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Review

Chemogenomics approaches to novel target discovery

Pages 411-419 | Published online: 09 Jan 2014

References

  • Schreiber SL. Chemical genetics resulting from a passion for synthetic organic chemistry. Bioorg. Med. Chem.6(8), 1127–1152 (1998).
  • Harris CJ, Stevens AP. Chemogenomics: structuring the drug discovery process to gene families. Drug Discov. Today11(19–20), 880–888 (2006).
  • Huang Y, Sadee W. Drug sensitivity and resistance genes in cancer chemotherapy: a chemogenomics approach. Drug Discov. Today8(8), 356–363 (2003).
  • Smukste I, Stockwell BR. Advances in chemical genetics. Annu. Rev. Genomics Hum. Genet.6, 261–286 (2005).
  • Mestres J. Computational chemogenomics approaches to systematic knowledge-based drug discovery. Curr. Opin Drug Discov. Devel.7(3), 304–313 (2004).
  • MDL Comprehensive Medicinal Chemistry (CMC-3D) Database: MDL Information Systems Inc., San Leandro, CA. Pergamon Press, NY, USA. 6 (1990).
  • World Drug Index. Derwent Information Ltd, London, UK.
  • Olah M, Bologa C, Oprea TI. An automated PLS search for biologically relevant QSAR descriptors. J. Comput. Aided Mol. Des.18(7–9), 437–449 (2004).
  • Strausberg RL, Schreiber SL. From knowing to controlling: a path from genomics to drugs using small molecule probes. Science300(5617), 294–295 (2003).
  • Weinstein JN, Myers TG, O’Connor PM et al. An information-intensive approach to the molecular pharmacology of cancer. Science275(5298), 343–349 (1997).
  • Roth BL, Kroeze WK, Patel S, Lopez E. The multiplicity of serotonin receptors: uselessly diverse molecules or an embarrassment of riches? Neuroscientist6, 252–262 (2000).
  • Bredel M, Jacoby E. Chemogenomics: an emerging strategy for rapid target and drug discovery. Nat. Rev. Genet.5(4), 262–275 (2004).
  • Paolini GV, Shapland RH, van Hoorn WP, Mason JS, Hopkins AL. Global mapping of pharmacological space. Nat. Biotechnol.24(7), 805–815 (2006).
  • Caron PR, Mullican MD, Mashal RD, Wilson KP, Su MS, Murcko MA. Chemogenomic approaches to drug discovery. Curr. Opin. Chem. Biol.5(4), 464–470 (2001).
  • Stockwell BR. Chemical genetics: ligand-based discovery of gene function. Nat. Rev. Genet.1(2), 116–125 (2000).
  • Stockwell BR. Frontiers in chemical genetics. Trends Biotechnol.18(11), 449–455 (2000).
  • Bishop AC, Buzko O, Shokat KM. Magic bullets for protein kinases. Trends Cell Biol.11(4), 167–172 (2001).
  • Jacoby E. Chemogenomics, Knowledge-Based Approaches to Drug Discovery. Imperial College Press, London, UK (2006).
  • Deveraux QL, Aza-Blanc P, Wagner KW, Bauerschlag D, Cooke MP, Hampton GM. Exposing oncogenic dependencies for cancer drug target discovery and validation using RNAi. Semin. Cancer Biol.13(4), 293–300 (2003).
  • Zaarur N, Gabai VL, Porco JA Jr, Calderwood S, Sherman MY. Targeting heat shock response to sensitize cancer cells to proteasome and Hsp90 inhibitors. Cancer Res.66(3), 1783–1791 (2006).
  • Kaelin WG. The concept of synthetic lethality in the context of anticancer therapy. Nat. Rev. Cancer5, 689–698 (2005).
  • Aza-Blanc P, Cooper CL, Wagner K, Batalov S, Deveraux QL, Cooke MP. Identification of modulators of TRAILHinduced apoptosis via RNAiHbased phenotypic screening. Mol. Cell12(3), 627–637 (2003).
  • Lackner MR, Kindt RM, Carroll PM et al. Chemical genetics identifies Rab geranylgeranyl transferase as an apoptotic target of farnesyl transferase inhibitors. Cancer Cell7, 325–336 (2005).
  • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature391(6669), 806–811 (1998).
  • Sachse C, Echeverri CJ. Oncology studies using siRNA libraries: the dawn of RNAi-based genomics. Oncogene23(51), 8384–9391 (2004).
  • Tiscornia G, Singer O, Ikawa M, Verma IM. A general method for gene knock-down in mice by using lentiviral vectors expressing small interfering RNA. Proc. Natl Acad. Sci. USA100(4), 1844–1848 (2003).
  • Alisky JM, Davidson BL. Towards therapy using RNA interference.Am. J. Pharmacogenomics4(1), 45–51 (2004).
  • Kim TK. Chemical genomics and medicinal systems biology: chemical control of genomic networks in human systems biology for innovative medicine. J. Biochem. Mol. Biol.37(1), 53–58 (2004).
  • Hartman JL, Garvik B, Hartwell L. Principles for the buffering of genetic variation. Science291(5506) 1001–1004 (2001).
  • Samani AA, Yakar S, Leroith D, Brodt P. The role of the IGF system in cancer growth and metastasis: overview and recent insights. Endocr. Rev.28(1), 20–47 (2007).
  • Ozanne BW, Spence HJ, McGarry LC, Hennigan RF. Invasion is a genetic program regulated by transcription factors. Curr. Opin Genet. Dev.16(1), 65–70 (2006).
  • Syed V, Zhang X, Lau KM, Cheng R, Mukherjee K, Ho SM. Profiling estrogen-regulated gene expression changes in normal and malignant human ovarian surface epithelial cells. Oncogene24(55), 8128–8143 (2005).
  • Marsh I. Easing the chemistry bottleneck: careers in high-throughput chemistry. Nat. Rev. Drug Discov.1(11), 925 (2002).
  • Zarraga IG, Schwarz ER. Coxibs and heart disease: what we have learned and what else we need to know. J. Am. Coll. Cardiol.49(1), 1–14 (2007).
  • Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat. Biotechnol.25(2), 197–206 (2007).
  • Mestres J, Martin-Couce L, Gregori-Puigjane E, Cases M, Boyer S. Ligand-based approach to in silico pharmacology: nuclear receptor profiling. J. Chem. Inf. Model.46(6), 2725–2736 (2006).
  • Cleves AE, Jain AN. Robust ligand-based modeling of the biological targets of known drugs. J. Med. Chem.49(10), 2921–2938 (2006).
  • MacKeigan JP, Murphy LO, Blenis J. Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance. Nat. Cell Biol.7(6), 591–600 (2005).
  • Bartz SR, Zhang Z, Burchard J et al. Small interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Mol. Cell. Biol.26(24), 9377–9386 (2006).
  • Jaeschke A, Karasarides M, Ventura JJ et al. JNK2 is a positive regulator of the c-Jun transcription factor. Mol. Cell23(6), 899–911 (2006).
  • Collins I, Workman P. New approaches to molecular cancer therapeutics. Nat. Chem. Biol.2(12), 689–700 (2006).
  • Wishart MJ, Denu JM, Williams JA, Dixon JE. A single mutation converts a novel phosphotyrosine binding domain into a dual-specificity phosphatase. J. Biol. Chem.270(45), 26782–26785 (1995).
  • Socinski MA. Cytotoxic chemotherapy in advanced non-small cell lung cancer: a review of standard treatment paradigms. Clin. Cancer Res.10(12 Pt 2), S4210–S4214 (2004).
  • Fridman JS, Lowe SW. Control of apoptosis by p53. Oncogene22(56), 9030–9040 (2003).
  • Yarden RI, Pardo-Reoyo S, Sgagias M, Cowan KH, Brody LC. BRCA1 regulates the G2/M checkpoint by activating Chk1 kinase upon DNA damage. Nat. Genet.30(3), 285–289 (2002).
  • Ewart-Toland A, Briassouli P, de Koning JP et al. Identification of Stk6/STK15 as a candidate low-penetrance tumor-susceptibility gene in mouse and human. Nat. Genet.34(4), 403–412 (2003).
  • Vogel C, Hager C, Bastians H. Mechanisms of mitotic cell death induced by chemotherapy-mediated G2 checkpoint abrogation. Cancer Res.67(1), 339–345 (2007).
  • Bishop AC, Buzko O, Shokat KM. Magic bullets for protein kinases. Trends Cell Biol.11(4), 167–172 (2001).
  • Bishop AC, Ubersax JA, Petsch DT et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature407(6802), 395–401 (2000).
  • Sabapathy K, Hochedlinger K, Nam SY, Bauer A, Karin M, Wagner EF. Distinct roles for JNK1 and JNK2 in regulating JNK activity and c-Jun-dependent cell proliferation. Mol. Cell15(5), 713–725 (2004).
  • Lin X, Ruan X, Anderson MG et al. siRNA-mediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Res.33(14), 4527–4535 (2005).
  • Kraynack BA, Baker BF. Small interfering RNAs containing full 2´-O-methylribonucleotide-modified sense strands display Argonaute2/eIF2C2-dependent activity. RNA12(1), 163–176 (2006).
  • Ross-Macdonald P. Forward in reverse: how reverse genetics complements chemical genetics. Pharmacogenomics6(4), 429–434 (2005).
  • Evanko D. Systems biology for beginners. Nat. Methods3(12), 964–965 (2006).
  • Gilbert D, Fuss H, Gu X et al. Computational methodologies for modelling, analysis and simulation of signalling networks. Brief Bioinform.7(4), 339–353 (2006).
  • Moffat J, Grueneberg DA, Yang X et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell124(6), 1283–1298 (2006).
  • Ngo VN, Davis RE, Lamy L et al. A loss-of-function RNA interference screen for molecular targets in cancer. Nature441(7089), 106–110 (2006).
  • Wu MT, Wu RH, Hung CF, Cheng TL, Tsai WH, Chang WT. Simple and efficient DNA vector-based RNAi systems in mammalian cells. Biochem. Biophys. Res. Commun.330(1), 53–59 (2005).
  • Deininger MW, Goldman JM, Lydon N, Melo JV. The tyrosine kinase inhibitor CGP57148B selectively inhibits the growth of BCR–ABL-positive cells. Blood90(9), 3691–3698 (1997).
  • Druker BJ, Sawyers CL, Kantarjian H et al. Activity of a specific inhibitor of the BCR–ABL tyrosine kinase in the blast crisis of chronic myeloid leukemia and acute lymphoblastic leukemia with the Philadelphia chromosome. N. Engl. J. Med.344(14), 1038–1042 (2001).

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