Metabolomics for bioactivity assessment of natural products

Phytotherapy Research

Volumn 25, Issue 2, 2011, Pages 157-169

  Yuliana, Nancy Dewi ^a,b   Khatib, Alfi ^b,c   Choi, Young Hae ^a   Verpoorte, Robert ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

^b BOGOR AGRICULTURAL UNIVERSITY   (Indonesia)

^c UNIVERSITY PUTRA MALAYSIA   (Malaysia)

Author keywords

bioactivity; drug discovery; metabolomics; natural product

Indexed keywords

NATURAL PRODUCT; PLANT EXTRACT;

DRUG ACTIVITY; DRUG RESEARCH; DRUG STRUCTURE; HUMAN; METABOLITE; METABOLOMICS; NONHUMAN; PHYTOCHEMISTRY; REVIEW;

BIOLOGICAL PRODUCTS; DRUG DISCOVERY; METABOLOMICS; TECHNOLOGY, PHARMACEUTICAL;

EID: 79551667692     PISSN: 0951418X     EISSN: 10991573     Source Type: Journal    
DOI: 10.1002/ptr.3258     Document Type: Review

References (94)

1. 1H-NMR spectroscopy and chemometrics. Planta Med 68: 734-738.
2. 1H NMR spectroscopy and chemometrics. J Pharm Biomed Anal 35: 117-126.
3. Bajorath J,. 2002. Integration of virtual and high-throughput screening. Nat Rev Drug Discov 1: 882-894.
4. Beekwilder J, Jonker H, Meesters P, et al. 2005. Antioxidants in raspberry; On-line analysis links antioxidant activity to a diversity of individual metabolites. Agric Food Chem 53: 3313-3320.
5. Bhalla R, Narasimhan K, Swarup S,. 2005. Metabolomics and its role in understanding cellular responses in plants. Plant Cell Rep 24: 562-571.
6. Biao-Yi Z, Yu Y, Zeng-Liang Y,. 2008. Investigation of antimicrobial model of Hemsleya pengxianensis W.J. Chang and its main active component by metabolomics technique. J Ethnopharmacol 116: 89-95.
7. Bindseil KU, Jakupovic J, Wolf D, et al. 2001. Pure compound libraries; a new perspective for natural product based drug discovery. Drug Discov Today 6: 840-847.
8. Bleicher KH, Bohm H-J, Muller K, et al. 2003. Hit and lead generation: beyond high-throughput screening. Nat Rev Drug Discov 2: 369-378.
9. Böröczky K, Laatsch H, Döbler IW, et al. 2006. Cluster analysis as selection and dereplication tool for the identification of new natural compounds from large sample sets. Chem Biodiversity 3: 622-634.
10. Butler MS,. 2004. The role of natural product chemistry in drug discovery. J Nat Prod 67: 2141-2153.
11. Cardoso-Taketa AT, Pereda-Miranda R, Choi YH, et al. 2008. Metabolic profiling of the Mexican anxiolytic and sedative plant Galphimia glauca using nuclear magnetic resonance spectroscopy and multivariate data analysis. Planta Med 74: 1295-1301.
12. 1H NMR spectroscopy and principal component analysis. J Nat Prod 67: 953-957.
13. Choi YH, Sertic S, Kim HK, et al. 2005. Classification of Ilex species based on metabolomic fingerprinting using nuclear magnetic resonance and multivariate data analysis. J Agric Food Chem 53: 1237-1245.
14. Colquhoun IJ,. 2007. Use of NMR for metabolic profiling in plant systems. J Pestic Sci 32: 200-212.
15. Cui Q, Lewis IA, Hegeman AD, et al. 2008. Metabolite identification via the Madison Metabolomics Consortium Database. Nat Biotech 26: 162-164.
16. Dickson M, Gagnon JP,. 2004. Key factors in the rising cost of new drug discovery and development. Nat Rev Drug Discov 3: 417-429.
17. Dunn WB, Ellis DI,. 2005. Metabolomics: Current analytical platforms and methodologies. Trends Anal Chem 24: 285-294.
18. Entzeroth M,. 2003. Emerging trends in high-throughput screening. Curr Opin Pharmacol 3: 522-529.
19. Exarchou V, Krucker M, van Beek TA, et al. 2005. LC-NMR coupling technology: recent advancements and applications in natural products analysis. Magn Reson Chem 43: 681-687.
20. Famei Li, Xiumei Lu, Huiping Liu, et al. 2007. A pharmaco-metabonomic study on the therapeutic basis and metabolic effects of Epimedium brevicornum Maxim on hydrocortisone-induced rat using UPLC-MS. Biomed Chromatogr 21: 397-405.
21. Feher M, Schmidt JM,. 2003. Property distributions: Differences between drugs, natural products, and molecules from combinatorial chemistry. J Chem Inf Comput Sci 43: 218-227.
22. Fiehn O,. 2002. Metabolomics-the link between genotypes and phenotypes. Plant Mol Biol 48: 155-171.
23. Fiehn O, Kopka J, Trethewey RN, et al. 2000. Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry. Anal Chem 72: 3573-3580.
24. Gabrielsson J, Jonsson H, Airiau C, et al. 2006. OPLS methodology for analysis of pre-processing effects on spectroscopic data. Chemom Intell Lab Syst 84: 153-158.
25. Gõmez-Hens A, Aguilar-Caballos MP,. 2007. Modern analytical approaches to high-throughput drug discovery. Trends Anal Chem 26: 171-182.
26. Hall RD,. 2006. Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytol 169: 453-468.
27. Henkel T, Brunne RM, Müller H, et al. 1999. Statistical investigation into the structural complementarity of natural products and synthetic compounds. Angew Chem Int Ed 38: 643-647.
28. Ingkaninan K, Hazekamp A, de Best CM, et al. 2000. The application of HPLC with on-line coupled UV/MS: Biochemical detection for isolation of an acetylcholinesterase inhibitor from Narcissus Sir Winston Churchill. J Nat Prod 63: 803-806.
29. Jahangir M, Kim HK, Choi YH, et al. 2008. Metabolomic response of Brassica rapa submitted to pre-harvest bacterial contamination. Food Chem 107: 362-368.
30. Jiang H, Xie Z, Koo HJ, et al. 2006. Metabolic profiling and phylogenetic analysis of medicinal Zingiber species: Tools for authentication of ginger (Zingiber officinale Rosc.). Phytochemistry 67: 1673-1685.
31. Kell DB,. 2004. Metabolomics and systems biology: making sense of the soup. Curr Opin Microbiol 7: 296-307.
32. 1H-NMR spectroscopy and principal component analysis. Chem Pharm Bull 53: 105-109.
33. Koehn FE,. 2008. High impact technologies for natural products screening. In Natural Compounds as Drugs Volume I. Birkhäuser, Basel, 175-210.
34. Koehn FE, Carter GT,. 2005. The evolving role of natural products in drug discovery. Nat Rev Drug Discov 4: 206-220.
35. Krug D, Zurek G, Revermann O, et al. 2008. Discovering the hidden secondary metabolome of Myxococcus xanthus: a study of intraspecific diversity. Appl Environ Microbiol 74: 3058-3068.
36. Landro JA, Taylor ICA, Stirtan WG, et al. 2000. HTS in the new millennium: The role of pharmacology and flexibility. J Pharmacol Toxicol Methods 44: 273-289.
37. Leiss K, Choi Y, Abdel-Farid I, et al. 2009. NMR metabolomics of thrips (Frankliniella occidentalis) resistance in Senecio hybrids. J Chem Ecol 35: 219-229.
38. Li L, Sun B, Zhang Q, et al. 2008a. Metabonomic study on the toxicity of Hei-Shun-Pian, the processed lateral root of Aconitum carmichaelii Debx. (Ranunculaceae). J Ethnopharmacol 116: 561-568.
39. Li P, Qi L-W, Liu EH, et al. 2008b. Analysis of Chinese herbal medicines with holistic approaches and integrated evaluation models. Trends Anal Chem 27: 66-77.
40. Liu L, Li Y-F, Cheng Y-Y,. 2008. A method for the production and characterization of fractionated libraries from Chinese herbal formulas. J Chromatogr B 862: 196-204.
41. Ma C, Wang H, Lu X, et al. 2008. Metabolic fingerprinting investigation of Artemisia annua L. in different stages of development by gas chromatography and gas chromatography-mass spectrometry. J Chromatogr A 1186: 412-419.
42. Macarron R,. 2006. Critical review of the role of HTS in drug discovery. Drug Discov Today 11: 277-279.
43. McChesney JD, Venkataraman SK, Henri JT,. 2007. Plant natural products: Back to the future or into extinction? Phytochemistry 68: 2015-2022.
44. Mendes P, Camacho D, de la Fuente A,. 2005. Modelling and simulation for metabolomics data analysis. Biochem Soc Trans 33: 1427-1429.
45. Mishra KP, Ganju L, Sairam M, et al. 2008. A review of high throughput technology for the screening of natural products. Biomed Pharmacother 62: 94-98.
46. Moco S, Bino RJ, Vorst O, et al. 2006. A liquid chromatography-mass spectrometry-based metabolome database for tomato. Plant Physiol 141: 1205-1218.
47. Myers PL,. 1997. Will combinatorial chemistry deliver real medicines? Curr Opin Biotechnol 8: 701-707.
48. Newman DJ, Cragg GM,. 2007. Natural products as sources of new drugs over the last 25 years. J Nat Prod 70: 461-477.
49. Newman DJ, Cragg GM, Snader KM,. 2003. Natural products as sources of new drugs over the period 1981-2002. J Nat Prod 66: 1022-1037.
50. Nicholson JK, Connelly J, Lindon JC, et al. 2002. Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov 1: 153-161.
51. Nisbet LJ, Moore M,. 1997. Will natural products remain an important source of drug research for the future? Curr Opin Biotechnol 8: 708-712.
52. Nobeli I, Thornton JM,. 2006. A bioinformatician's view of the metabolome. Bioessays 28: 534-545.
53. Ortholand J-Y, Ganesan A,. 2004. Natural products and combinatorial chemistry: back to the future. Curr Opin Chem Biol 8: 271-280. (Pubitemid 38759402)
54. Pierens GK, Palframan ME, Tranter CJ, et al. 2005. A robust clustering approach for NMR spectra of natural product extracts. Magn Reson Chem 43: 359-365.
55. Pieters L, Vlietinck AJ,. 2005. Bioguided isolation of pharmacologically active plant components, still a valuable strategy for the finding of new lead compounds? J Ethnopharmacol 100: 57-60.
56. Politi M, Chávez MI, Cañada FJ, et al. 2005. Screening by NMR: A new approach for the study of bioactive natural products? The example of Pleurotus ostreatus hot water extract. Eur J Org Chem 2005: 1392-1396.
57. Poulsen S, Davis R, Keys T,. 2006. Screening a natural product-based combinatorial library using FTICR mass spectrometry. Bioorg Med Chem 14: 510-515. (Pubitemid 41767611)
58. 1H-NMR spectral data from complex pharmaceutical preparations: St. John's Wort. Planta Med 72: 556-563.
59. Rochfort S,. 2005. Metabolomics reviewed: A new omics platform technology for systems biology and implications for natural products research. J Nat Prod 68: 1813-1820.
60. Rollinger JM, Stuppner H, Langer T,. 2008. Virtual screening for the discovery of bioactive natural products. In Natural Compounds as Drugs Volume I, Petersen F, Amstutz R, (eds). Birkhäuser Verlag: Basel, 211-249.
61. Roos G, Röseler C, Büter KB, et al. 2004. Classification and correlation of St. John's Wort extracts by nuclear magnetic resonance spectroscopy, multivariate data analysis and pharmacological activity. Planta Med 70: 771-777.
62. Schenk T, Breel GJ, Koevoets P, et al. 2003. Screening of natural products extracts for the presence of phosphodiesterase inhibitors using liquid chromatography coupled online to parallel biochemical detection and chemical characterization. J Biomol Screen 8: 421-429.
63. Schmid I, Sattler I, Grabley S, et al. 1999. Natural products in high throughput screening: automated high-quality sample preparation. J Biomol Screen 4: 15-25.
64. Schobel U, Frenay M, Van Elswijk DA, et al. 2001. High resolution screening of plant natural product extracts for estrogen receptor a and f3 binding activity using an online HPLC-MS biochemical detection system. J Biomol Screen 6: 291-303.
65. Schroeder FC, Gibson DM, Churchill ACL, et al. 2007. Differential analysis of 2D NMR spectra: new natural products from a pilot-scale fungal extract library. Angew Chem Int Ed 119: 919-922.
66. Shyur L-F, Yang N-S,. 2008. Metabolomics for phytomedicine research and drug development. Curr Opin Chem Biol 12: 66-71.
67. Smith A,. 2002. Screening for drug discovery: The leading question. Nature 418: 453-459.
68. Sumner LW, Mendes P, Dixon RA,. 2003. Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 62: 817-836.
69. Thomas JJ, Shen Z, Crowell JE, et al. 2001. Desorption/ionization on silicon (DIOS): A diverse mass spectrometry platform for protein characterization. Proc Natl Acad Sci USA 98: 4932-4937. (Pubitemid 32397060)
70. Tikunov Y, Lommen A, de Vos CHR, et al. 2005. A novel approach for nontargeted data analysis for metabolomics: Large-scale profiling of tomato fruit volatiles. Plant Physiol 139: 1125-1137.
71. Ulrich-Merzenich G, Zeitler H, Jobst D, et al. 2007. Application of the '-Omic-' technologies in phytomedicine. Phytomedicine 14: 70-82.
72. Vaidyanathan S, Jones D, Broadhurst D, et al. 2005. A laser desorption ionisation mass spectrometry approach for high throughput metabolomics. Metabolomics 1: 243-250.
73. van der Greef J, Smilde AK,. 2005. Symbiosis of chemometrics and metabolomics: past, present, and future. J Chemometr 19: 376-386.
74. van der Kooy F, Verpoorte R, Meyer JJM,. 2008. Metabolomic quality control of claimed anti-malarial Artemisia afra herbal remedy and A. afra and A. annua plant extracts. S Afr J Bot 74: 186-189.
75. van Elswijk DA, Irth H,. 2002. Analytical tools for the detection and characterization of biologically active compounds from nature. Phytochem Rev 1: 427-439.
76. Verpoorte R,. 1998. Exploration of nature's chemodiversity: the role of secondary metabolites as leads in drug development. Drug Discov Today 3: 232-238.
77. Verpoorte R, Choi Y, Kim H,. 2007. NMR-based metabolomics at work in phytochemistry. Phytochem Rev 6: 3-14.
78. Verpoorte R, Choi Y, Mustafa N, et al. 2008. Metabolomics: back to basics. Phytochem Rev 7: 525-537.
79. Verpoorte R, Choi YH, Kim HK,. 2005. Ethnopharmacology and systems biology: A perfect holistic match. J Ethnopharmacol 100: 53-56.
80. Verpoorte R, Kim H, Choi Y,. 2006. Plants as source for medicines: New perspectives. In Medicinal and Aromatic Plants: Agricultural, Commercial, Ecological, Legal, Pharmacological and Social Aspects, Bogers R, Craker L, Lange D, (eds). Wageningen UR: Wageningen, 261-273.
81. Walters WP, Namchuk M,. 2003. Designing screens: how to make your hits a hit. Nat Rev Drug Discov 2: 259-266.
82. Wang M, Lamers R-JAN, Korthout HAAJ, et al. 2005. Metabolomics in the context of systems biology: bridging traditional Chinese medicine and molecular pharmacology. Phytother Res 19: 173-182.
83. Wang P, Liang Y, Zhou N, et al. 2007. Screening and analysis of the multiple absorbed bioactive components and metabolites of Dangguibuxue decoction by the metabolic fingerprinting technique and liquid chromatography/diode-array detection mass spectrometry. Rapid Commun Mass Spectrom 21: 99-106.
84. Wang Y, Tang H, Nicholson JK, et al. 2004. Metabolomic strategy for the classification and quality control of phytomedicine: a case study of chamomile flower (Matricaria recutita L.). Planta Med 70: 250-255.
85. Ward JL, Baker JM, Beale MH,. 2007. Recent applications of NMR spectroscopy in plant metabolomics. FEBS J 274: 1126-1131.
86. Williams G,. 2004. Advances in high throughput screening. Drug Discov Today 9: 515.
87. Williard X, Pop I, Bourel L, et al. 1996. Combinatorial chemistry: a rational approach to chemical diversity. Eur J Med Chem 31: 87-98.
88. Wold S, Sjöström M, Eriksson L,. 2001a. PLS-regression: a basic tool of chemometrics. Chemom Intell Lab Syst 58: 109-130.
89. Wold S, Trygg J, Berglund A, et al. 2001b. Some recent developments in PLS modeling. Chemom Intell Lab Syst 58: 131-150.
90. Wolfender J-L, Queiroz EF, Hostettmann K,. 2006. The importance of hyphenated techniques in the discovery of new lead compounds from nature. Expert Opin Drug Discov 1: 237-260.
91. Wu B, Yan S, Lin Z, et al. 2008. Metabonomic study on ageing: NMR-based investigation into rat urinary metabolites and the effect of the total flavone of Epimedium. Mol Biosyst 4: 855-861.
92. Yi L-Z, Yuan D-L, Liang Y-Z, et al. 2007. Quality control and discrimination of Pericarpium Citri Reticulatae and Pericarpium Citri Reticulatae Viride based on high-performance liquid chromatographic fingerprints and multivariate statistical analysis. Anal Chim Acta 588: 207-215.
93. Zhang X, Wu H, Liao P, et al. 2006. NMR-based metabonomic study on the subacute toxicity of aristolochic acid in rats. Food Chem Toxicol 44: 1006-1014.
94. Zhao X, Zhang Y, Meng X, et al. 2008. Effect of a traditional Chinese medicine preparation Xindi soft capsule on rat model of acute blood stasis: A urinary metabonomics study based on liquid chromatography-mass spectrometry. J Chromatogr B 873: 151-158.