Systems biology tools for toxicology

Archives of Toxicology

Volumn 86, Issue 8, 2012, Pages 1251-1271

  Geenen, Suzanne ^a,b   Taylor, Peter Neal ^a   Snoep, Jacky L ^a,c,d   Wilson, Ian D ^b   Kenna, J Gerry ^b   Westerhoff, Hans V ^a,d,e  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b ASTRAZENECA   (United Kingdom)

^c STELLENBOSCH UNIVERSITY   (South Africa)

^d VU UNIVERSITY AMSTERDAM   (Netherlands)

^e UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

Biomarkers; Computational tools; Glutathione; Paracetamol toxicity; Systems biology; Toxicology

Indexed keywords

BIOLOGICAL MARKER; GLUTATHIONE; GLUTATHIONE SYNTHASE; METHIONINE; PARACETAMOL; PYROGLUTAMIC ACID; XENOBIOTIC AGENT;

CATABOLISM; COMPUTER MODEL; COMPUTER SIMULATION; DRUG DETOXIFICATION; DRUG EFFICACY; DRUG TOXICITY; ELEMENTARY MODE ANALYSIS; ENZYME ACTIVITY; FLUX BALANCE ANALYSIS; GENE MUTATION; GLUTATHIONE METABOLISM; HIERARCHICAL REGULATION ANALYSIS; HUMAN; INFORMATION PROCESSING; MATHEMATICAL MODEL; METABOLIC FLUX ANALYSIS; METABOLIC REGULATION; METABOLITE; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; REVIEW; RISK BENEFIT ANALYSIS; ROBUSTNESS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; STATISTICAL PARAMETERS; STEADY STATE; SYSTEMS BIOLOGY; TOXICOKINETICS; TOXICOLOGY;

ANIMALS; COMPUTER SIMULATION; GENOTYPE; GLUTATHIONE; HUMANS; LIVER; METABOLIC DETOXICATION, DRUG; METABOLOMICS; MODELS, BIOLOGICAL; PHARMACOGENETICS; PHARMACOKINETICS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK ASSESSMENT; RISK FACTORS; SYSTEMS BIOLOGY; TOXICOLOGY;

ANIMALIA;

EID: 84866034431     PISSN: 03405761     EISSN: 14320738     Source Type: Journal    
DOI: 10.1007/s00204-012-0857-8     Document Type: Review

References (75)

1. Aderem A (2005) Systems biology: its practice and challenges. Cell 121(4):511-513 (Pubitemid 40720005)
2. Alberghina L, Westerhoff H (2005) Systems biology: definitions and perspectives p. 273
3. Albert R, Jeong H, Barabasi A-L (2000) Error and attack tolerance of complex networks. Nature 406(6794):378-382 (Pubitemid 30625551)
4. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427(6977):839-843 (Pubitemid 38297745)
5. Alves R, Antunes F, Salvador A (2006) Tools for kinetic modeling of biochemical networks. Nat Biotechnol 24(6):667-672 (Pubitemid 43884436)
6. Andersen ME (1995) Development of physiologically based pharmacokinetic and physiologically based pharmacodymamic models for applications in toxicology and risk assessment. Toxicol Lett 79(1-3):35-44
7. Arai K, Lee K, Berthiaume F, Tompkins RG, Yarmush ML (2001) Intrahepatic amino acid and glucose metabolism in a D-galactosamine- induced rat liver failure model. Hepatology 34(2):360-371. doi:10.1053/jhep.2001.26515 (Pubitemid 32702349)
8. Bakker BM, Walsh MC, ter Kuile BH, Mensonides FIC, Michels PAM, Opperdoes FR, Westerhoff HV (1999) Contribution of glucose transport to the control of the glycolytic flux in Trypanosoma brucei. Proc Nat Acad Sci USA 96(18):10098-10103 (Pubitemid 29422518)
9. Bakker BM, Mensonides FIC, Teusink B, van Hoek P, Michels PAM, Westerhoff HV (2000) Compartmentation protects trypanosomes from the dangerous design of glycolysis. Proc Nat Acad Sci USA 97(5):2087-2092 (Pubitemid 30134026)
10. Bakker BM, Assmus HE, Bruggeman F, Haanstra JR, Klipp E, Westerhoff H (2002) Network-based selectivity of antiparasitic inhibitors. Mol Biol Rep 29(1):1-5. doi:10.1023/a:1020397513646 (Pubitemid 35021849)
11. Barabasi A, Oltvai Z (2004) Network biology: understanding the cell's functional organisation. Nat Rev 43(2):101-113 (Pubitemid 38160277)
12. Barkai N, Leibler S (1997) Robustness in simple biochemical networks. Nature 387(6636):913-917 (Pubitemid 27289593)
13. Chen Y-D, Westerhoff HV (1986) How do inhibitors and modifiers of individual enzymes affect steady-state fluxes and concentrations in metabolic systems? Math Modell 7(9-12):1173-1180
14. Chung W-H, Hung S-I, Hong H-S, Hsih M-S, Yang L-C, Ho H-C, Wu J-Y, Chen Y-T (2004) Medical genetics: a marker for Stevens- Johnson syndrome. Nature 428(6982):486
15. Ciardiello F, Caputo R, Bianco R, Damiano V, Pomatico G, De Placido S, Bianco AR, Tortora G (2000) Antitumor effect and potentiation of cytotoxic drugs activity in human cancer cells by ZD-1839 (Iressa), an epidermal growth factor receptor-selective tyrosine kinase inhibitor. Clin Cancer Res 6(5):2053-2063 (Pubitemid 30305105)
16. Cornish-Bowden A (ed) (1995) Fundamentals of enzyme kinetics. Portland press Ltd, London
17. Croal BL, Glen ACA, Kelly CJG, Logan RW (1998) Transient 5-oxoprolinuria (pyroglutamic aciduria) with systemic acidosis in an adult receiving antibiotic therapy. Clin Chem 44(2):336-340 (Pubitemid 28087733)
18. Curien G, Bastien O, Robert-Genthon M, Cornish-Bowden A, Cardenas ML, Dumas R (2009) Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters. Mol Syst Biol 5:271
19. Daniels BC, Chen Y-J, Sethna JP, Gutenkunst RN, Myers CR (2008) Sloppiness, robustness, and evolvability in systems biology. Curr Opin Biotechnol 19(4):389-395
20. Daran-Lapujade P, Rossell S, van Gulik WM, Luttik MAH, de Groot MJL, Slijper M, Heck AJR, Daran J-M, de Winde JH, Westerhoff HV, Pronk JT, Bakker BM (2007) The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc Nat Acad Sci 104(40):15753-15758. doi:10.1073/pnas.0707476104 (Pubitemid 350035372)
21. Eunen KV, Bouwman J, Alexander L, Hans VW, Barbara MB (2009) Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker's yeast. FEBS J 276(19):5521-5536
22. Geenen S, du Preez FB, Reed M, Frederik Nijhout H, Gerry Kenna J, Wilson ID, Westerhoff HV, Snoep JL (in press) A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism. Eur J Pharmaceut Sci. doi:10.1016/j.ejps.2011.08.017
23. Grimbs S, Selbig J, Bulik S, Holzhutter H-G, Steuer R (2007) The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks. Mol Syst Biol 3:146
24. Groen AK, Van der Meer R, Westerhoff HV, Wanders RJA, Akerboom TPM, Tager JM (1982a) Control of metabolic fluxes. In: Siess H (ed) Metabolic Compartmentation. Academic Press, New York, pp 9-37
25. Groen AK, Wanders RJ, Westerhoff HV, van der Meer R, Tager JM (1982b) Quantification of the contribution of various steps to the control of mitochondrial respiration. J Biol Chem 257(6):2754- 2757
26. Haldane J (1930) Enzymes longmans. Green and Co, UK
27. Haldane JBS (1931) The molecular statistics of an enzyme action. Proceedings of the royal society of london series B, containing papers of a biological character 108(759):559-567
28. Härdin HM, Zagaris A, Krab K, Westerhoff HV (2009) Simplified yet highly accurate enzyme kinetics for cases of low substrate concentrations. FEBS J 276(19):5491-5506. doi:10.1111/j.1742-4658.2009.07233.x
29. Heinrich R, Rapoport TA (1974) A linear steady-state treatment of enzymatic chains. Eur J Biochem 42(1):89-95. doi:10.1111/j.1432-1033.1974. tb03318.x
30. Helfert S, Estevez AM, Bakker B, Michels P, Clayton C (2001) Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei. Biochem J 357(1):117-125 (Pubitemid 32642909)
31. Hofmann U, Maier K, Anja N, Gabriele V, Reuss M, Klaus M (2008) Identification of metabolic fluxes in hepatic cells from transient 13C-labeling experiments: part I. Experimental observations. Biotechnol Bioeng 100(2):344-354 (Pubitemid 351758176)
32. Hofmeyr J-HS (1995) Metabolic regulation: a control analytic perspective. J Bioenerg Biomembr 27(5):479-490 (Pubitemid 26006041)
33. Höhme S, Hengstler JG, Brulport M, Schäfer M, Bauer A, Gebhardt R, Drasdo D (2007) Mathematical modelling of liver regeneration after intoxication with CCl4. Chem Biol Interact 168(1): 74-93 (Pubitemid 46671421)
34. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U (2006) COPASI-a complex pathway simulator. Bioinformatics 22(24):3067-3074. doi:10.1093/bioin formatics/btl485
35. Hornberg J, Bruggeman F, Bakker B, Westerhoff H (2007) Metabolic control analysis to identify optimal drug targets. Prog Drug Res 64:171-189 (Pubitemid 351495009)
36. Kacser H, Burns J (1973) The control of flux. Symp Soc Exp Biol 27:65-104
37. Kauffman KJ, Prakash P, Edwards JS (2003) Advances in flux balance analysis. Curr Opin Biotechnol 14(5):491-496 (Pubitemid 37298033)
38. Ketterer B, Coles B, Meyer DJ (1983) The role of glutathione in detoxication. Environ Health Perspect 49:59-69 (Pubitemid 13098339)
39. Kholodenko BN, Molenaar D, Schuster S, Heinrich R, Westerhoff HV (1995) Defining control coefficients in non-ideal metabolic pathways. Biophys Chem 56:215-226
40. Kitano H (2002) Systems biology: a brief overview. Science 295(5560):1662-1664. doi:10.1126/science.1069492 (Pubitemid 34202893)
41. Koefoed S, Otten MF, Koebmann BJ, Bruggeman FJ, Bakker BM, Snoep JL, Krab K, van Spanning RJM, van Verseveld HW, Jensen PR, Koster JG, Westerhoff HV (2002) A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life. Biochimica et Biophysica Acta (BBA) Bioenerg 1555(1-3):75-82 (Pubitemid 35246009)
42. Krishnan K, Andersen ME (2010) Quantitative modelling in toxicology. Wiley, New York
43. Liebermeister W, Klipp E (2006) Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Model 3:41
44. Maier K, Hofmann U, Reuss M, Klaus M (2008) Identification of metabolic fluxes in hepatic cells from transient 13C-labeling experiments: part II. Flux estimation. Biotechnol Bioeng 100(2): 355-370 (Pubitemid 351758177)
45. Maier K, Hofmann U, Bauer A, Niebel A, Vacun G, Reuss M, Mauch K (2009) Quantification of statin effects on hepatic cholesterol synthesis by transient 13C-flux analysis. Metab Eng 11(4-5): 292-309
46. Materi W, Wishart DS (2007) Computational systems biology in drug discovery and development: methods and applications. Drug Discovery Today 12(7-8):295-303 (Pubitemid 46467486)
47. Michaelis L, Menten ML (1913) Die Kinetik der Invertinwirkung. Biochemische Zeitschrift 49:333-369
48. Mulquiney PJ, Kuchel PW (1999) Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: computer simulation and metabolic control analysis. Biochem J 342(3):597-604 (Pubitemid 29452644)
49. Olivier B, Snoep J (2004) Web-based kinetic modelling using JWS online. Bioinformatics 20(13):2143-2144 (Pubitemid 39236569)
50. Onsager L (1931) Reciprocal relations in irreversible processes. II. Phys Rev 38(12):2265-2279
51. Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO (2003) Metabolic pathways in the post-genome era. Trends Biochem Sci 28(5):250-258 (Pubitemid 36588667)
52. Park BK, Boobis A, Clarke S, Goldring CEP, Jones D, Kenna JG, Lambert C, Laverty HG, Naisbitt DJ, Nelson S, Nicoll-Griffith DA, Obach RS, Routledge P, Smith DA, Tweedie DJ, Vermeulen N, Williams DP, Wilson ID, Baillie TA (2011) Managing the challenge of chemically reactive metabolites in drug development. Nature Rev Drug Discov 10(4):292-306
53. Poolman MG, Venkatesh KV, Pidcock MK, Fell DA (2004) A method for the determination of flux in elementary modes, and its application to Lactobacillus rhamnosus. Biotechnol Bioeng 88(5):601-612 (Pubitemid 39656808)
54. Raman K, Chandra N (2009) Flux balance analysis of biological systems: applications and challenges. Briefings in Bioinformatics. doi:10.1093/bib/bbp011
55. Reed MC, Thomas R, Pavisic J, James S, Ulrich CM, Nijhout HF (2008) A mathematical model of glutathione metabolism. Theor Biol Med Modell 5(8):1-16. doi:10.1186/1742-4682-5-8 (Pubitemid 351728047)
56. Rodriguez B, Burrage K, Gavaghan D, Grau V, Kohl P, Noble D (2010) The systems biology approach to drug development: application to toxicity assessment of cardiac drugs. Clin Pharmacol Ther 88(1):130-134
57. Rossell S, Weijden CCvd, Lindenbergh A, Tuijl Av, Christof F, Bakker BM, Westerhoff HV (2006) Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc Nat Acad Sci USA 103(7):2166-2171 (Pubitemid 43271641)
58. Schilling CH, Letscher D, Palsson BO (2000) Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol 203:229-248
59. Schuster S, Dandekar T, Fell DA (1999) Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol 17(2): 53-60 (Pubitemid 29332898)
60. Schwartz J-M, Kanehisa M (2005) A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics 21(suppl-2):ii204-ii205. doi:10.1093/bioinformatics/bti1132 (Pubitemid 41535449)
61. Schwartz JM, Kanehisa M (2006) Quantitative element are mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinform 7:186
62. Shi Z-Z, Habib GM, Rhead WJ, Gahl WA, He X, Sazer S, Lieberman MW (1996) Mutations in the glutathione synthetase gene cause 5-oxoprolinuria. Nat Genet 14(3):361-365
63. Simeonidis E, Murabito E, Smallbone K, Westerhoff HV (2010) Why does yeast ferment? A flux balance analysis study. Biochem Soc Trans 38:1225-1229
64. Soga T, Baran R, Suematsu M, Ueno Y, Ikeda S, Sakurakawa T, Kakazu Y, Ishikawa T, Robert M, Nishioka T, Tomita M (2006) Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption. J Biol Chem 281(24):16768-16776. doi:10.1074/jbc. M601876200
65. Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature 420(6912):190-193 (Pubitemid 35340124)
66. Swat M, Kielbasa SM, Polak S, Olivier B, Bruggeman FJ, Tulloch MQ, Snoep JL, Verhoeven AJ, Westerhoff HV (2011) What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokineticspharmacodynamics platform. Interface Focus 1(1):16-23. doi: 10.1098/rsfs.2010.0011
67. ter Kuile BH, Westerhoff HV (2001) Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett 500(3):169-171 (Pubitemid 32607554)
68. Wakeling AE, Guy SP, Woodburn JR, Ashton SE, Curry BJ, Barker AJ, Gibson KH (2002) ZD1839 (Iressa). Cancer Res 62(20): 5749-5754
69. Westerhoff HV (2007) Multi-factorial disease and robustness: where systems biology makes a difference. FEBS J 274(suppl 1):342
70. Westerhoff HV, Kell DB (1984) How do enzyme activities control metabolite concentrations? An additional theorem in the theory of metabolic control. Eur J Biochem 142:425-430 (Pubitemid 14093625)
71. Westerhoff HV, van Dam K (1987) Thermodynamics and control of biological free-energy transduction. Elsevier, Amsterdam
72. Westerhoff HV, Mosekilde E, Noe CR, Clemensen AM (2008) Integrating systems approaches into pharmaceutical sciences. Eur J Pharm Sci 35(1-2):1-4
73. Westerhoff H, Kolodkin A, Conradie R, Wilkinson S, Bruggeman F, Krab K, van Schuppen J, Hardin H, Bakker B, Moné M, Rybakova KN, Eijken M, van Leeuwen H, Snoep J (2009) Systems biology towards life in silico: mathematics of the control of living cells. J Math Biol 58(1):7-34
74. Westerhoff HV, Verma M, Nardelli M, Adamczyk M, van Eunen K, Simeonidis E, Bakker BM (2010) Systems biochemistry in practice: experimenting with modelling and understanding, with regulation and control. Biochem Soc Trans 38:1189-1196
75. WiechertW(2001) 13C metabolic flux analysis. Metab Eng 3(3):195- 206 http://www.brenda-enzymes.org/.http://www.brenda-enzymes.org/http://www.ebi.ac. uk/biomodels-main/