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Combinatorial Chemistry & High Throughput Screening

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ISSN (Print): 1386-2073
ISSN (Online): 1875-5402

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Research Article

Relating Substructures and Side Effects of Drugs with Chemical-chemical Interactions

Author(s): Bo Zhou*, Xian Zhao, Jing Lu, Zuntao Sun, Min Liu, Yilu Zhou, Rongzhi Liu and Yihua Wang

Volume 23, Issue 4, 2020

Page: [285 - 294] Pages: 10

DOI: 10.2174/1386207322666190702102752

Price: $65

Abstract

Background: Drugs are very important for human life because they can provide treatment, cure, prevention, or diagnosis of different diseases. However, they also cause side effects, which can increase the risks for humans and pharmaceuticals companies. It is essential to identify drug side effects in drug discovery. To date, lots of computational methods have been proposed to predict the side effects of drugs and most of them used the fact that similar drugs always have similar side effects. However, previous studies did not analyze which substructures are highly related to which kind of side effect.

Method: In this study, we conducted a computational investigation. In this regard, we extracted a drug set for each side effect, which consisted of drugs having the side effect. Also, for each substructure, a set was constructed by picking up drugs owing such substructure. The relationship between one side effect and one substructure was evaluated based on linkages between drugs in their corresponding drug sets, resulting in an Es value. Then, the statistical significance of Es value was measured by a permutation test.

Results and Conclusion: A number of highly related pairs of side effects and substructures were obtained and some were extensively analyzed to confirm the reliability of the results reported in this study.

Keywords: Side effect, chemical substructure, chemical-chemical interaction, permutation test, statistical significance, tardive dyskinesia.

« Previous Next »
[1]
Pauwels, E.; Stoven, V.; Yamanishi, Y. Predicting drug side-effect profiles: a chemical fragment-based approach. BMC Bioinformatics, 2011, 12, 169.
[http://dx.doi.org/10.1186/1471-2105-12-169] [PMID: 21586169]
[2]
Liu, M.; Wu, Y.; Chen, Y.; Sun, J.; Zhao, Z.; Chen, X.W.; Matheny, M.E.; Xu, H. Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. J. Am. Med. Inform. Assoc., 2012, 19(e1), e28-e35.
[http://dx.doi.org/10.1136/amiajnl-2011-000699] [PMID: 22718037]
[3]
Cheng, F.; Li, W.; Wang, X.; Zhou, Y.; Wu, Z.; Shen, J.; Tang, Y. Adverse drug events: database construction and in silico prediction. J. Chem. Inf. Model., 2013, 53(4), 744-752.
[http://dx.doi.org/10.1021/ci4000079] [PMID: 23521697]
[4]
Yamanishi, Y.; Pauwels, E.; Kotera, M. Drug side-effect prediction based on the integration of chemical and biological spaces. J. Chem. Inf. Model., 2012, 52(12), 3284-3292.
[http://dx.doi.org/10.1021/ci2005548] [PMID: 23157436]
[5]
Breiman, L. Random forests. Mach. Learn., 2001, 45(1), 5-32.
[http://dx.doi.org/10.1023/A:1010933404324]
[6]
Zhao, X.; Chen, L.; Lu, J. A similarity-based method for prediction of drug side effects with heterogeneous information. Math. Biosci., 2018, 306, 136-144.
[http://dx.doi.org/10.1016/j.mbs.2018.09.010] [PMID: 30296417]
[7]
Chen, L.; Huang, T.; Zhang, J.; Zheng, M.Y.; Feng, K.Y.; Cai, Y.D.; Chou, K.C. Predicting drugs side effects based on chemical-chemical interactions and protein-chemical interactions. BioMed Res. Int., 2013, 2013, 485034
[http://dx.doi.org/10.1155/2013/485034] [PMID: 24078917]
[8]
Zhang, W.; Liu, F.; Luo, L.; Zhang, J. Predicting drug side effects by multi-label learning and ensemble learning. BMC Bioinformatics, 2015, 16(1), 365.
[http://dx.doi.org/10.1186/s12859-015-0774-y] [PMID: 26537615]
[9]
Kuhn, M.; Campillos, M.; Letunic, I.; Jensen, L.J.; Bork, P. A side effect resource to capture phenotypic effects of drugs. Mol. Syst. Biol., 2010, 6, 343.
[http://dx.doi.org/10.1038/msb.2009.98] [PMID: 20087340]
[10]
Kuhn, M.; Letunic, I.; Jensen, L.J.; Bork, P. The SIDER database of drugs and side effects. Nucleic Acids Res., 2016, 44(D1), D1075-D1079.
[http://dx.doi.org/10.1093/nar/gkv1075] [PMID: 26481350]
[11]
RDKit. Open-source cheminformatics, available at:. http://www.rdkit.org
[12]
Rogers, D.; Hahn, M. Extended-connectivity fingerprints. J. Chem. Inf. Model., 2010, 50(5), 742-754.
[http://dx.doi.org/10.1021/ci100050t] [PMID: 20426451]
[13]
Kuhn, M.; von Mering, C.; Campillos, M.; Jensen, L.J.; Bork, P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res., 2008, 36(Database issue), D684-D688.
[PMID: 18084021]
[14]
Kuhn, M.; Szklarczyk, D.; Pletscher-Frankild, S.; Blicher, T.H.; von Mering, C.; Jensen, L.J.; Bork, P. STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res., 2014, 42(Database issue), D401-D407.
[http://dx.doi.org/10.1093/nar/gkt1207] [PMID: 24293645]
[15]
Chen, L.; Liu, T.; Zhao, X. Inferring anatomical therapeutic chemical (ATC) class of drugs using shortest path and random walk with restart algorithms. BBA - Mol Basis Dis., 2018, 1864(6, Part B), 2228-2240.
[16]
Liu, T.; Chen, L.; Pan, X. An integrated multi-label classifier with chemical-chemical interactions for prediction of chemical toxicity effects. Comb. Chem. High Throughput Screen., 2018, 21(6), 403-410.
[http://dx.doi.org/10.2174/1386207321666180601075428] [PMID: 29852864]
[17]
Chen, L.; Zeng, W.M.; Cai, Y.D.; Feng, K.Y.; Chou, K.C. Predicting Anatomical Therapeutic Chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities. PLoS One, 2012, 7(4), e35254
[http://dx.doi.org/10.1371/journal.pone.0035254] [PMID: 22514724]
[18]
Cheng, X.; Zhao, S-G.; Xiao, X.; Chou, K.C. iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals. Bioinformatics, 2017, 33(3), 341-346.
[http://dx.doi.org/10.1093/bioinformatics/btx387] [PMID: 28172617]
[19]
Hu, L.L.; Chen, C.; Huang, T.; Cai, Y.D.; Chou, K.C. Predicting biological functions of compounds based on chemical-chemical interactions. PLoS One, 2011, 6(12), e29491
[http://dx.doi.org/10.1371/journal.pone.0029491] [PMID: 22220213]
[20]
Chen, L.; Lu, J.; Zhang, N.; Huang, T.; Cai, Y.D. A hybrid method for prediction and repositioning of drug Anatomical Therapeutic Chemical classes. Mol. Biosyst., 2014, 10(4), 868-877.
[http://dx.doi.org/10.1039/c3mb70490d] [PMID: 24492783]
[21]
Gao, Y.F.; Chen, L.; Cai, Y.D.; Feng, K.Y.; Huang, T.; Jiang, Y. Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins. PLoS One, 2012, 7(9), e45944
[http://dx.doi.org/10.1371/journal.pone.0045944] [PMID: 23029334]
[22]
Chen, L.; Chu, C.; Lu, J.; Kong, X.; Huang, T.; Cai, Y.D. A computational method for the identification of new candidate carcinogenic and non-carcinogenic chemicals. Mol. Biosyst., 2015, 11(9), 2541-2550.
[http://dx.doi.org/10.1039/C5MB00276A] [PMID: 26194467]
[23]
Huang, G.; Lu, Y.; Lu, C.; Zheng, M.; Cai, Y.D. Prediction of drug indications based on chemical interactions and chemical similarities. BioMed Res. Int., 2015, 2015, 584546
[http://dx.doi.org/10.1155/2015/584546] [PMID: 25821813]
[24]
Chen, L.; Lu, J.; Huang, T.; Yin, J.; Wei, L.; Cai, Y.D. Finding candidate drugs for hepatitis C based on chemical-chemical and chemical-protein interactions. PLoS One, 2014, 9(9), e107767
[http://dx.doi.org/10.1371/journal.pone.0107767] [PMID: 25225900]
[25]
Lu, J.; Huang, G.; Li, H.P.; Feng, K.Y.; Chen, L.; Zheng, M-Y.; Cai, Y.D. Prediction of cancer drugs by chemical-chemical interactions. PLoS One, 2014, 9(2), e87791
[http://dx.doi.org/10.1371/journal.pone.0087791] [PMID: 24498372]
[26]
Liu, L.; Chen, L.; Zhang, Y.H.; Wei, L.; Cheng, S.; Kong, X.; Zheng, M.; Huang, T.; Cai, Y.D. Analysis and prediction of drug-drug interaction by minimum redundancy maximum relevance and incremental feature selection. J. Biomol. Struct. Dyn., 2017, 35(2), 312-329.
[http://dx.doi.org/10.1080/07391102.2016.1138142] [PMID: 26750516]
[27]
Guo, Z.H.; Chen, L.; Zhao, X. A network integration method for deciphering the types of metabolic pathway of chemicals with heterogeneous information. Comb. Chem. High Throughput Screen., 2018, 21(9), 670-680.
[http://dx.doi.org/10.2174/1386207322666181206112641] [PMID: 30520371]
[28]
Zhao, X.; Chen, L.; Guo, Z-H.; Liu, T. Predicting drug side effects with compact integration of heterogeneous networks. Curr. Bioinform., 2019, 8, 709-720.
[http://dx.doi.org/10.2174/1574893614666190220114644]
[29]
Wang, T.; Chen, L.; Zhao, X. Prediction of drug combinations with a network embedding method. Comb. Chem. High Throughput Screen., 2018, 21(10), 789-797.
[http://dx.doi.org/10.2174/1386207322666181226170140] [PMID: 30747059]
[30]
Waln, O.; Jankovic, J. An update on tardive dyskinesia: from phenomenology to treatment. Tremor Other Hyperkinet. Mov. (N. Y.), 2013, 3, 3.
[PMID: 23858394]
[31]
Lockwood, J.T.; Remington, G. Emerging drugs for antipsychotic-induced tardive dyskinesia: investigational drugs in Phase II and Phase III clinical trials. Expert Opin. Emerg. Drugs, 2015, 20(3), 407-421.
[http://dx.doi.org/10.1517/14728214.2015.1050376] [PMID: 26166007]
[32]
Galili, R.; Mosberg, ; Gil-Ad, I.; Weizman, A.; Melamed, E.; Offen, D. Haloperidol-induced neurotoxicity--possible implications for tardive dyskinesia. J. Neural Transm. (Vienna), 2000, 107(4), 479-490.
[http://dx.doi.org/10.1007/s007020070089] [PMID: 11215758]
[33]
Correll, C.U.; Schenk, E.M. Tardive dyskinesia and new antipsychotics. Curr. Opin. Psychiatry, 2008, 21(2), 151-156.
[http://dx.doi.org/10.1097/YCO.0b013e3282f53132] [PMID: 18332662]
[34]
Kane, J.M.; Woerner, M.G.; Pollack, S.; Safferman, A.Z.; Lieberman, J.A. Does clozapine cause tardive dyskinesia? J. Clin. Psychiatry, 1993, 54(9), 327-330.
[PMID: 8104929]
[35]
Woods, S.W.; Morgenstern, H.; Saksa, J.R.; Walsh, B.C.; Sullivan, M.C.; Money, R.; Hawkins, K.A.; Gueorguieva, R.V.; Glazer, W.M. Incidence of tardive dyskinesia with atypical versus conventional antipsychotic medications: a prospective cohort study. J. Clin. Psychiatry, 2010, 71(4), 463-474.
[http://dx.doi.org/10.4088/JCP.07m03890yel] [PMID: 20156410]
[36]
Peluso, M.J.; Lewis, S.W.; Barnes, T.R.; Jones, P.B. Extrapyramidal motor side-effects of first- and second-generation antipsychotic drugs. Br. J. Psychiatry, 2012, 200(5), 387-392.
[http://dx.doi.org/10.1192/bjp.bp.111.101485] [PMID: 22442101]
[37]
Miller, D.D.; Caroff, S.N.; Davis, S.M.; Rosenheck, R.A.; McEvoy, J.P.; Saltz, B.L.; Riggio, S.; Chakos, M.H.; Swartz, M.S.; Keefe, R.S.; Stroup, T.S.; Lieberman, J.A. Extrapyramidal side-effects of antipsychotics in a randomised trial. Br. J. Psychiatry, 2008, 193(4), 279-288.
[http://dx.doi.org/10.1192/bjp.bp.108.050088] [PMID: 18827289]
[38]
Clayton, A.H. Antidepressant-induced tardive dyskinesia: review and case report. Psychopharmacol. Bull., 1995, 31(2), 259-264.
[PMID: 7491377]
[39]
Ganzini, L.; Casey, D.E.; Hoffman, W.F.; McCall, A.L. The prevalence of metoclopramide-induced tardive dyskinesia and acute extrapyramidal movement disorders. Arch. Intern. Med., 1993, 153(12), 1469-1475.
[http://dx.doi.org/10.1001/archinte.1993.00410120051007] [PMID: 8512437]
[40]
Kenney, C.; Hunter, C.; Davidson, A.; Jankovic, J. Metoclopramide, an increasingly recognized cause of tardive dyskinesia. J. Clin. Pharmacol., 2008, 48(3), 379-384.
[http://dx.doi.org/10.1177/0091270007312258] [PMID: 18223146]
[41]
Lau Moon Lin, M.; Robinson, P.D.; Flank, J.; Sung, L.; Dupuis, L.L. The safety of metoclopramide in children: a systematic review and meta-analysis. Drug Saf., 2016, 39(7), 675-687.
[http://dx.doi.org/10.1007/s40264-016-0418-9] [PMID: 27003816]
[42]
Rao, A.S.; Camilleri, M. Review article: metoclopramide and tardive dyskinesia. Aliment. Pharmacol. Ther., 2010, 31(1), 11-19.
[http://dx.doi.org/10.1111/j.1365-2036.2009.04189.x] [PMID: 19886950]
[43]
Wijemanne, S.; Jankovic, J.; Evans, R.W. Movement disorders from the use of metoclopramide and other antiemetics in the treatment of migraine. Headache, 2016, 56(1), 153-161.
[http://dx.doi.org/10.1111/head.12712] [PMID: 26573884]

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