Study of drug function based on similarity of pathway fingerprint

doi:10.1007/s13238-012-2011-z

Prot Cell

2012, Vol. 3

Issue (2) : 132-139 https://doi.org/10.1007/s13238-012-2011-z PMID: 22426982

RESEARCH ARTICLE

Study of drug function based on similarity of pathway fingerprint

Hao Ye^1,2, Kailin Tang², Linlin Yang^1,2, Zhiwei Cao³, Yixue Li^1,2(

)

1. State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai 200237, China; 2. Shanghai Center for Bioinformation Technology, Shanghai 200235, China; 3. School of Life Science and Technology, Tongji University, Shanghai 200092, China

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Abstract

Drugs sharing similar therapeutic function may not bind to the same group of targets. However, their targets may be involved in similar pathway profiles which are associated with certain pathological process. In this study, pathway fingerprint was introduced to indicate the profile of significant pathways being influenced by the targets of drugs. Then drug-drug network was further constructed based on significant similarity of pathway fingerprints. In this way, the functions of a drug may be hinted by the enriched therapeutic functions of its neighboring drugs. In the test of 911 FDA approved drugs with more than one known target, 471 drugs could be connected into networks. 760 significant associations of drug-therapeutic function were generated, among which around 60% of them were supported by scientific literatures or ATC codes of drug functional classification. Therefore, pathway fingerprints may be useful to further study on the potential function of known drugs, or the unknown function of new drugs.

Keywords pathway fingerprint drug-drug network therapeutic target function prediction

Corresponding Author(s): Li Yixue,Email:yxli@scbit.org

Issue Date: 01 February 2012

Cite this article:

Hao Ye,Kailin Tang,Linlin Yang, et al. Study of drug function based on similarity of pathway fingerprint[J]. Prot Cell, 2012, 3(2): 132-139.

URL:

https://academic.hep.com.cn/pac/EN/10.1007/s13238-012-2011-z
https://academic.hep.com.cn/pac/EN/Y2012/V3/I2/132

1	Adams, C.P., and Brantner, V.V. (2006). Estimating the cost of new drug development: is it really 802 million dollars? Health Aff (Millwood) 25, 420-428 . doi: 10.1377/hlthaff.25.2.420
2	Anandarajah, A.P., Schwarz, E.M., Totterman, S., Monu, J., Feng, C.Y., Shao, T., Haas-Smith, S.A., and Ritchlin, C.T. (2008). The effect of etanercept on osteoclast precursor frequency and enhancing bone marrow oedema in patients with psoriatic arthritis. Ann Rheum Dis 67, 296-301 . doi: 10.1136/ard.2007.076091
3	Andraos, J. (2008). Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws: new methods based on directed graphs. Can J Chem 86, 342-357 . doi: 10.1139/v08-020
4	Azzoli, C.G., Krug, L.M., Miller, V.A., Kris, M.G., and Mass, R. (2002). Trastuzumab in the treatment of non-small cell lung cancer. Semin Oncol 29, 59-65 . doi: 10.1053/sonc.2002.31526
5	Barabási, A.L., and Oltvai, Z.N. (2004). Network biology: understanding the cell’s functional organization. Nat Rev Genet 5, 101-113 . doi: 10.1038/nrg1272
6	Chen, L., Feng, K.Y., Cai, Y.D., Chou, K.C., and Li, H.P. (2010). Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. BMC Bioinformatics 11, 293. doi: 10.1186/1471-2105-11-293
7	Chong, C.R., and Sullivan, D.J. Jr. (2007). New uses for old drugs. Nature 448, 645-646 . doi: 10.1038/448645a
8	Chou, K.C. (1989). Low-frequency resonance and cooperativity of hemoglobin. Trends Biochem Sci 14, 212-213 . doi: 10.1016/0968-0004(89)90026-1
9	Chou, K.C. (1995). A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins 21, 319-344 . doi: 10.1002/prot.340210406
10	Chou, K.C. (1996). Review: Prediction of HIV protease cleavage sites in proteins. Anal Biochem 233, 1-14 . doi: 10.1006/abio.1996.0001
11	Chou, K. C. (2001). Prediction of protein cellular attributes using pseudo amino acid composition. PROTEINS: Structure, Function, and Genetics (Erratum: ibid, 2001, 44, 60) 43, 246-255 .
12	Chou, K.C. (2010). Graphic rule for drug metabolism systems. Curr Drug Metab 11, 369-378 . doi: 10.2174/138920010791514261
13	Chou, K.C., and Shen, H.B. (2007). Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. Biochem Biophys Res Commun 357, 633-640 . doi: 10.1016/j.bbrc.2007.03.162
14	Chou, K.C., Wu, Z.C., and Xiao, X. (2011). iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins. PLoS One 6, e18258. doi: 10.1371/journal.pone.0018258
15	Deitchman, D., Braselton, J.P., Hayes, D.C., and Stratman, R.L. (1980). The ganglion-blocked, angiotensin II-supported rat: a model for demonstrating antihypertensive vasodilator activity. J Pharmacol Methods 3, 311-321 . doi: 10.1016/0160-5402(80)90073-X
16	Delord, J.P., Quideau, S., Rochaix, P., Caselles, O., Couderc, B., Hennebelle, I., Courbon, F., Canal, P., and Allal, B.C. (2010). Trastuzumab induced in vivo tissue remodelling associated in vitro with inhibition of the active forms of AKT and PTEN and RhoB induction in an ovarian carcinoma model. Br J Cancer 103, 61-72 . doi: 10.1038/sj.bjc.6605699
17	Fintini, D., Brufani, C., and Cappa, M. (2009). Profile of mecasermin for the long-term treatment of growth failure in children and adolescents with severe primary IGF-1 deficiency. Ther Clin Risk Manag 5, 553-559 .
18	Fodor, M. (2011). [Current views on the metabolic syndrome and the effects of antipsychotic drugs]. Psychiatr Hung 26, 196-200 .
19	He, Z., Zhang, J., Shi, X.H., Hu, L.L., Kong, X., Cai, Y.D., and Chou, K.C. (2010). Predicting drug-target interaction networks based on functional groups and biological features. PLoS One 5, e9603. doi: 10.1371/journal.pone.0009603
20	Hu, L.L., Chen, C., Huang, T., Cai, Y.D., and Chou, K.C. (2011a). Predicting biological functions of compounds based on chemical-chemical interactions. PLoS One 6, e29491. doi: 10.1371/journal.pone.0029491
21	Hu, L.L., Huang, T., Cai, Y.D., and Chou, K.C. (2011b). Prediction of body fluids where proteins are secreted into based on protein interaction network. PLoS One 6, e22989. doi: 10.1371/journal.pone.0022989
22	Huang, T., Shi, X.H., Wang, P., He, Z., Feng, K.Y., Hu, L., Kong, X., Li, Y.X., Cai, Y.D., and Chou, K.C. (2010). Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PloS One 5, e10972. doi: 10.1371/journal.pone.0010972
23	Huang, W., Sherman, B.T., and Lempicki, R.A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44-57 . doi: 10.1038/nprot.2008.211
24	Kamikawa, Y., and Shimo, Y. (1987). Different spasmolytic effects of smooth muscle relaxants on the guinea-pig esophageal muscularis mucosae contracted by carbachol or high potassium in vitro. Eur J Pharmacol 136, 39-48 . doi: 10.1016/0014-2999(87)90776-X
25	Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M. (2010). KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38, D355-D360 . doi: 10.1093/nar/gkp896
26	Keating, G.M. (2008). Mecasermin. BioDrugs 22, 177-188 . doi: 10.2165/00063030-200822030-00004
27	Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V., . (2011). DrugBank 3.0: a comprehensive resource for ‘omics’ research on drugs. Nucleic Acids Res 39, D1035-D1041 . doi: 10.1093/nar/gkq1126
28	Kondo, N., Ishiguro, Y., Kimura, M., Sano, D., Fujita, K., Sakakibara, A., Taguchi, T., Toth, G., Matsuda, H., and Tsukuda, M. (2008). Antitumor effect of gefitinib on head and neck squamous cell carcinoma enhanced by trastuzumab. Oncol Rep 20, 373-378 .
29	Krantz, A. (1998). Protein-site targeting. Diversification of the drug discovery process. Nat Biotechnol 16, 1294. doi: 10.1038/4243
30	Lazner, F., Gowen, M., Pavasovic, D., and Kola, I. (1999). Osteopetrosis and osteoporosis: two sides of the same coin. Hum Mol Genet 8, 1839-1846 . doi: 10.1093/hmg/8.10.1839
31	Liao, C.H., Chang, C.S., Wei, W.C., Chang, S.N., Liao, C.C., Lane, H.Y., and Sung, F.C. (2011). Schizophrenia patients at higher risk of diabetes, hypertension and hyperlipidemia: a population-based study. Schizophr Res 126, 110-116 . doi: 10.1016/j.schres.2010.12.007
32	Mineo, J.F., Bordron, A., Quintin-Roué, I., Loisel, S., Ster, K.L., Buhé, V., Lagarde, N., and Berthou, C. (2004). Recombinant humanised anti-HER2/neu antibody (Herceptin) induces cellular death of glioblastomas. Br J Cancer 91, 1195-1199 .
33	Nacher, J.C., and Schwartz, J.M. (2008). A global view of drug-therapy interactions. BMC Pharmacol 8, 5. doi: 10.1186/1471-2210-8-5
34	Timberlake, W.H., and Schwab, R.S. (1952) Experimental preparation W-483 in the treatment of Parkinson’s disease. N Engl J Med 247, 98-100 doi: 10.1056/NEJM195207172470306
35	Tobinick, E.L. (2009). The value of drug repositioning in the current pharmaceutical market. Drug News Perspect 22, 119-125 . doi: 10.1358/dnp.2009.22.2.1343228
36	Wermuth, C.G. (2004). Multitargeted drugs: the end of the “onetarget-one-disease” philosophy? Drug Discov Today 9, 826-827 . doi: 10.1016/S1359-6446(04)03213-1
37	Willett, P., Barnard, J.M., and Downs, G.M. (1998). Chemical similarity searching. J Chem Inf Comput Sci 38, 983-996 . doi: 10.1021/ci9800211
38	Xiao, X., Lin, W.Z., and Chou, K.C. (2008). Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes. J Comput Chem 29, 2018-2024 . doi: 10.1002/jcc.20955
39	Xiao, X., Wang, P., and Chou, K.C. (2009). GPCR-CA: A cellular automaton image approach for predicting G-protein-coupled receptor functional classes. J Comput Chem 30, 1414-1423 . doi: 10.1002/jcc.21163
40	Yildirim, M.A., Goh, K.I., Cusick, M.E., Barabási, A.L., and Vidal, M. (2007). Drug-target network. Nat Biotechnol 25, 1119-1126 . doi: 10.1038/nbt1338
41	Zhou, G.P., and Deng, M.H. (1984). An extension of Chou’s graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways. Biochem J 222, 169-176 .

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