Towards a bioinformatics analysis of anti-alzheimer's herbalmedicines from a target network perspective

Briefings in Bioinformatics

Volumn 14, Issue 3, 2013, Pages 327-343

  Sun, Yi ^a   Zhu, Ruixin ^a   Ye, Hao ^b   Tang, Kailin ^b   Zhao, Jing ^b   Chen, Yujia ^a   Liu, Qi ^a   Cao, Zhiwei ^a  

^a TONGJI UNIVERSITY   (China)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

Alzheimer's disease (AD); Herbal medicine; Network pharmacology; Therapeutic target

Indexed keywords

ALZHEIMER DISEASE; ALZHEIMER'S DISEASE (AD); ARTICLE; BIOLOGY; FOOD AND DRUG ADMINISTRATION; HERBAL MEDICINE; HUMAN; NETWORK PHARMACOLOGY; PHYTOTHERAPY; THERAPEUTIC TARGET; UNITED STATES;

ALZHEIMER'S DISEASE (AD); HERBAL MEDICINE; NETWORK PHARMACOLOGY; THERAPEUTIC TARGET;

ALZHEIMER DISEASE; COMPUTATIONAL BIOLOGY; HERBAL MEDICINE; HUMANS; PHYTOTHERAPY; UNITED STATES; UNITED STATES FOOD AND DRUG ADMINISTRATION;

EID: 84878485512     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbs025     Document Type: Article

References (109)

1. Kitano H. A robustness-based approach to systems-oriented drug design. Nat RevDrug Discov 2007;6:202-10.
2. Reddy PH, McWeeney S, Park BS, et al. Gene expression profiles of transcripts in amyloid precursor protein transgenic mice: up-regulation of mitochondrial metabolism and apoptotic genes is an early cellular change in Alzheimer's disease. HumMol Genet 2004;13:1225-40.
3. LaFerla FM. Pathways linking Abeta and tau pathologies. Biochem SocTrans;38:993-5.
4. Citron M. Alzheimer's disease: strategies for disease modification. Nat RevDrug Discov 2010;9:387-98.
5. Bajda M, Guzior N, Ignasik M, et al. Multi-target-directed ligands in Alzheimer's disease treatment. Curr Med Chem 2011;18:4949-75.
6. Salawu FK, Umar JT, Olokoba AB. Alzheimer's disease: a review of recent developments. AnnAfrMed 2011;10:73-9.
7. Melnikova I. Therapies for Alzheimer's disease. Nat Rev Drug Discov 2007;6:341-2.
8. Luo Y, Smith JV, Paramasivam V, et al. Inhibition of amyloid-beta aggregation and caspase-3 activation by the Ginkgo biloba extract EGb761. Proc Natl Acad Sci USA 2002;99:12197-202.
9. Watanabe CM, Wolffram S, Ader P, et al. The in vivo neuromodulatory effects of the herbal medicine ginkgo biloba. Proc Natl Acad Sci USA 2001;98:6577-580.
10. Wu Y, Wu Z, Butko P, etal. Amyloid-beta-induced pathological behaviors are suppressed by Ginkgo biloba extract EGb 761 and ginkgolides in transgenic Caenorhabditis elegans. JNeurosci 2006;26:13102-13.
11. Perry NS, Bollen C, Perry EK, et al. Salvia for dementia therapy: review of pharmacological activity and pilot tolerability clinical trial. Pharmacol Biochem Behav 2003;75:651-9.
12. Little JT, Walsh S, Aisen PS. An update on huperzine A as a treatment for Alzheimer's disease. Expert Opin InvestigDrugs 2008;17:209-15.
13. Anekonda TS, Reddy PH. Can herbs provide a new generation of drugs for treating Alzheimer's disease?. Brain Res Brain Res Rev 2005;50:361-76.
14. Bermudez-Lugo JA, Rosales-Hernandez MC, Deeb O, et al. In silico methods to assist drug developers in acetylcholinesterase inhibitor design. Curr Med Chem 2011;18: 1122-36.
15. Chekmarev D, Kholodovych V, Kortagere S, et al. Predicting inhibitors of acetylcholinesterase by regression and classification machine learning approaches with combinations of molecular descriptors. Pharm Res 2009;26: 2216-24.
16. Al-Rashid ZF, Hsung RP. (p)-Arisugacin A-computational evidence of a dual binding site covalent inhibitor of acetylcholinesterase. BioorgMedChemLett 2011;21:2687-91.
17. da Silva VB, de Andrade P, Kawano DF, et al. In silico design and search for acetylcholinesterase inhibitors in Alzheimer's disease with a suitable pharmacokinetic profile and low toxicity. FutureMed Chem 2011;3:947-60.
18. Adhami HR, Linder T, Kaehlig H, et al. Catechol alkenyls from Semecarpus anacardium: acetylcholinesterase inhibition and binding mode predictions. J Ethnopharmacol 2012;139:142-8.
19. John S, Thangapandian S, Sakkiah S, et al. Potent BACE-1 inhibitor design using pharmacophore modeling, in silico screening and molecular docking studies. BMC Bioinformatics 2011;12(Suppl. 1):S28.
20. Vijayan RS, Prabu M, Mascarenhas NM, et al. Hybrid structure-based virtual screening protocol for the identification of novel BACE1 inhibitors. JChem InfModel 2009;49: 647-57.
21. Monceaux CJ, Hirata-Fukae C, Lam PC, et al. Triazole-linked reduced amide isosteres: an approach for the fragment-based drug discovery of anti-Alzheimer's BACE1 inhibitors. BioorgMed Chem Lett 2011;21:3992-6.
22. Yang XG, Lv W, Chen YZ, et al. In silico prediction and screening of gamma-secretase inhibitors by molecular descriptors and machine learning methods. J Comput Chem 2010;31:1249-58.
23. Lamb J, Crawford ED, Peck D, etal. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 2006;313:1929-35.
24. Williams G. A searchable cross-platform gene expression database reveals connections between drug treatments and disease. BMCGenomics 2012;13:12.
25. Kong W, Mou X, Hu X. Exploring matrix factorization techniques for significant genes identification of Alzheimer's disease microarray gene expression data. BMC Bioinformatics 2011;12(Suppl 5):S7.
26. Huang Y, Sun X, Hu G. An integrated genetics approach for identifying protein signal pathways of Alzheimer's disease. ComputMethods Biomech Biomed Eng 2011;14:371-8.
27. Yanashima R, Kitagawa N, Matsubara Y, et al. Network features and pathway analyses of a signal transduction cascade. FrontNeuroinform 2009;3:13.
28. Miller JA, Oldham MC, Geschwind DH. A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci 2008;28:1410-20.
29. Li J, Zhu X, Chen JY. Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLoSComput Biol 2009;5: e1000450.
30. Yang L, Chen J, Shi L, et al. Identifying unexpected therapeutic targets via chemical-protein interactome. PLoS One 2010;5:e9568.
31. Perreau VM, Orchard S, Adlard PA, et al. A domain level interaction network of amyloid precursor protein and Abeta of Alzheimer's disease. Proteomics 2010;10:2377-95.
32. Chen JY, Shen C, Sivachenko AY. Mining Alzheimer disease relevant proteins from integrated protein interactome data. Pac Symp Biocomput 2006;367-78.
33. Mathur S, Dinakarpandian D. Drug repositioning using disease associated biological processes and network analysis of drug targets. AMIA Annu Symp Proc 2011;2011:305-11.
34. Zhao S, Iyengar R. Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. Annu Rev PharmacolToxicol 2012;52:505-21.
35. Berger SI, Iyengar R. Network analyses in systems pharmacology. Bioinformatics 2009;25:2466-72.
36. Zhao J, Jiang P, Zhang W. Molecular networks for the study of TCM pharmacology. Brief Bioinform 2010;11: 417-30.
37. Mazza M, Capuano A, Bria P, et al. Ginkgo biloba and donepezil: a comparison in the treatment of Alzheimer's dementia in a randomized placebo-ccontrolled double-blind study. EurJNeurol 2006;13:981-5.
38. Tavazoie S, Hughes JD, Campbell MJ, et al. Systematic determination of genetic network architecture. Nat Genet 1999;22:281-5.
39. Erhardt RA, Schneider R, Blaschke C. Status of text-mining techniques applied to biomedical text. Drug DiscovToday 2006;11:315-25.
40. Truffinet P, Bordet R, Menard J. Relevance of the evaluation criteria used in clinical trials for Alzheimer's disease. Therapie 2009;64:139-8.
41. Wesnes KA. Assessing change in cognitive function in dementia: the relative utilities of the Alzheimer's disease assessment scale-cognitive subscale and the cognitive drug research system. NeurodegenerDis 2008;5:261-3.
42. Flaks MK, Forlenza OV, Pereira FS, et al. Short cognitive performance test: diagnostic accuracy and education bias in older Brazilian adults. Arch Clin Neuropsychol 2009; 24:301-6.
43. Schneider LS, Clark CM, Doody R, etal. ADCS Prevention Instrument Project: ADCS-clinicians' global impression of change scales (ADCS-CGIC), self-rated and study partner-rated versions. Alzheimer Dis Assoc Disord 2006;20: S124-38.
44. Lancu I, Olmer A. [The minimental state examination-an up-to-date review]. Harefuah 2006;145:687-90, 701.
45. Ji ZL, Zhou H, Wang JF, et al. Traditional Chinese medicine information database. J Ethnopharmacol 2006;103:501.
46. Zhang Z, Wang X, Chen Q, et al. [Clinical efficacy and safety of huperzine Alpha in treatment of mild to moderate Alzheimer disease, a placebo-ccontrolled, double-blind, randomized trial]. ZhonghuaYi Xue ZaZhi 2002;82:941-4.
47. Ye H, Ye L, Kang H, et al. HIT: linking herbal active ingredients to targets. Nucleic Acids Res 2011;39:D1055-9.
48. Yildirim MA, Goh KI, Cusick ME, et al. Drug-target network. Nat Biotechnol 2007;25:1119-26.
49. Hamosh A, Scott AF, Amberger JS, et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005;33: D514-7.
50. Keshava Prasad TS, Goel R, Kandasamy K, et al. Human Protein Reference Database-2009 update. Nucleic Acids Res 2009;37:D767-72.
51. Ceol A, Chatr Aryamontri A, Licata L, et al. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 2009;38:D532-9.
52. Kerrien S, Alam-Faruque Y, Aranda B, et al. IntAct-open source resource for molecular interaction data. NucleicAcids Res 2007;35:D561-5.
53. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, et al. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 2011;39:D698-704.
54. Xenarios I, Salwinski L, Duan XJ, etal. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002;30: 303-5.
55. Mewes HW, Frishman D, Guldener U, et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res 2002;30:31-4.
56. Maslova S, Sneppen K, Zaliznyaka A. Detection of topological patterns in ccomplex networks: correlation profile of the internet. Phys AStatTheor Phys 2003;333:529-40.
57. Wishart DS, Knox C, Guo AC, et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 2006;34:D668-72.
58. Birks J. Cholinesterase inhibitors for Alzheimer's disease. CochraneDatabase SystRev 2006;1:CD005593.
59. Robinson DM, Keating GM. Memantine: a review of its use in Alzheimer's disease. Drugs 2006;66:1515-34.
60. Qi WN, Chen LE, Zhang L, et al. Reperfusion injury in skeletal muscle is reduced in inducible nitric oxide synthase knockout mice. JAppl Physiol 2004;97:1323-8.
61. Colton CA, Wilcock DM, Wink DA, et al. The effects of NOS2 gene deletion on mice expressing mutated human AbetaPP. JAlzheimersDis 2008;15:571-87.
62. Lashuel HA, Hartley D, Petre BM, et al. Neurodegenerative disease: amyloid pores from pathogenic mutations. Nature 2002;418:291.
63. Firuzi O, Zhuo J, Chinnici CM, et al. 5-Lipoxygenase gene disruption reduces amyloid-beta pathology in a mouse model of Alzheimer's disease. FASEB J 2008;22:1169-78.
64. Manev H, Chen H, Dzitoyeva S, etal. Cyclooxygenases and 5-lipoxygenase in Alzheimer's disease. ProgNeuropsychopharmacol Biol Psychiatry 2011;35:315-9.
65. Gnjec A, D'Costa KJ, Laws SM, et al. Association of alleles carried at TNFA-850 and BAT1-22 with Alzheimer's disease. J Neuroinflammation 2008;5:36.
66. Luckhaus C, Sand PG. Estrogen Receptor 1 gene (ESR1) variants in Alzheimer's disease. Results of a meta-analysis. Aging Clin Exp Res 2007;19:165-8.
67. Liu HP, Lin WY, Wu BT, et al. Evaluation of the poly(ADP-ribose) polymerase-1 gene variants in Alzheimer's disease. JClin Lab Anal;24:182-6.
68. Ogata H, Goto S, Sato K, et al. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999;27:29-34.
69. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000;28:27-30.
70. Drakkar Soft. Pathway Diagrammer. http://download.cnet. com/Pathway-Diagrammer/3000-2054_4-10844649.html (Oct 24th, 2009-9th Jan, 2012).
71. Furey ML. The prominent role of stimulus processing: cholinergic function and dysfunction in cognition. Curr Opin Neurol 2011;24:364-70.
72. Goussakov I, Miller MB, Stutzmann GE. NMDA-mediated Ca(2p) influx drives aberrant ryanodine receptor activation in dendrites of young Alzheimer's disease mice. J Neurosci 2010;30:12128-37.
73. Wang R, Yan H, Tang XC. Progress in studies of huperzine A, a natural cholinesterase inhibitor from Chinese herbal medicine. Acta Pharmacol Sin 2006;27:1-26.
74. Gordon RK, Nigam SV, Weitz JA, et al. The NMDA receptor ion channel: a site for binding of Huperzine A. JAppl Toxicol 2001;21(Suppl. 1):S47-51.
75. Kim HK, Park HR, Lee JS, et al. Down-regulation of iNOS and TNF-alpha expression by kaempferol via NF-kappaB inactivation in aged rat gingival tissues. Biogerontology 2007; 8:399-408.
76. Brathe A, Gundersen LL, Malterud KE, et al. 6-substituted purines as inhibitors of 15-lipoxygenase; a structure-activity study. Arch Pharm 2005;338:159-66.
77. Kawai M, Hirano T, Higa S, et al. Flavonoids and related compounds as anti-allergic substances. Allergol Int 2007;56: 113-23.
78. Shishodia S, Majumdar S, Bcanerjee S, et al. Ursolic acid inhibits nuclear factor-kappaB activation induced by carcinogenic agents through suppression of IkappaBalpha kinase and p65 phosphorylation: correlation with down-regulation of cyclooxygenase 2, matrix metalloproteinase 9, and cyclin D1. Cancer Res 2003;63:4375-83.
79. Akiyama H, Barger S, Barnum S, et al. Inflammation and Alzheimer's disease. Neurobiol Aging 2000;21:383-421.
80. Swardfager W, Lanctot K, Rothenburg L, et al. A meta-analysis of cytokines in Alzheimer's disease. Biol Psychiatry 2010;68:930-41.
81. Chen D, Daniel KG, Chen MS, et al. Dietary flavonoids as proteasome inhibitors and apoptosis inducers in human leukemia cells. Biochem Pharmacol 2005;69:1421-32.
82. Leung LK, Po LS, Lau TY, et al. Effect of dietary flavonols on oestrogen receptor transactivation and cell death induction. Br J Nutr 2004;91:831-9.
83. Lim H, Kim HP. Inhibition of mammalian collagenase, matrix metalloproteinase-1, by naturally-occurring flavonoids. PlantaMed 2007;73:1267-74.
84. Geraets L, Moonen HJ, Brauers K, et al. Dietary flavones and flavonoles are inhibitors of poly(ADP-ribose)- polymerase-1 in pulmonary epithelial cells. J Nutr 2007; 137:2190-5.
85. Hayeshi R, Mutingwende I, Mavengere W, et al. The inhibition of human glutathione S-transferases activity by plant polyphenolic compounds ellagic acid and curcumin. Food ChemToxicol 2007;45:286-95.
86. Hsu CL, Lo WH, Yen GC. Gallic acid induces apoptosis in 3T3-L1 pre-adipocytes via a Fas- and mitochondrialmediated pathway. JAgric FoodChem 2007;55:7359-65.
87. Choi YH, Kong KR, Kim YA, et al. Induction of Bax and activation of caspases during beta-sitosterol-mediated apoptosis in human colon cancer cells. Int J Oncol 2003;23: 1657-62.
88. Behrens MI, Lendon C, Roe CM. A common biological mechanism in cancer and Alzheimer's disease? Curr Alzheimer Res 2009;6:196-204.
89. Fang XK, Gao J, Zhu DN. Kaempferol and quercetin isolated from Euonymus alatus improve glucose uptake of 3T3-L1 cells without adipogenesis activity. Life Sci 2008;82:615-22.
90. Logendra S, Ribnicky DM, Yang H, et al. Bioassay-guided isolation of aldose reductase inhibitors from Artemisia dracunculus. Phytochemistry 2006;67:1539-46.
91. Jones A, Kulozik P, Ostertag A, et al. Common pathological processes and transcriptional pathways in Alzheimer's disease and type 2 diabetes. JAlzheimersDis 2009;16:787-808.
92. Ramana KV. Aldose reductase: new insights for an old enzyme. Biomol Concepts 2011;2:103-14.
93. Ramana KV, Srivastava SK. Aldose reductase: a novel therapeutic target for inflammatory pathologies. IntJ BiochemCell Biol 2010;42:17-20.
94. Yu JT, Chang RC, Tan L. Calcium dysregulation in Alzheimer's disease: from mechanisms to therapeutic opportunities. ProgNeurobiol 2009;89:240-55.
95. Li L, Stanton JD, Tolson AH, et al. Bioactive terpenoids and flavonoids from Ginkgo biloba extract induce the expression of hepatic drug-metabolizing enzymes through pregnane X receptor, constitutive androstane receptor, and aryl hydrocarbon receptor-mediated pathways. Pharm Res 2009; 26:872-82.
96. Ansari MA, Abdul HM, Joshi G, et al. Protective effect of quercetin in primary neurons against Abeta(1-42): relevance to Alzheimer's disease. JNutr Biochem 2009;20:269-75.
97. Babiloni C, Babiloni F, Carducci F, et al. Movement-related electroencephalographic reactivity in Alzheimer disease. Neuroimage 2000;12:139-46.
98. Roe CM, Behrens MI, Xiong C, et al. Alzheimer disease and cancer. Neurology 2005;64:895-8.
99. Arvanitakis Z, Wilson RS, Bienias JL, et al. Diabetes mellitus and risk of Alzheimer disease and decline in cognitive function. Arch Neurol 2004;61:661-6.
100. Rangel-Ordonez L, Noldner M, Schubert-Zsilavecz M, et al. Plasma levels and distribution of flavonoids in rat brain after single and repeated doses of standardized Ginkgo biloba extract EGb 761(R). Planta Med 2010;76: 1683-90.
101. Kuhn M, Campillos M, Letunic I, et al. A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol 2010;6:343.
102. Ji ZL, Han LY, Yap CW, et al. Drug adverse reaction target database (DART): proteins related to adverse drug reactions. Drug Saf 2003;26:685-90.
103. Atias N, Sharan R. An algorithmic framework for predicting side effects of drugs. JComput Biol 2011;18:207-18.
104. Lee S, Lee KH, Song M, et al. Building the process-drugside effect network to discover the relationship between biological processes and side effects. BMC Bioinformatics 2011;12(Suppl. 2):S2.
105. Ma C, Kang H, Liu Q, et al. Insight into potential toxicity mechanisms of melamine: an in silico study. Toxicology 2011;283:96-100.
106. Brouwers L, Iskar M, Zeller G, et al. Network neighbors of drug targets contribute to drug side-effect similarity. PLoS One 2011;6:e22187.
107. Goh KI, Cusick ME, Valle D, et al. The human disease network. ProcNatl Acad SciUSA 2007;104:8685-90.
108. Zhang X, Zhang R, Jiang Y, et al. The expanded human disease network combining protein-protein interaction information. EurJ Hum Genet 2011;19:783-8.
109. Wyss-Coray T, Rogers J. Inflammation in Alzheimer disease-a brief review of the basic science and clinical literature. Cold SpringHarb PerspectMed 2012;2:a006346.