Science. 273:1996;1236-1238.
17. Weinstein JN, Myers TG, O'Connor PM, Friend SH, Fornace AJ Jr., Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NLet al. An information-intensive approach to the molecular pharmacology of cancer. Science. 275:1997;343-349. This paper employees the strategy that molecular markers can help define chemotherapeutic mechanisms and suggest molecular target pathways. It shows how data-rich approaches can use complete spectrums of information to impact a target disease.
18. Anderson NL, Anderson NG Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis. 19:1998;1853-1861.
19. Li G, Waltham M, Anderson NL, Unsworth E, Treston A, Weinstein JN Rapid mass spectrometric identification of proteins from two-dimensional polyacrylamide gels after in gel proteolytic digestion. Electrophoresis. 18:1997;391-402.
20. Scheler C, Lamer S, Pan Z, Li XP, Salnikow J, Jungblut P Peptide mass fingerprint sequence coverage from differently stained proteins on two-dimensional electrophoresis patterns by matrix assisted laser desorption/ionization-mass spectrometry (MALDI-MS). Electrophoresis. 19:1998;918-927.
21. Myers TG, Anderson NL, Waltham M, Li G, Buolamwini JK, Scudiero DA, Paull KD, Sausville EA, Weinstein JN A protein expression database for the molecular pharmacology of cancer. Electrophoresis. 18:1997;647-653. The authors create a comprehesive protein expression database and illustrate the use of comprehensive protein profiling to correlate drug action with potential molecular targets.
22. Anderson NL, Esquer-Blasco R, Richardson F, Foxworthy P, Eacho P The effects of peroxisome proliferators on protein abundances in mouse liver. Toxicol Appl Pharmacol. 137:1996;75-89.
23. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16:1998;301-306.
24. Schena M, Shalon D, Davis RW, Brown PO Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270:1995;467-470.
25. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 14:1996;457-460.
26. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA. 93:1996;10614-10619.
27. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 14:1996;1675-1680.
28. Shalon D, Smith SJ, Brown PO A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6:1996;639-645.
29. Wodicka L, Dong H, Mittmann M, Ho MH, Lockhart DJ Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol. 15:1997;1359-1367.
30. Heller RA, Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci USA. 94:1997;2150-2155. This paper describes one of the first uses of microarray profiling to identify candidate inflammatory genes. Similar strategies are being applied in many disease states.
31. DeRisi JL, Iyer VR, Brown PO Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 278:1997;680-686.
32. Gray NS, Wodicka L, Thunnissen AM, Norman TC, Kwon S, Espinoza FH, Morgan DO, Barnes G, LeClerc S, Meijer Let al. Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Science. 281:1998;533-538. The authors combine structure-based drug design, combinitorial chemistry and oligonucleotide arrays in the assessment of new kinase inhibitors. This is a good preview of how drug discovery strategies evolve to incorporate genomics information.
33. Christoffersen RE, Marr JJ Ribozymes as human therapeutic agents. J Med Chem. 38:1995;2023-20237.
34. Nadeau JH, Dunn PJ Genomic strategies for defining and dissecting developmental and physiological pathways. Curr Opin Genet Dev. 8:1998;311-315.
35. Zhao JJ, Lemke G Rules for ribozymes. Mol Cell Neurosci. 11:1998;92-97. This paper outlines basic and advanced strategies for ribozymes generation.
36. Jankowsky E, Schwenzer B Oligonucleotide facilitators enable a hammerhead ribozyme to cleave long RNA substrates with multiple-turnover activity. Eur J Biochem. 254:1998;129-134.
37. Juhl H, Downing SG, Wellstein A, Czubayko F HER-2/neu is rate-limiting for ovarian cancer growth. Conditional depletion of HER-2/neu by ribozyme targeting. J Biol Chem. 272:1997;29482-29486. This paper Illustrates the use of ribozymes to identify rate-limiting steps in disease.
38. Vaugh JP, Iglehart JD, Demirdji S, Davis P, Babiss LE, Carruthers MH, Mark JR Antisense DNA downregulation of the ERBB2 oncogene measured by a flow cytometric assay. Proc Natl Acad Sci USA. 92:1995;8338-8342.
39. Fan Z, Mendelsohn J Therapeutic application of anti-growth factor receptor antibodies. Curr Opin Oncol. 10:1998;67-73.
40. Rondon IJ, Marasco WA Intracellular antibodies (intrabodies) for gene therapy of infectious diseases. Annu Rev Microbiol. 51:1997;257-283.
41. Wright M, Grim J, Deshane J, Kim M, Strong TV, Siegal GP, Curiel DT An intracellular anti-erbB-2 single-chain antibody is specifically cytotoxic to human breast carcinoma cells overexpressing erbB-2. Gene Ther. 4:1997;317-322. This paper illustrates the potential of intrabodies for validating molecular targets.
42. Grim J, Deshane J, Siegal GP, Alvarez RD, DiFiore P, Curiel DT The level of erbB2 expression predicts sensitivity to the cytotoxic effects of an intracellular anti-erbB2 sFv. J Mol Med. 76:1998;451-458.
43. Piche A, Grim J, Rancourt C, Gomez-Navarro J, Reed JC, Curiel DT Modulation of Bcl-2 protein levels by an intracellular anti-Bcl-2 single-chain antibody increases drug-induced cytotoxicity in the breast cancer cell line MCF-7. Cancer Res. 58:1998;2134-2140. This work targeted an intracellular regulator, Bcl-2, with neutralized intrabodies to increase drug sensitivity.
44. Grim J, Deshane J, Siegal GP, Alvarez RD, Di Fiore P, Curiel DT The level of erbB2 expression predicts sensitivity to the cytotoxic effects of an intracellular anti-erbB2 sFv. J Mol Med. 76:1998;451-458.