The end game of chemical genetics: Target identification

Future Medicinal Chemistry

Volumn 1, Issue 4, 2009, Pages 727-736

  Kasper, Amanda C ^a   Baker, Joseph B ^a   Kim, Hyoungsu ^a   Hong, Jiyong ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; INDOMETACIN; NATURAL PRODUCT; TACROLIMUS;

AFFINITY CHROMATOGRAPHY; ARTICLE; CHEMICAL GENETICS; DNA MICROARRAY; DRUG PURIFICATION; DRUG SCREENING; DRUG TARGETING; GENE OVEREXPRESSION; HUMAN; MOLECULAR LIBRARY; PHENOTYPE; PRIORITY JOURNAL; RNA INTERFERENCE;

CHROMATOGRAPHY, AFFINITY; GENE EXPRESSION PROFILING; HAPLOINSUFFICIENCY; MICROARRAY ANALYSIS; PROTEINS; RNA INTERFERENCE; SIGNAL TRANSDUCTION; SMALL MOLECULE LIBRARIES;

EID: 77953469804     PISSN: 17568919     EISSN: None     Source Type: Journal    
DOI: 10.4155/fmc.09.52     Document Type: Article

References (50)

1. Schreiber SL. The small-molecule approach to biology. Chem. Eng. News. 81(9), 51-61 (2003).
2. Burdine L, Kodadek T. Target identification in chemical genetics. The (often) missing link. Chem. Biol. 11(5), 593-597 (2004)
3. Ding S, Schultz PG. A role for chemistry in stem cell biology. Nat. Biotechnol. 22(7), 833-840 (2004).
4. Stockwell BR. Exploring biology with small organic molecules. Nature 432, 846-854 (2004).
5. Boshoff HI, Dowd CS. Systems biological approaches in infectious diseases. In: Prog. Drug. Res. (Volume 64). Bischoff HI, Barry III CE (Eds). Birkhauser, Basel, Switzerland, 49-78 (2007).
6. Bauer A, Stockwell BR. Neurobiological applications of small molecule screening. Chem. Rev. 108(5), 1774-1786 (2008).
7. Lehar J, Stockwell BR, Giaever G, Nislow C. Combination chemical genetics. Nat. Chem. Biol. 4(11), 674-681 (2008).
8. Russell K, Michne WF. The value of chemical genetics in drug discovery. In: Methods Principles Med. Chem. (Volume 22). Kubinyi H, Müller G, Wiley VCH (Eds). Verlag GmbH & Co. KGaA, Weinheim, Germany, 69-96 (2004).
9. Thorpe DS. Forward and reverse chemical genetics using SPOS-based combinatorial chemistry. Comb. Chem. High Throughput Screen. 6(7), 623-647 (2003).
10. Low W-K, Dang Y, Schneider-Poetsch T et al. Isolation and identification of eukaryotic initiation factor 4A as a molecular target for the marine natural product pateamine A. Meth. Enzymol. 431, 303-324 (2007).
11. Cuatrecasas P. Protein purification by affinity chromatography: derivatizations of agarose and polyacrylamide beads. J. Biol. Chem. 245(12), 3059-3065 (1970).
12. George O, Bryant BK, Chinnasamy R, Corona C, Arterburn JB, Shuster CB. Bisphenol A directly targets tubulin to disrupt spindle organization in embryonic and somatic cells. ACS Chem. Biol. 3(3), 167-179 (2008).
13. Oda Y, Owa T, Sato T et al. Quantitative chemical proteomics for identifying candidate drug targets. Anal. Chem. 75(9), 2159-2165 (2003).
14. Yamamoto K, Yamazaki A, Takeuchi M, Tanaka A. A versatile method of identifying specific binding proteins on affinity resins. Anal. Biochem. 352(1), 15-23 (2006).
15. Livnah O, Bayer EA, Wilchek M, Sussman JL. Three-dimensional structures of avidin and the avidin-biotin complex. Proc. Natl Acad. Sci. USA 90(11), 5076-5080 (1993).
16. Sato S, Kwon Y, Kamisuki S et al. Polyproline-rod approach to isolating protein targets of bioactive small molecules. Isolation of a new target of indomethacin. J. Am. Chem. Soc. 129(4), 873-880 (2007).
17. Leuenroth SJ, Okuhara D, Shotwell JD et al. Triptolide is a traditional Chinese medicinederived inhibitor of polycystic kidney disease. Proc. Natl Acad. Sci. USA 104(11), 4389-4394 (2007).
18. Giaever G, Shoemaker DD, Jones TW et al. Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat. Genet. 21(3), 278-283 (1999).
19. Baetz K, McHardy L, Gable K et al. Yeast genome-wide drug-induced haploinsufficiency screen to determine drug mode of action. Proc. Natl Acad. Sci. USA 101(13), 4525-4530 (2004).
20. Bays N, Margolis, J. Yeast as a budding technology in target validation. Drug Discov. Today 1(2), 157-162 (2004).
21. Lain S, Hollick JJ, Campbell J et al. Discovery, in vivo activity, and mechanism of action of a small-molecule inhibitor p53 activator. Cancer Cell 13(5), 454-463 (2008).
22. Lum PY, Armour CD, Stepaniants SB et al. Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 116(1), 121-137 (2004).
23. Bjornsti M-A. Cancer therapeutics in yeast. Cancer Cell 2(4), 267-273 (2002).
24. Luesch H, Wu TYH, Ren P, Gray NS, Schultz PG. A genome-wide overexpression screen in yeast for small-molecule target identification. Chem. Biol. 12, 55-63 (2005).
25. Luesch H, Chanda SK, Raya RM et al. A functional genomics approach to the mode of action of apratoxin A. Nat. Chem. Biol. 2(3), 158-167 (2006).
26. Hardiman G. Microarray platforms - comparisons and contrasts. Pharmacogenomics 5(5), 487-502 (2004).
27. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235), 467-470 (1995).
28. Lockhart DJ, Dong H, Byrne MC et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14(13), 1675-1680 (1996).
29. Churchill GA. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 32(Suppl. 4), 490-495 (2002).
30. Quackenbush J. Microarray data normalization and transformation. Nat. Genet. 32(Suppl. 4) 496-501 (2002).
31. Irizarry RA, Hobbs B, Collin F et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4(2), 249-264 (2003).
32. Marton MJ, DeRisi JL, Bennett HA et al. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med. 4(11), 1293-1301 (1998).
33. MacBeath G, Koehler AN, Schreiber SL. Printing small molecules as microarrays and detecting protein-ligand interactions en masse. J. Am. Chem. Soc. 121(34), 7967-7968 (1999).
34. Kuruvilla FG, Shamji AF, Sternson SM, Hergenrother PJ, Schreiber SL. Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 416, 653-657 (2002).
35. Barnes-Seeman D, Park SB, Koehler AN, Schreiber SL. Expanding the functional group compatibility of small-molecule microarrays: discovery of novel calmodulin ligands. Angew. Chem. Int. Ed. Engl. 42(21), 2376-2379 (2003).
36. Winssinger N, Ficarro S, Shultz PG, Harris JL. Profiling protein function with small molecule microarrays. Proc. Natl Acad. Sci. USA 99(17), 11139-11144 (2002).
37. Kanoh N, Kumashiro S, Simizu S et al. Immobilization of natural products on glass slides by using a photoaffinity reaction and the detection of protein-small-molecule interactions. Angew. Chem. Int. Ed. Engl. 42(45), 5584-5587 (2003).
38. Li S, Bowerman D, Marthandan N et al. Photolithographic synthesis of peptoids. J. Am. Chem. Soc. 126(13), 4088-4089 (2004).
39. Salisbury CM, Maly DJ, Ellman JA. Peptide microarrays for the determination of protease substrate specificity. J. Am. Chem. Soc. 124(50), 14868-14870 (2002).
40. Hall DA, Ptacek J, Snyder M. Protein microarray technology. Mech. Ageing Dev. 128(1), 161-167 (2007).
41. Tully SE, Rawat M, Hsieh-Wilson LC. Discovery of a TNF-αantagonist using chondroitin sulfate microarrays. J. Am. Chem. Soc. 128(24), 7740-7741 (2006).
42. Castanotto D, Rossi JJ. The promises and pitfalls of RNA-interference- based therapeutics. Nature 457, 426-433 (2009).
43. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811 (1998).
44. McCaffrey AP, Meuse L, Pham TT, Conklin DS, Hannon GJ, Kay MA. RNA interference in adult mice. Nature 418, 38-39 (2002).
45. Hannon GJ. RNA interference. Nature 418, 244-251 (2002).
46. Eggert US, Kiger AA, Richter C et al. Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol. 2(12), 2135-2143 (2004).
47. Eggert US, Field CM, Mitchison TJ. Small molecules in an RNAi world. Mol. Biosyst. 2(2), 93-96 (2006).
48. Vanhaesebroeck B, Rohn JL, Waterfield MD. Gene targeting: attention to detail. Cell 118(3), 274-276 (2004).
49. Hall J. Unravelling the general properties of siRNAs: strength in numbers and lessons from the past. Nat. Rev. Genet. 5, 552-557 (2004).
50. Sledz CA, Holko M, de Veer MJ, Silverman RH, Williams BRG. Activation of the interferon system by short-interfering RNAs. Nat. Cell Biol. 5(9), 834-839 (2003).