Systematic Approach for Analyzing Drug Combination by Using Target-Enzyme Distance |
Park, Jaesub
(Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology)
Lee, Sunjae (Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology) Kim, Kiseong (Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology) Lee, Doheon (Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology) |
1 | Li, J. W., and Vederas, J. C. (2009). Drug discovery and natural products: end of an era or an endless frontier? Science 325, 161-165. DOI ScienceOn |
2 | Lehar, J., Krueger, A. S., Avery, W., Heilbut, A. M., Johansen, L. M., Price, E. R., Rickles, R. J., Short, G. F., 3rd, Staunton, J. E., Jin, X., et al. (2009). Synergistic drug combinations tend to improve therapeutically relevant selectivity. Nat Biotechnol 27, 659-666. DOI ScienceOn |
3 | Zhao, X. M., Iskar, M., Zeller, G., Kuhn, M., van Noort, V., and Bork, P. (2011). Prediction of drug combinations by integrating molecular and pharmacological data. PLoS Comput Biol 7, e1002323. DOI |
4 | Zhang, B. B., Zhou, G., and Li, C. (2009). AMPK: an emerging drug target for diabetes and the metabolic syndrome. Cell Metab 9, 407-416. DOI ScienceOn |
5 | Robert, C., Green, M. (2005). Diagnosis and Management of Alzheimer's Disease and Other Dementias. 2 Edition.: Professional Communications. |
6 | Chang, R. L., Xie, L., Bourne, P. E., and Palsson, B. O. (2010). Drug offtarget effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol 6, e1000938. DOI ScienceOn |
7 | Folger, O., Jerby, L., Frezza, C., Gottlieb, E., Ruppin, E., and Shlomi, T. (2011). Predicting selective drug targets in cancer through metabolic networks. Mol Syst Biol 7, 501. |
8 | Gottlieb, A., Stein, G. Y., Oron, Y., Ruppin, E., and Sharan, R. (2012). INDI: a computational framework for inferring drug interactions and their associated recommendations. Mol Syst Biol 8, 592. |
9 | Bibi, Z. (2008). Role of cytochrome P450 in drug interactions. Nutr Metab (Lond) 5, 27. DOI ScienceOn |
10 | Barabasi, A. L., and Oltvai, Z. N. (2004). Network biology: understanding the cell's functional organization. Nat Rev Genet 5, 101-113. DOI ScienceOn |
11 | Zimmermann, G. R., Lehár, J., and Keith, C. T. (2007). Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discov Today 12, 34-42. DOI ScienceOn |
12 | Vander Heiden, M. G. (2011). Targeting cancer metabolism: a therapeutic window opens. Nat Rev Drug Discov 10, 671-684. DOI ScienceOn |
13 | Chong, Z. Z., Wang, S., Shang, Y. C., and Maiese, K. (2012). Targeting cardiovascular disease with novel SIRT1 pathways. Future Cardiol 8, 89-100. DOI |
14 | Huang, J., Niu, C., Green, C. D., Yang, L., Mei, H., and Han, J. D. (2013). Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network. PLoS Comput Biol 9, e1002998. DOI |
15 | Liu, Y., Hu, B., Fu, C., and Chen, X. (2010). DCDB: drug combination database. Bioinformatics 26, 587-588. DOI ScienceOn |
16 | Jia, J., Zhu, F., Ma, X., Cao, Z., Li, Y., and Chen, Y. Z. (2009). Mechanisms of drug combinations: interaction and network perspectives. Nat Rev Drug Discov 8, 111-128. DOI ScienceOn |
17 | Mathivanan, S., Ahmed, M., Ahn, N. G., Alexandre, H., Amanchy, R., Andrews, P. C., Bader, J. S., Balgley, B. M., Bantscheff, M., Bennett, K. L., et al. (2008). Human Proteinpedia enables sharing of human protein data. Nat Biotechnol 26, 164-167. DOI ScienceOn |
18 | Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R., and Palsson, B. O. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104, 1777-1782. DOI ScienceOn |
19 | Wolfram Research, I. (2010). Mathematica Edition: Version 8.0. Champaign, Illinois: Wolfram Research, Inc. |
20 | Ashburn, T. T., and Thor, K. B. (2004). Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 3, 673-683. DOI ScienceOn |