메뉴 건너뛰기




Volumn 13, Issue 5, 2013, Pages 778-785

Metabolically re-modeling the drug pipeline

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT; CHORISMIC ACID; HALOFANTRINE; TORCETRAPIB;

EID: 84892974755     PISSN: 14714892     EISSN: 14714973     Source Type: Journal    
DOI: 10.1016/j.coph.2013.05.006     Document Type: Review
Times cited : (28)

References (69)
  • 1
    • 78651297594 scopus 로고    scopus 로고
    • The problems with today's pharmaceutical business - An outsider's view
    • Kessel M: The problems with today's pharmaceutical business - an outsider's view. Nat Biotechnol 2011, 29: 27-33.
    • (2011) Nat Biotechnol , vol.29 , pp. 27-33
    • Kessel, M.1
  • 3
    • 73449101512 scopus 로고    scopus 로고
    • Lessons from 60 years of pharmaceutical innovation
    • Munos B: Lessons from 60 years of pharmaceutical innovation. Nat Rev Drug Discov 2009, 8: 959-968.
    • (2009) Nat Rev Drug Discov , vol.8 , pp. 959-968
    • Munos, B.1
  • 4
    • 33750579770 scopus 로고    scopus 로고
    • Drug discovery in jeopardy
    • DOI 10.1172/JCI29999
    • Cuatrecasas P: Drug discovery in jeopardy. J Clin Invest 2006, 116: 2837-2842. (Pubitemid 44684465)
    • (2006) Journal of Clinical Investigation , vol.116 , Issue.11 , pp. 2837-2842
    • Cuatrecasas, P.1
  • 6
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: The next paradigm in drug discovery
    • Hopkins AL: Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 2008, 4: 682-690.
    • (2008) Nat Chem Biol , vol.4 , pp. 682-690
    • Hopkins, A.L.1
  • 7
    • 84866128045 scopus 로고    scopus 로고
    • Shrinking the metabolic solution space using experimental datasets
    • Reed JL: Shrinking the metabolic solution space using experimental datasets. PLoS Comput Biol 2012, 8:e1002662.
    • (2012) PLoS Comput Biol , vol.8
    • Reed, J.L.1
  • 12
    • 84878949529 scopus 로고    scopus 로고
    • Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells
    • Sahoo S, Thiele I: Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells. Hum Mol Genet 2013.
    • (2013) Hum Mol Genet
    • Sahoo, S.1    Thiele, I.2
  • 14
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism
    • Jerby L, Shlomi T, Ruppin E: Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol 2010, 6.
    • (2010) Mol Syst Biol , pp. 6
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 16
    • 84863662483 scopus 로고    scopus 로고
    • Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
    • Agren R, Bordel S, Mardinoglu A, Pornputtapong N, Nookaew I, Nielsen J: Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput Biol 2012, 8:e1002518.
    • (2012) PLoS Comput Biol , vol.8
    • Agren, R.1    Bordel, S.2    Mardinoglu, A.3    Pornputtapong, N.4    Nookaew, I.5    Nielsen, J.6
  • 17
    • 84870933131 scopus 로고    scopus 로고
    • Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
    • Wang Y, Eddy J, Price N: Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol 2012, 6:153.
    • (2012) BMC Syst Biol , vol.6 , pp. 153
    • Wang, Y.1    Eddy, J.2    Price, N.3
  • 20
    • 78049445175 scopus 로고    scopus 로고
    • Drug off-target effects predicted using structural analysis in the context of a metabolic network model
    • Chang RL, Xie L, Xie L, Bourne PE, Palsson B: Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol 2010, 6:e1000938.
    • (2010) PLoS Comput Biol , vol.6
    • Chang, R.L.1    Xie, L.2    Xie, L.3    Bourne, P.E.4    Palsson, B.5
  • 23
    • 45749090110 scopus 로고    scopus 로고
    • An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
    • Rantanen A, Rousu J, Jouhten P, Zamboni N, Maaheimo H, Ukkonen E: An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments. BMC Bioinformatics 2008, 9:266.
    • (2008) BMC Bioinformatics , vol.9 , pp. 266
    • Rantanen, A.1    Rousu, J.2    Jouhten, P.3    Zamboni, N.4    Maaheimo, H.5    Ukkonen, E.6
  • 25
    • 25844495901 scopus 로고    scopus 로고
    • Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
    • DOI 10.1101/gr.3832305
    • Fong SS, Joyce AR, Palsson BO: Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res 2005, 15: 1365-1372. (Pubitemid 41400902)
    • (2005) Genome Research , vol.15 , Issue.10 , pp. 1365-1372
    • Fong, S.S.1    Joyce, A.R.2    Palsson, B.O.3
  • 26
    • 0038293216 scopus 로고    scopus 로고
    • Optimization-based framework for inferring and testing hypothesized metabolic objective functions
    • DOI 10.1002/bit.10617
    • Burgard A, Maranas C: Optimization-based framework for inferring and testing hypothesized metabolic objective functions. Biotechnol Bioeng 2003, 82: 670-677. (Pubitemid 36576230)
    • (2003) Biotechnology and Bioengineering , vol.82 , Issue.6 , pp. 670-677
    • Burgard, A.P.1    Maranas, C.D.2
  • 27
    • 84866525910 scopus 로고    scopus 로고
    • Comparative multi-goal tradeoffs in systems engineering of microbial metabolism
    • Byrne D, Dumitriu A, Segre D: Comparative multi-goal tradeoffs in systems engineering of microbial metabolism. BMC Syst Biol 2012, 6:127.
    • (2012) BMC Syst Biol , vol.6 , pp. 127
    • Byrne, D.1    Dumitriu, A.2    Segre, D.3
  • 28
    • 84855929956 scopus 로고    scopus 로고
    • Using the reconstructed genome-scale human metabolic network to study physiology and pathology
    • Bordbar A, Palsson BO: Using the reconstructed genome-scale human metabolic network to study physiology and pathology. J Intern Med 2012, 271: 131-141.
    • (2012) J Intern Med , vol.271 , pp. 131-141
    • Bordbar, A.1    Palsson, B.O.2
  • 29
    • 84857999389 scopus 로고    scopus 로고
    • A metabolic network approach for the identification and prioritization of antimicrobial drug targets
    • Chavali AK, D'Auria KM, Hewlett EL, Pearson RD, Papin JA: A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends Microbiol 2012, 20: 113-123.
    • (2012) Trends Microbiol , vol.20 , pp. 113-123
    • Chavali, A.K.1    D'Auria, K.M.2    Hewlett, E.L.3    Pearson, R.D.4    Papin, J.A.5
  • 30
  • 32
    • 79956140184 scopus 로고    scopus 로고
    • Getting pharmaceutical R&D back on target
    • Bunnage ME: Getting pharmaceutical R&D back on target. Nat Chem Biol 2011, 7: 335-339.
    • (2011) Nat Chem Biol , vol.7 , pp. 335-339
    • Bunnage, M.E.1
  • 34
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • DOI 10.1016/S0167-7799(98)01290-6, PII S0167779998012906
    • Schuster S, Dandekar T, Fell DA: Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol 1999, 17: 53-60. (Pubitemid 29332898)
    • (1999) Trends in Biotechnology , vol.17 , Issue.2 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 35
    • 35348934254 scopus 로고    scopus 로고
    • Genome-scale reconstruction of metabolic network in bacillus subtilis based on high-throughput phenotyping and gene essentiality data
    • Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R: Genome-scale reconstruction of metabolic network in bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 2007, 282: 28791-28797.
    • (2007) J Biol Chem , vol.282 , pp. 28791-28797
    • Oh, Y.K.1    Palsson, B.O.2    Park, S.M.3    Schilling, C.H.4    Mahadevan, R.5
  • 37
    • 84860222515 scopus 로고    scopus 로고
    • Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease
    • Chavali AK, Blazier AS, Tlaxca JL, Jensen PA, Pearson RD, Papin JA: Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease. BMC Syst Biol 2012, 6:27.
    • (2012) BMC Syst Biol , vol.6 , pp. 27
    • Chavali, A.K.1    Blazier, A.S.2    Tlaxca, J.L.3    Jensen, P.A.4    Pearson, R.D.5    Papin, J.A.6
  • 39
    • 77955334006 scopus 로고    scopus 로고
    • Identification of novel bacterial histidine biosynthesis inhibitors using docking, ensemble rescoring, and whole-cell assays
    • Henriksen ST, Liu J, Estiu G, Oltvai ZN, Wiest O: Identification of novel bacterial histidine biosynthesis inhibitors using docking, ensemble rescoring, and whole-cell assays. Bioorg Med Chem 2010, 18: 5148-5156.
    • (2010) Bioorg Med Chem , vol.18 , pp. 5148-5156
    • Henriksen, S.T.1    Liu, J.2    Estiu, G.3    Oltvai, Z.N.4    Wiest, O.5
  • 40
    • 2442636351 scopus 로고    scopus 로고
    • Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery
    • DOI 10.1101/gr.2050304
    • Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB: Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res 2004, 14: 917-924. (Pubitemid 38660510)
    • (2004) Genome Research , vol.14 , Issue.5 , pp. 917-924
    • Yeh, I.1    Hanekamp, T.2    Tsoka, S.3    Karp, P.D.4    Altman, R.B.5
  • 41
    • 33747890136 scopus 로고    scopus 로고
    • Observing local and global properties of metabolic pathways: 'Load points' and 'choke points' in the metabolic networks
    • DOI 10.1093/bioinformatics/btl181
    • Rahman SA, Schomburg D: Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks. Bioinformatics 2006, 22: 1767-1774. (Pubitemid 44288340)
    • (2006) Bioinformatics , vol.22 , Issue.14 , pp. 1767-1774
    • Rahman, S.A.1    Schomburg, D.2
  • 42
    • 75749144228 scopus 로고    scopus 로고
    • Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE
    • Kim HU, Kim TY, Lee SY: Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE. Mol Biosyst 2010, 6: 339-348.
    • (2010) Mol Biosyst , vol.6 , pp. 339-348
    • Kim, H.U.1    Kim, T.Y.2    Lee, S.Y.3
  • 44
    • 77049123018 scopus 로고    scopus 로고
    • Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks
    • Kim TY, Kim HU, Lee SY: Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks. Metab Eng 2010, 12: 105-111.
    • (2010) Metab Eng , vol.12 , pp. 105-111
    • Kim, T.Y.1    Kim, H.U.2    Lee, S.Y.3
  • 48
    • 73149122136 scopus 로고    scopus 로고
    • Applications of genome-scale metabolic reconstructions
    • Oberhardt MA, Palsson BO, Papin JA: Applications of genome-scale metabolic reconstructions. Mol Syst Biol 2009, 5:320.
    • (2009) Mol Syst Biol , vol.5 , pp. 320
    • Oberhardt, M.A.1    Palsson, B.O.2    Papin, J.A.3
  • 49
    • 84873587763 scopus 로고    scopus 로고
    • Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production
    • Brynildsen MP, Winkler JA, Spina CS, MacDonald IC, Collins JJ: Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production. Nat Biotechnol 2013, 31: 160-165.
    • (2013) Nat Biotechnol , vol.31 , pp. 160-165
    • Brynildsen, M.P.1    Winkler, J.A.2    Spina, C.S.3    Macdonald, I.C.4    Collins, J.J.5
  • 51
    • 77958537509 scopus 로고    scopus 로고
    • Insight into human alveolar macrophage and M. Tuberculosis interactions via metabolic reconstructions
    • Bordbar A, Lewis NE, Schellenberger J, Palsson BO, Jamshidi N: Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Biol 2010, 6.
    • (2010) Mol Syst Biol , pp. 6
    • Bordbar, A.1    Lewis, N.E.2    Schellenberger, J.3    Palsson, B.O.4    Jamshidi, N.5
  • 52
    • 84865425410 scopus 로고    scopus 로고
    • Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer
    • Facchetti G, Zampieri M, Altafini C: Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer. BMC Syst Biol 2012, 6:115.
    • (2012) BMC Syst Biol , vol.6 , pp. 115
    • Facchetti, G.1    Zampieri, M.2    Altafini, C.3
  • 53
    • 77957837882 scopus 로고    scopus 로고
    • Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection
    • Oberhardt MA, Goldberg JB, Hogardt M, Papin JA: Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection. J Bacteriol 2010, 192: 5534-5548.
    • (2010) J Bacteriol , vol.192 , pp. 5534-5548
    • Oberhardt, M.A.1    Goldberg, J.B.2    Hogardt, M.3    Papin, J.A.4
  • 55
    • 77956456621 scopus 로고    scopus 로고
    • Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis
    • Huthmacher C, Hoppe A, Bulik S, Holzhutter HG: Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC Syst Biol 2010, 4:120.
    • (2010) BMC Syst Biol , vol.4 , pp. 120
    • Huthmacher, C.1    Hoppe, A.2    Bulik, S.3    Holzhutter, H.G.4
  • 56
    • 84866893169 scopus 로고    scopus 로고
    • Integrative genomic analysis identifies isoleucine and CodY as regulators of Listeria monocytogenes virulence
    • Lobel L, Sigal N, Borovok I, Ruppin E, Herskovits AA: Integrative genomic analysis identifies isoleucine and CodY as regulators of Listeria monocytogenes virulence. PLoS Genet 2012, 8:e1002887.
    • (2012) PLoS Genet , vol.8
    • Lobel, L.1    Sigal, N.2    Borovok, I.3    Ruppin, E.4    Herskovits, A.A.5
  • 59
    • 78049255973 scopus 로고    scopus 로고
    • Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
    • Chandrasekaran S, Price ND: Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2010, 107: 17845-17850.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 17845-17850
    • Chandrasekaran, S.1    Price, N.D.2
  • 61
    • 34748925493 scopus 로고    scopus 로고
    • Prediction of human pharmacokinetics using physiologically based modeling: A retrospective analysis of 26 clinically tested drugs
    • DOI 10.1124/dmd.107.015644
    • De Buck SS, Sinha VK, Fenu LA, Nijsen MJ, Mackie CE, Gilissen RA: Prediction of human pharmacokinetics using physiologically based modeling: a retrospective analysis of 26 clinically tested drugs. Drug Metab Dispos 2007, 35: 1766-1780. (Pubitemid 47481568)
    • (2007) Drug Metabolism and Disposition , vol.35 , Issue.10 , pp. 1766-1780
    • De Buck, S.S.1    Sinha, V.K.2    Fenu, L.A.3    Nijsen, M.J.4    Mackie, C.E.5    Gilissen, R.A.H.J.6
  • 64
    • 84865358026 scopus 로고    scopus 로고
    • The design of long-term effective uranium bioremediation strategy using a community metabolic model
    • Zhuang K, Ma E, Lovley DR, Mahadevan R: The design of long-term effective uranium bioremediation strategy using a community metabolic model. Biotechnol Bioeng 2012, 109: 2475-2483.
    • (2012) Biotechnol Bioeng , vol.109 , pp. 2475-2483
    • Zhuang, K.1    Ma, E.2    Lovley, D.R.3    Mahadevan, R.4
  • 65
    • 44949252217 scopus 로고    scopus 로고
    • Strategies for systems-level metabolic engineering
    • DOI 10.1002/biot.200700240
    • Kim TY, Sohn SB, Kim HU, Lee SY: Strategies for systems-level metabolic engineering. Biotechnol J 2008, 3: 612-623. (Pubitemid 351803371)
    • (2008) Biotechnology Journal , vol.3 , Issue.5 , pp. 612-623
    • Kim, T.Y.1    Sohn, S.B.2    Kim, H.U.3    Lee, S.Y.4
  • 66
    • 77957556494 scopus 로고    scopus 로고
    • Predicting enzyme targets for cancer drugs by profiling human metabolic reactions in NCI- 60 cell lines
    • Li L, Zhou X, Ching WK, Wang P: Predicting enzyme targets for cancer drugs by profiling human metabolic reactions in NCI- 60 cell lines. BMC Bioinformatics 2010, 11:501.
    • (2010) BMC Bioinformatics , vol.11 , pp. 501
    • Li, L.1    Zhou, X.2    Ching, W.K.3    Wang, P.4
  • 69
    • 79953303482 scopus 로고    scopus 로고
    • Metabolic modeling of endosymbiont genome reduction on a temporal scale
    • Yizhak K, Tuller T, Papp B, Ruppin E: Metabolic modeling of endosymbiont genome reduction on a temporal scale. Mol Syst Biol 2011, 7.
    • (2011) Mol Syst Biol , pp. 7
    • Yizhak, K.1    Tuller, T.2    Papp, B.3    Ruppin, E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.