Systems biology approaches and metabolomics for understanding Japanese traditional Kampo medicine

Current Pharmacogenomics and Personalized Medicine

Volumn 10, Issue 2, 2012, Pages 111-124

  Afendi, Farit Mochamad ^a   Katsuragi, Tetsuo ^a   Kato, Akira ^a   Nishihara, Noritaka ^b   Nakamura, Kensuke ^a   Nakamura, Yukiko ^a   Tanaka, Ken ^c   Morita, Aki Hirai ^a   Altaf Ul Amin, ^a   Takahashi, Hiroki ^a   Kanaya, Shigehiko ^a  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b OKAYAMA UNIVERSITY OF SCIENCE   (Japan)

^c UNIVERSITY OF TOYAMA   (Japan)

Author keywords

Bioinformatics; Convergence of innovations; Emerging biotechnologies; Japanese traditional Kampo medicine; KNApSAcK; Metabolomics; Personalized medicine and Asia Pacific; Systems biology

Indexed keywords

ACONITINE; ALANINE; ARTEMISININ; CAFFEINE; CANNABIS; CATECHIN; CINNAMALDEHYDE; CINNAMIC ACID; EPICATECHIN; EPIGALLOCATECHIN; EPIGALLOCATECHIN GALLATE; EUGENOL; FUROCOUMARIN; GLUTAMINE; GLYCYRRHIZIC ACID; HYPACONITINE; ISOLEUCINE; KAMPO; LEUCINE; LIQUIRITIN; MESACONITINE; ONONIN; PROTOCATECHUIC ACID; QUINIC ACID; SCOPOLAMINE; THEANINE; THREONINE; TRANSCRIPTOME; UNINDEXED DRUG; VALINE;

ACONITE; ANGELICA; ARTEMISIA ANNUA; ARTICLE; ASIA; ASTRAGALUS MEMBRANACEUS; BARLEY; CIMICIFUGA; CINNAMOMUM; CURCUMA; DATA BASE; DIOSCOREA BULBIFERA; EPHEDRA; GAS CHROMATOGRAPHY; GENOMICS; GLYCYRRHIZA URALENSIS; HERB; HUMAN; JAPAN; LIVER CANCER; LIVER CIRRHOSIS; LONICERA JAPONICA; MALARIA; MENSTRUATION DISORDER; METABOLOMICS; MULTIVARIATE ANALYSIS; NONHUMAN; PANAX; PERILLA FRUTESCENS; PERSONALIZED MEDICINE; PROTON NUCLEAR MAGNETIC RESONANCE; SYSTEMS BIOLOGY; TEA; TIME OF FLIGHT MASS SPECTROMETRY; TRADITIONAL MEDICINE; TRITICUM TURGIDUM;

EID: 84861748486     PISSN: 18756921     EISSN: 18756913     Source Type: Journal    
DOI: 10.2174/187569212800626377     Document Type: Article

References (91)

1. Ikegami F, Fujii Y, Satoh T. Toxicological considerations of Kampo medicines in clinical use. Toxicology 2004; 187: 221-8.
2. Shi J, Liu YL, Fang YX, et al. Traditional Chinese medicine in treatment of opiate addiction. Acta Pharmacol Sinica 2006; 27: 1303-8.
3. Ji HF, Li XJ, Zhang HY. Natural products and drug discovery. EMBO reports 2009; 10: 194-200.
4. Hijikata Y, Miyamae Y, Takatsu H, et al. Two Kampo medicines, Jidabokuippo and Hachimijiogan alleviate sprains, bruises and arthritis. eCAM 2007; 4: 463-7.
5. Ulrich-Merzenich G, Panek D, Zeitler H, et al. New perspectives for synergy research with the "omic"-technologies. Phytomedicine 2009; 16: 495-508.
6. Wagner H, Ulrich-Merzenich G. Synergy research: approaching a new generation of phytopharmaceuticals. Phytomedicine 2009; 16: 97-110.
7. Wagner H. Synergy research: approaching a new generation of phytopharmaceuticals. Fitoterapia 2011; 82: 34-7.
8. Nicholson JK, Wilson ID. Understanding 'global' systems biology: metabonomics and the continuum of metabolism. Nat Rev Drug Discov 2003; 2: 668-76.
9. Fiehn O. Metabolomics-the link between genotypes and phenotypes. Plant Mol Biol 2002; 48: 155-71.
10. Raamsdonk LM, Teusink B, Broadhurst D, et al. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol, 2001; 19: 45-50.
11. Fell DA. Beyond genomics. Trends Genet 2001; 17: 680-2.
12. Nicholson JK, Connelly J, Lindon JC. Innovation: Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov 2002; 1: 153-61.
13. Shockcor JP, Holmes E. Metabonomic applications in toxicity screening and disease diagnosis. Curr Top Med Chem 2002; 2: 35-51.
14. Kino H. Systems biology, a brief overview. Science 2002; 295: 1662-4.
15. Wang M, Lamers RJAN, Korthout HAAJ, et al. Metabolomics in the context of systems biology: bridging traditional Chinese medicine and molecular pharmacology. Phytother Res 2005; 19: 173-82.
16. Lindon JC, Nicholson JK. Holmes E. Contemporary issues in toxicology: the role of metabonomics in toxicology and its evaluation by the COMET project. Toxicol Appl Pharmacol 2003; 187: 137-46.
17. Li P, Yang LP, Gong YW. Application of systems biology technology in research of traditional Chinese medicine. J Trad Chin Med 2009; 29: 153-7.
18. Tan G, Lou Z, Jing J, et al. Screening and analysis of aconitum alkaloids and their metabolites in rat urine after oral administration of aconite roots extract using LC-TOFMS-based metabolomics. Biomed Chromatrogr 2011; 25: 1343-51.
19. Sun B, Wu S, Li L, et al. A metabolomic analysis of the toxicity of Aconitum sp. alkaloids in rats using gas chromatography/mass spectrometry. Rapid Commun Mass Spectrom 2009; 23: 1221-8.
20. Sun B, Li L, Wu S, et al. Metabolomics analysis of biofluids from rats treated with Aconitum alkaoids using nuclear magnetic resonance and gas chromatography/time-of flight mass spectrometry. Anal Biochem 2009; 395: 125-33.
21. Tianniam S, Tarachiwin L, Bamba T, et al. Metabolic profiling of Angelica acutiloba roots utilizing gas chromatography/time-offlight mass spectrometry for quality assessment based on cultivation area and cultivar via multivariate pattern recognition. J Biosci Bioeng 2008; 105: 659-9.
22. Hatip-Al-Khatib I, Egashira N, Mishima K, et al. Ditermination of the effectiveness of components of the herbal medicine Toki-Shakuyaku-San and fractions of Angelica acutiloba in improving the scopolamine-induced impairment of rat's spatial cognition in eight-armed radial maze test. J. Pharmacol Sci 2004; 96: 33-41.
23. Zhao Q, Murakami Y, Tohda M, et al. Preventive effect of Chotosan, a Kampo medicine, on transient ischemia-induced learning deficit is mediated by stimulation of muscarinic M1 but not nicotinic receptor. Biol Pharm Bull 2005; 28: 1873-8.
24. Murakami Y, Zhao Q, Harada K, et al. Choto-san a Kampo formula, improves chronic cerebral hypoperfusion-induced spatial learning deficit via stimulation of muascarinic M1 receptor. Pharmacol Biochem Behav 2005; 81: 616-25.
25. Shimizu M, Mitsuzawa T, Suzuki S, et al. Evaluation of Angelicae Radix (Touki) by the inhibitory effect on platelet aggregation. Chem Parm Bull 1991; 39: 2046-8.
26. Yim TK, Wu WK, Pak WF, et al. Myocardial protection against ischaemia reperfusion injury by a Polygomum multiflorum extract supplemented "Dang-Gui decoction for enriching blood", a compound formulation, ex vivo. Phytother Res 2000; 14: 195-9.
27. Liu J, Burdette JE, Xu H, et al. Evaluation of estrogenic activity of plant extracts for the potential trealment of menopausal symptoms. J Agric Food Chem 2001; 49: 2472-9.
28. Wilasrusmee C, Kittur S, Siddiqui J, et al. In vitro immunomodulatory effects of ten commonly used herbs on murine lymphocytes. J. Altern. Complement Med 2002; 8: 467-75.
29. Liao JF, Jan YM, Huang SY, et al. Evaluation with receptor binding assay on the water extracts of ten CNS-active Chinese herbal drugs. Proc Natl Sci Counc Repub China B 1995; 19: 151-8.
30. Mitsuhashi H, Nagai U, Muramatsu T, et al. Studied on the constituents of Umbelliferae plants II. Isolation of the active principles of Ligusticum root. Chem Pharm Bull 1960; 8: 243-5.
31. Kang SY, Lee KY, Sung SH, et al. Coumarins isolated from Angelica gigas inhibit acetylcholinesterase: structure-activity relationships. J Nat Prod 2001; 64: 683-5.
32. Hayasaka T, Katoh, A, Shojo M, et al. Investigation of the pharmacological effect of tokishakuyakusan by global transcriptional analysis in humans. J Trad Med 2010; 27(20): 66-77.
33. Zhao KJ, Dong TT, Tu PF, et al. Molecular genetic and chemical assessment of radix Angelica (Danggui) in China. J Agric Food Chem 2003; 51: 2576-83.
34. Hu YQ, Tan RX, Chu MY, et al. Apoptosis in human hepatoma cell line SMMC-7721 induced by water-soluble macromolecular components of Artemisia capillaris Thunberg. Cancer Sci 2000; 91: 113-7.
35. Yang CC, Lee MR, Hsu SI, et al. Supercritical fluids extraction of capillarisin form Artemisia capillaries and its inhibition of in vitro growth of hepatoma cells. J. Supercritical Fluids 2007; 42: 96-103.
36. Liu C, Zhao Y, Wang Y, et al. Artemisinin: current state and perspectives for biotechnological production of an antimalarial drug. Appl Microbiol Biotechnol 2006: 72; 11-20.
37. Baker M. Synthetic genomes: The next step for synthetic genome. Nature 2011; 473: 403-8.
38. Ro DK, Paradise EM, Ouellet M, et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 2006; 440: 940-3.
39. Tanaka K, Tamura T, Fukuda S, et al. Quality evaluation of Astragali Radix using a multivariate statistical approach. Phytochemistry 2008; 69: 2081-7.
40. Sinclair S. Chinese herbs: a clinical review of Astragalus, Ligusticum and Schizandrae. Altern Med Rev 1998; 3: 338-44.
41. Xu F, Zhang Y, Xiao S, et al. Absorption and metabolism of Astragali Radix decoction: in silico, in vitro, and a case study in vivo. Drug Metab Dispos 2006; 34: 913-24.
42. Ma XQ, Shi Q, Duan JA, et al. Chemical analysis of Radix Astragali (Huangqi) in China: a comparison with its adulterants and seasonal variations. J. Agric Food Chem 2002; 50: 4861-6.
43. Anetai M, Aoyagi M, Shibata T, et al. Preparation and chemical evaluation of Astragali Radix produced in Hokkaido (in Japanese). Natural Med 1998; 52: 10-3.
44. Lee JE, Lee BJ, Chung JO, et al. Geographical and climatic dependencies of green tea (Camellia sinensis) metabolites: A 1H NMR-based metabolomics study. J Agric Food Chem 2010; 58: 10582-9.
45. Lee JE, Lee BJ, Hwang JA, et al. Metabolic dependence of green tea on plucking positions revisited: a metabolomic study. J Agric Food Chem 2011; 59: 10579-85.
46. Russo EB. History of cannabis and its preparation in saga, science, and sobriquet. Chem Biodiversity 2007; 4: 1614-48.
47. Fischedic JT, Hazekamp A, Erkelens T, et al. Metabolic fingerprinting of Cannabis sativa L., cannabinoids and terpenoids for chemotaxonomic and drug standardization purposes. Phytochemistry 2010; 71: 2058-73.
48. Wang HK, Sakurai N, Shin C, et al. LC/TIS-MS fingerprint profiling of Cimicifuga species and analysis of 23-epi-26-deoxyactein in Cimicifuga racemosa commercial products. J Agric Food Chem 2005; 53: 1379-86.
49. He K, Pauli GF, Zheng B, et al. Cimicifuga species identification by high performance liquid chromatography-photodiode array/mass spectrometric/evaporative light scattering detection for quality control of black cohosh products. J Chromatogr A 2006; 1112: 241-54.
50. Yang J, Chen LH, Zhang Q, et al. Quality assessment of cortex cinnamomi by HPLC chemical fingerprint, principle component analysis and cluster analysis. J. Sep Sci 2007; 30: 1276-83.
51. Xiang Z, Wang XQ, Cai XJ, et al. Metabolomics study on quality control and discrimination of three curcuma species based on gas chromatograph-mass spectrometry. Phytochem Anal 2011; 22: 411-8.
52. Cao H, Sasaki Y, Fushimi H, et al. Molecular analysis of medicinally-used Chinese and Japanese Curcuma based on 18S rRNA gene and trnK gene sequence. Biol Pharm Bull 2001; 24(2): 1389-94.
53. Tanaka K, Kuba Y, Ina A, et al. Prediction of cyclooxygenase inhibitory activity of curcuma rhizome from chromatograms by multivariate analysis. Chem Pharm Bull 2008; 56: 936-40.
54. Liu Y, Huang R, Liu L, et al. Metabolomics study of urine from Sprague-Dawley rats exposed to Huang-yao-zi using 1H NMR spectroscopy. J Pharmaceutical Biomed Anal 2010; 52: 136-41.
55. Kim KH, Choi SU, Choi SZ, et al. Withanolides from the rhizomes of Dioscorea japonica and their cytotoxicity. J Agric Food Chem 2011; 59: 6980-4.
56. 1H-NMR spectroscopy and principal component analysis. Chem Pharm Bull 2005; 53(1): 105-9.
57. Kojima M, Hayashi S, Shibata T, et al. Variation of glycyrrhizin and liquiritin contents within a population of 5-year-old licorice (Glycyrrhiza uralensis) plants cultivated under the same coditions. Biol Pharm Bull 2011; 34(8): 1334-7.
58. Roessner U, Patterson JH, Forbes MG, et al. An investigation of boron toxicity in barley using metabolomics. Plant Physiol 2006; 142: 1087-101.
59. Bollina V, Kumaraswamy GK, Kushalappa AC, et al. Mass spectrometry-based metabolomics application to identify quantitative resistance-related metabolites in barley against Fusarium head blight. Mol Plant Pathol 2010; 11: 769-82.
60. Bennett MD, Smith JB. Nuclear DNA amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci 1976; 274: 227-74.
61. Wicker T, Taudien S, Houben, A, et al. A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant J 2009; 59: 712-22.
62. Sun C, Teng Y, Li G. Metabonomics study of the protective effects of Lonicera japonica extract on acute liver injury in dimethylnitrosamine treated rats. J Pharm Biomed Anal 2010; 53: 98-102.
63. Lee MH, Yoon S, Moon JO, et al. The flavonoid naringenin inhibits dimethylnitrosamine-induced liver damage in rats. Biol Pharm Bull 2004; 27: 72-6.
64. Lange BM, Mahmoud SS, Wildung MR, et al. Improving peppermint essential oil yield and composition by metabolic engineering. Proc Natl Acad Sci USA 2011; 108: 16944-9.
65. Yamazaki M, Nakajima J, Yamanashi M, et al. Metabolomics and differential gene expression in anthocyanin chemo-varietal forms of Perilla frutescens. Phytochemistry 2003; 62: 987-95.
66. Angelova N, Kong HW, van der Heijden R, et al. Recent methodology in the phytochemical analysis of ginseng, Phytochem Anal 2008; 19: 2-16.
67. Yang SY, Kim HK, Lafeber AWM, et al. Application of twodimensional nuclear magnetic resonance spectroscopy to quality control of ginseng commercial products. Planta Med 2006; 72: 364-9.
68. Krugman T, Peleg Z, Quansah L, et al. Alteration in expression of hormone-related genes in wild emmer wheat roots associated with drought adaptation mechanisms. Funct Integr Genomics 2011; 11(4): 565-83.
69. Xue GP, McIntyre CL, Glassop D, et al. Use of expression analysis to dissect alterations in carbohydrate metabolism in wheat leaves during drought stress. Plant Mol Biol 2008; 67: 197-214.
70. 2 enrichment on sysnthesis of some primary and secondary metabolites in ginger (Zingiber officinale Roscoe). Int J Mol Sci 2011; 12: 1101-14.
71. Okada T, Afendi FM, Altaf-Ul-Amin M, et al. Metabolomics of medicinal plants: the importance of multivariate analysis of analytical chemical data. Curr Comp Aided Drug Design 2010; 6: 179-96.
72. Nandagopal N, Elowitz MB. Synthetic biology: integrated gene circuits. Science 2011; 333: 1244-8.
73. Gao H, Zhuo Y, Ashforth E, et al. Engineering of a genomereduced host: practical application of synthetic biology in the overproduction of desired secondary metabolites. Protein Cell 2010: 1(7); 621-6.
74. Katoh, A. Fukuda S, Fukusaki E, et al. Systems biology in a commercial quality study of the Japanese Angelica Radix: toward an understanding of traditional medicinal plants. Am J Chinese Med 2011; 39: 757-77.
75. Afendi, FM, Okada, T, Yamazaki, M, et al. KNApSAcK Family Databases: Integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol 2012; 53: e1.1-12.
76. Adnyana IK, Soemardji AA. Evaluation of pharmacological efficacy of Jamu medicine. Toyama: University of Toyama Institute of Natural Medicine 2007.
77. Pramono S. Jamu in Indonesian daily life and industry. Toyama: University of Toyama Institute of Natural Medicine 2007.
78. Sangat HM, Zuhud EAM, Damayanti EK. Kamus Penyakit dan Tumbuhan Obat Indonesia: Etnofitomedika (in Javanese). Jakarta: Yayasan Obor Indonesia 2000.
79. Penso G. WHO inventory of medicinal plants used in different countries. Geneva: WHO 1980.
80. Watanabe K, Matsuura K, Gao P, et al. Traditional Japanese Kampo medicine: clinical research between modernity and traditional medicine-The state of research and methodological suggestions for the future. eCAM 2011; (doi:10.1093/ecam/neq067)
81. Terasawa K. Evidence-based reconstruction of Kampo medicine: Part I-Is Kampo CAM? eCAM 2004; 1(1): 11-6.
82. Terasawa K. Evidence-based reconstruction of Kampo medicine: Part II-The concept of Sho. eCAM 2004; 1(2): 119-23.
83. Terasawa K. Evidence-based reconstruction of Kampo medicine: Part III-How should Kampo be evaluated? eCAM 2004; 1(3): 219-22.
84. Centler F, Kaleta C, di Fenizio PS, et al. Computing chemical organizations in biological networks. Bioinformatics 2008; 24: 1611-8.
85. Sanchez R, Morgado E, Grau R. A genetic code Boolean structure I. The meaning of Boolean deductions. Bull Math Biol 2005; 67: 1-14.
86. Amemiya CT, Power TP, Prohaska SJ. Complex Hox cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proc Natl Acad Sci USA 2010; 23: 3622-7.
87. Randic M, Lers N, Vukicevic D, et al. Canonical labeling of proteome maps. J Proteome Res 2005; 4: 1347-52.
88. Sontrop HMJ, Verhaegh WFJ, Reinders MJT, et al. An evaluation protocol for subtype-specific breast cancer event prediction. PLoS One 2011; 6: e21681.
89. Afendi FM, Altaf-Ul-Amin M, Kanaya S. Permutation test in evaluating the significance of plants in PLS-DA model of Jamu ingredients. The 7th Asian Crop Science Association Conference, ACSAC 2011 (September 27-30 2011, Bogor Agricultural University, Bogor, Indonesia) 2011.
90. Yun H, Hou L, Song M, et al. Genomics and Traditional Chinese Medicine: A new driver for novel molecular-targeted personalized medicine? Curr Pharmacogenomics Person Med 2012; 10(1): 16-21.
91. Ozdemir V, Fisher E, Dove ES, et al. End of the beginning and public health pharmacogenomics: Knowledge in 'Mode 2' and P5 medicine. Curr Pharmacogenomics Person Med 2012; 10(1): 1-6.