A systems biology approach to identify effective cocktail drugs

BMC Systems Biology

Volumn 4, Issue SUPPL. 2, 2010, Pages

  Wu, Zikai ^a,b   Zhao, Xing Ming ^a   Chen, Luonan ^c,d  

^a SHANGHAI UNIVERSITY   (China)

^b UNIVERSITY OF SHANGHAI FOR SCIENCE AND TECHNOLOGY   (China)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^d NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

2,4 THIAZOLIDINEDIONE DERIVATIVE; ANTIDIABETIC AGENT; METFORMIN; ROSIGLITAZONE;

ARTICLE; CHEMICAL STRUCTURE; DRUG COMBINATION; DRUG INTERACTION; GENE EXPRESSION PROFILING; GENETICS; NON INSULIN DEPENDENT DIABETES MELLITUS; PILOT STUDY; SYSTEMS BIOLOGY;

DIABETES MELLITUS, TYPE 2; DRUG INTERACTIONS; DRUG THERAPY, COMBINATION; GENE EXPRESSION PROFILING; HYPOGLYCEMIC AGENTS; METFORMIN; MODELS, MOLECULAR; PILOT PROJECTS; SYSTEMS BIOLOGY; THIAZOLIDINEDIONES;

EID: 77956836440     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-7     Document Type: Article

References (43)

1. Chen LN, Wang RS, Zhang XS. Biomolecular Networks: Methods and Applications in Systems Biology. 2009, New Jersey, USA: Wiley Interscience.
2. Lindsay MA. Target discovery. Nat Rev Drug Discov 2003, 2:831-838. 10.1038/nrd1202, 14526386.
3. Yang K, Bai HJ, Ouyang Q, Lai LH, Tang C. Finding multiple traget optimal intervention in disease-related molecular network. Molecular Systems Biology 2008, 4:228. 2673713, 18985027, 10.1038/msb.2008.60.
4. Chou TC. Theoretical Basis, Experimental Design, and Computerized Simulation of Synergism and Antagonism in Drug Combination Studies. Pharmacol Rev 2006, 58(3):621-680. 10.1124/pr.58.3.10, 16968952.
5. Loewe S. The problem of synergism and antagonism of combined drugs. Arzneimittelforschung 1953, 3:285-290.
6. Fitzgerald JB, Schoeberl B, Nielsen UB, orger PK. Systems biology and combination therapy in the quest for clinical efficacy. Nat Chem Bioc 2006, 2(9):458-466.
7. Bliss CI. The calculation of microbial assays. Bacteriol Rev 1956, 20:243-258. 180866, 13403845.
8. Agrawal N, Pallos J, Slepko N, Apostol BL, Bodai L, Chang LW, Chiang AS. Thompson LM, Marsh JL, Identification of combinatorial drug combination regimens for treatment of Huntington's disease using Drosophila. Proc Natl Acad Sci 2005, 102(10):3777-3781. 553288, 15716359, 10.1073/pnas.0500055102.
9. Cottarel G, Wierzbowski J. Combination drugs, an emerging option for antibacterial therapy. TRENDS Biotechnol 2007, 25(12):548-554.
10. Calzolari D, Bruschi S, Coquin L, Schofield J, Feala J, Reed JC, McCulloch AD. Paternostro G, Search Algorithms as a framework for the Optimization of Drug combinations. Plos Comput Biol 2008, 4(12):e1000249. 2590660, 19112483, 10.1371/journal.pcbi.1000249.
11. Borisy AA, Elliott PJ, Hurst NW, Lee MS, Lehál J, Price ER, Serbedzija G, Zimmermann GR, Foley MA, Stockwell BR, Keith CT. Systematic discovery of multicomponent therapeutics. Proc Natl Acad Sci 2003, 100(13):7977-7982. 164698, 12799470, 10.1073/pnas.1337088100.
12. Wong PK, Yu FQ, Shahangian A, Cheng GH, Sun R, Ho CM. Closed-loop control of cellular functions using comninatory drugs guided by a stochastic search algorithm. Proc Natl Acad Sci 2008, 105(13):5105-5110. 2278193, 18356295, 10.1073/pnas.0800823105.
13. Vazquez A. Optimal drug combinations and minimal hitting sets. BMC Systems Biology 2009, 3:81. 2738654, 19660129, 10.1186/1752-0509-3-81.
14. Maria T, Tusié L. Genes and Type 2 diabetes Mellitus. Arch Med Res 2005, 36:210-222. 10.1016/j.arcmed.2005.03.004, 15925011.
15. Fonseca V, Rosenstock J, Patwardhan, Salzman A. Effect of Metformin and Rosiglitazone Combination Therapy in Patients with Type 2 Diabetes Mellitus(A Randomized Controlled Trial). The Journal of the American Medical Association 2000, 283:1695-1702.
16. Gómez-Perez F, Fanghänel-Salmón G, Barbosa JA, Montes-Villareal J, Berry RA, Warsi G, Gould EM. Efficacy and safety of Rosiglitazone plus Metformin in Mexicans with type 2 diabetes. Diabetes Metab rev 2002, 18:127-134.
17. Bailey CJ, Day C. Avandamet: combined Metformin-Rosiglitazone treatment for insulin resistence in type 2 diabetes. Int J Clin Pract 2004, 58(9):867-876. 10.1111/j.1742-1241.2004.00318.x, 15529521.
18. Rosak C, Petzoldt R, Wolf R, Reblin T, Dehmel B, Seidel D. Rosliglitazone plus Metformin is effective and well telerated in clinical practice: results from large observational studies in people with type 2 diabetes. Int J Clin Pract 2005, 59(10):1131-1136. 10.1111/j.1368-5031.2005.00652.x, 16178978.
19. Rosenstock J, Rood J, Cobitz A, Biswas N, Chou H, Garber A. Initial treatment with Rosiglitazone/Metformin fixed-dose combination therapy compared with monotherapy with either Rosiglitazone or Metformin in patients with uncontrolled type 2 diabetes. Diabetes Obes Metab 2006, 8:650-660. 10.1111/j.1463-1326.2006.00659.x, 17026489.
20. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005, 33:D514-D517. 539987, 15608251, 10.1093/nar/gki033.
21. Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIMR). Nucleic Acids Res 2009, 37:D793-D796. 2686440, 18842627, 10.1093/nar/gkn665.
22. Tiffin N, Adie E, Turner F, Brunner HG, Van DMA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA. Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Res 2006, 34(10):3067-3081. 1475747, 16757574, 10.1093/nar/gkl381.
23. Harris MA. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32:D258-D261. 308770, 14681407, 10.1093/nar/gkh066.
24. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32:D277-D280. 308797, 14681412, 10.1093/nar/gkh063.
25. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat Protoc 2009, 4(1):44-57. 10.1038/nprot.2008.211, 19131956.
26. Lee SH, Demeterco C, Geron I, Abrahamsson A, Levine F, Itkin-Ansari P. Islet SpecificWnt Activation in Human Type II Diabetes. Experimental Diabetes Research 2009, 2009:doi:10.1155/2008/728763.
27. Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 2006, 34:D668-D672. 1347430, 16381955, 10.1093/nar/gkj067.
28. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 2008, 36:D901-D906. 2238889, 18048412, 10.1093/nar/gkm958.
29. Zhao F, Xuan Z, Liu L, Zhang MQ. TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res 2005, 33:D103-D107. 539958, 15608156, 10.1093/nar/gki004.
30. Cui Q, Yu Z, Purisima EO, Wang E. Principles of microRNA regulation of a human cellular signaling network. Molecular Systems Biology 2006, 2:46. 1681519, 16969338, 10.1038/msb4100089.
31. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30(1):207-210. 99122, 11752295, 10.1093/nar/30.1.207.
32. Barrett TY, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R. NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res 2002, 35:760-765.
33. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP, Subramanian A, Ross KN, et al. The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes and Disease. Science 2006, 313(29):1929-1935. 10.1126/science.1132939, 17008526.
34. Guo Z, Li Y, Gong X, Yao C, Ma W, Wang D, Li Y, Zhu J, Zhang M, Yang D, Wang J. Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network. Bioinformatics 2007, 23:2121-2128. 10.1093/bioinformatics/btm294, 17545181.
35. Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S. Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models. PLOS Genet 2007, 3:e96. 1904360, 17571924, 10.1371/journal.pgen.0030096.
36. Noisel J, Sanguinetti G, Wright P. Identifying differentially-expressed subnetworks with MMG. Bioinformatics 2008, 24:2792-2793. 10.1093/bioinformatics/btn499, 18819939.
37. Dittrich M, Klau G, Rosenwald A, Dandekarand T, Muller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008, 24:i223-i231. 2718639, 18586718, 10.1093/bioinformatics/btn161.
38. Ulitsky I, Karp M, Shamir R. Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles. Lect N Bioinformat(RECOMB2008) 2008, 4955:347-359.
39. Qiu YQ, Zhang SH, Zhang XS, Chen LN. Identifying differentially expressed pathways via a mixed integer linear programming model. IET Systems Biology 2009, 3(6):475-486. 10.1049/iet-syb.2008.0155, 19947773.
40. Zhao XM, Wang RS, Chen LN, Aihara K. Automatic modeling of signaling pathways based on network flow model. Journal of Bioinformatics and Computational Biology 2009, 7(2):309-322.
41. Zhao XM, Wang RS, Chen L, Aihara K. Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucl. Acids Res 2008, 36(9):e48.
42. Wu Z, Zhao X, Chen L. Identifying responsive functional modules from protein-protein interaction network. Molecules and Cells 2009, 27(3):271-277.
43. Lee HF, Dooly DR. Algorithms for the constrained maximum-Weight connected graph problem. Nav Res Log 1996, 43:985-1008.