What it takes to understand and cure a living system: Computational systems biology and a systems biology-driven pharmacokinetics- pharmacodynamics platform

Interface Focus

Volumn 1, Issue 1, 2011, Pages 16-23

  Swat, Maciej ^a,b   Kiełbasa, Szymon M ^c   Polak, Sebastian ^d   Olivier, Brett ^b   Bruggeman, Frank J ^b,e   Tulloch, Mark Quinton ^f   Snoep, Jacky L ^b,f,g   Verhoeven, Arthur J ^a   Westerhoff, Hans V ^b,f  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

^c MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^d JAGIELLONIAN UNIVERSITY MEDICAL COLLEGE   (Poland)

^e Life Sciences   (Netherlands)

^f UNIVERSITY OF MANCHESTER   (United Kingdom)

^g STELLENBOSCH UNIVERSITY   (South Africa)

Author keywords

Biology; Computational; Pharmacodynamics; Pharmacokinetics; Systems

Indexed keywords

EID: 79959885237     PISSN: 20428898     EISSN: 20428901     Source Type: Journal    
DOI: 10.1098/rsfs.2010.0011     Document Type: Article

References (30)

1. Westerhoff, H. V. & Palsson, B. O. 2004 The evolution of molecular biology into systems biology. Nat. Biotechnol. 22, 1249-1252. (doi:10.1038/nbt1020)
2. Alberghina, L. & Westerhoff, H. V. 2005 Systems biology: definitions and perspectives. Berlin, Germany: Springer.
3. Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J. H. S. & Westerhoff, H. V. (eds) 2007 Systems biology: philosophical foundations. Amsterdam, The Netherlands: Elsevier Science.
4. Noble, D. 2006 The music of life: biology beyond genes. Oxford, UK: Oxford University Press.
5. Westerhoff, H. V., Winder, C., Messiha, H., Simeonidis, E., Adamczyk, M., Verma, M., Bruggeman, F. J. & Dunn, W. 2009 Systems biology: the elements and principles of life. FEBS Lett. 583, 3882-3890. (doi:10.1016/j.febslet.2009. 11018)
6. Kohl, P. & Noble, D. 2009 Systems biology and the virtual physiological human. Mol. Syst. Biol. 5, 292. (doi:10.1038/msb.2009.51)
7. Noble, D. 2008 Computational models of the heart and their use in assessing the actions of drugs. J. Pharmacol. Sci. 107, 107-117. (doi:10.1254/jphs.CR0070042)
8. Westerhoff, H. V., Mosekilde, E., Noe, C. R. & Clemensen, A. M. 2008 Integrating systems approaches into pharmaceutical sciences. Eur. J. Pharm. Sci. 35, 1-4. (doi:10.1016/j.ejps.2008.05.011)
9. Snoep, J. L. & Westerhoff, H. V. 2004 The silicon cell initiative. Curr. Genom. 5, 687-697. (doi:10.2174/1389202043348553)
10. Teusink, B., Walsh, M. C., Van Dam, K. & Westerhoff, H. V. 1998 The danger of metabolic pathways with turbo design. Trends Biochem. Sci. 23, 162-169. (doi:10.1016/S0968-0004(98)01205-5)
11. Haanstra, J. R., Van Tuijl, A., Kessler, P., Reijnders, W., Michels, P. A. M., Westerhoff, H. V., Parsons, M. & Bakker, B. M. 2008 Compartmentation prevents a lethal turbo-explosion of glycolysis in trypanosomes. Proc. Natl Acad. Sci. USA 105, 17 718-17 723. (doi:10.1073/pnas. 0806664105)
12. Bakker, B. M., Krauth-Siegel, R. L., Clayton, C., Matthews, K., Girolami, M., Westerhoff, H. V., Michels, P. A., Breitling, R. & Barrett, M. P. The silicon trypanosome. Parasitology 137, 1333-1341. (doi:10.1017/S0031182010000466)
13. Westerhoff, H. V. & Van Dam, K. 1987 Thermodynamics and control of biological free-energy transduction. Amsterdam, The Netherlands: Elsevier Science Publishers B.V. (Biomedical Division).
14. Rowland, T. 2010 Clinical pharmacokinetics and pharmacodynamics: concepts and applications, 4th edn. Philadelphia, PA: Lippincott Williams & Wilkins.
15. Hucka, M. et al. 2003 The systems biology markup language (SBML): a medium for the representation and exchange of biochemical network models. Bioinformatics 19, 524-531. (doi:10.1093/bioinformatics/btg015)
16. Olivier, B. G. & Snoep, J. L. 2004 Web-based kinetic modelling using JWS online. Bioinformatics 20, 2143-2144. (doi:10.1093/bioinformatics/bth200)
17. Snoep, J. L., Bruggeman, F., Olivier, B. G. & Westerhoff, H. V. 2006 Towards building the silicon cell: a modular approach. Biosystems 83, 207-216. (doi:10.1016/j.biosystems. 2005.07.006)
18. Le Novere, N. et al. 2006 Biomodels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucl. Acids Res. 34, D689-D691. (doi:10.1093/nar/gkj092)
19. Nicolis, G. & Prigogine, I. 1977 Self-organization in nonequilibrium systems: from dissipative structures to order through fluctuations. New York, NY: John Wiley & Sons.
20. Bruggeman, F. J., Bluthgen, N. & Westerhoff, H. V. 2009 Noise management by molecular networks. PLoS Comput. Biol. 5, e1000506. (doi:10.1371/journal.pcbi.1000506)
21. Koefoed, S. et al. 2002 A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life. Biochim. Biophys. Acta 1555, 75-82.
22. Teusink, B. et al. 2000 Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur. J. Biochem. 267, 5313-5329. (doi:10.1046/j.1432-1327.2000.01527.x)
23. Westerhoff, H. V., Jensen, P. R., Snoep, J. L. & Kholodenko, B. N. 1998 Thermodynamics of complexity: the live cell. Thermochim. Acta 309, 111-120. (doi:10. 1016/S0040-6031(97)00353-5)
24. Novak, B., Csikasz-Nagy, A., Gyorffy, B., Chen, K. & Tyson, J. J. 1998 Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions. Biophys. Chem. 72, 185-200. (doi:10.1016/S0301-4622(98)00133-1)
25. Mager, D. E. 2001 Diversity of mechanism-based pharmacodynamics models. Drug Metab. Disp. 31, 510-519. (doi:10.1124/dmd.31.5.510)
26. Danhof, M. 2007 Mechanism-based pharmacokineticpharmacodynamic modeling: biophase distribution, receptor theory, and dynamical systems analysis. Annu. Rev. Pharmacol. Toxicol. 47, 357-400. (doi:10.1146/annurev.pharmtox.47.120505.105154)
27. Bakker, B. M., Assmus, H. E., Bruggeman, F., Haanstra, J. R., Klipp, E. & Westerhoff, H. 2002 Network-based selectivity of antiparasitic inhibitors. Mol. Biol. Rep. 29, 1-5. (doi:10.1023/A:1020397513646)
28. Bakker, B. M., Michels, P. A. M., Opperdoes, F. R. & Westerhoff, H. V. 1997 Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes. J. Biol. Chem. 272, 3207-3215.
29. Guiral, M., Viratelle, O., Westerhoff, H. V. & Lankelma, J. 1994 Cooperative P-glycoprotein mediated daunorubicin transport into DNA-loaded plasma-membrane vesicles. FEBS Lett. 346, 141-145. (doi:10.1016/0014-5793(94) 00447-1)
30. R Foundation 2008 R: regulatory compliance and validation issues. A guidance document for the use of R in regulated clinical trial environments. See: http://www.r-project.org/doc/R-FDA.pdf.