Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network

PLoS Computational Biology

Volumn 9, Issue 3, 2013, Pages

  Huang, Jialiang ^a,b,c   Niu, Chaoqun ^a,b   Green, Christopher D ^a   Yang, Lun ^d   Mei, Hongkang ^c   Han, Jing Dong J ^a  

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

^b INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^c GLAXOSMITHKLINE   (China)

^d GLAXOSMITHKLINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG INTERACTIONS; PROTEINS;

ADVERSE EVENTS; DRUG CONCENTRATION; DRUG DEVELOPMENT; DRUG TARGETS; DRUG-DRUG INTERACTIONS; FEASIBLE SOLUTION; FORMAL APPROACH; NETWORK CONNECTION; PROTEIN-PROTEIN INTERACTION NETWORKS; SIDE EFFECT;

FORECASTING;

DESIPRAMINE; MEMANTINE; TRICYCLIC ANTIDEPRESSANT AGENT; TRIMIPRAMINE; ZONISAMIDE;

ACCURACY; ALGORITHM; AREA UNDER THE CURVE; ARTICLE; BAYES THEOREM; CASE STUDY; CONTROLLED STUDY; DRUG POTENTIATION; DRUG TARGETING; DYSTHYMIA; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; MAJOR DEPRESSION; MOLECULAR INTERACTION; PHARMACODYNAMICS; PREDICTION; PROTEIN PROTEIN INTERACTION; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY AND SPECIFICITY; STATISTICAL MODEL;

EID: 84875992866     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002998     Document Type: Article

References (31)

1. Qato DM, Alexander GC, Conti RM, Johnson M, Schumm P, et al. (2008) Use of prescription and over-the-counter medications and dietary supplements among older adults in the United States. Jama 300: 2867-2878.
2. Kiran P, (2011) Typical Drug Interactions in Oncology. US Pharm 36: 7-9.
3. Tatro DS, (1992) Drug Interaction Facts. St Louis: JB Lippincott Co.
4. Beijnen JH, Schellens JH, (2004) Drug interactions in oncology. Lancet Oncol 5: 489-496.
5. Nemeroff CB, Preskorn SH, Devane CL, (2007) Antidepressant drug-drug interactions: clinical relevance and risk management. CNS Spectr 12: 1-13.
6. Huang SM, Temple R, Throckmorton DC, Lesko LJ, (2007) Drug interaction studies: study design, data analysis, and implications for dosing and labeling. Clin Pharmacol Ther 81: 298-304.
7. Gottlieb A, Stein GY, Oron Y, Ruppin E, Sharan R, (2012) INDI: a computational framework for inferring drug interactions and their associated recommendations. Mol Syst Biol 8: 592.
8. Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, et al. (2009) Predicting new molecular targets for known drugs. Nature 462: 175-181.
9. Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M, (2007) Drug-target network. Nat Biotechnol 25: 1119-1126.
10. Berger SI, Iyengar R, (2009) Network analyses in systems pharmacology. Bioinformatics 25: 2466-2472.
11. Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P, (2008) Drug target identification using side-effect similarity. Science 321: 263-266.
12. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, et al. (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313: 1929-1935.
13. Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P, (2008) STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res 36: D684-688.
14. Jon DD, Xu H, Zhiping W, Abhinita S, Shreyas DK, et al. (2012) Literature Based Drug Interaction Prediction with Clinical Assessment Using Electronic Medical Records: Novel Myopathy Associated Drug Interactions. PLoS Comput Biol 8: e1002614.
15. Tatonetti NP, Ye PP, Daneshjou R, Altman RB, (2012) Data-driven prediction of drug effects and interactions. Sci Transl Med 4: 125ra131.
16. Hopkins AL, (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4: 682-690.
17. Knox C, Law V, Jewison T, Liu P, Ly S, et al. (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res 39: D1035-1041.
18. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res 37: D767-772.
19. Berger SI, Iyengar R, (2010) Role of systems pharmacology in understanding drug adverse events. Wiley Interdiscip Rev Syst Biol Med 3: 129-135.
20. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
21. Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P, (2010) A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol 6: 343.
22. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690.
23. Ereshefsky L, (2009) Drug-drug interactions with the use of psychotropic medications. Interview by Diane M. Sloan. CNS Spectr 14: 1-8.
24. Nieuwstraten C, Labiris NR, Holbrook A, (2006) Systematic overview of drug interactions with antidepressant medications. Can J Psychiatry 51: 300-316.
25. Gillman PK, (2007) Tricyclic antidepressant pharmacology and therapeutic drug interactions updated. Br J Pharmacol 151: 737-748.
26. Selkoe DJ, (2002) Alzheimer's disease is a synaptic failure. Science 298: 789-791.
27. Kohling R, (2002) Voltage-gated sodium channels in epilepsy. Epilepsia 43: 1278-1295.
28. Zhao XM, Iskar M, Zeller G, Kuhn M, Noort V, et al. (2011) Prediction of drug combinations by integrating molecular and pharmacological data. PLoS Comput Biol 7: e1002323.
29. Xia K, Dong D, Han JD, (2006) IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. BMC Bioinformatics 7: 508.
30. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, et al. (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490: 556-560.
31. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.