Dereplication of microbial extracts and related analytical technologies

Journal of Antibiotics

Volumn 67, Issue 5, 2014, Pages 353-360

  Ito, Tatsuya ^a   Masubuchi, Miyako ^a  

^a CHUGAI PHARMACEUTICAL CO LTD   (Japan)

Author keywords

Dereplication; Microbial extract; Profiling; Quantification; Structure elucidation; UHPLC MS

Indexed keywords

ACETONITRILE; NATURAL PRODUCT;

ANALYTIC METHOD; CHEMICAL PROCEDURES; DEREPLICATION; ELECTROSPRAY; FERMENTATION; FRACTIONATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; REVIEW; SCREENING TEST; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; ULTRAVIOLET SPECTROSCOPY; X RAY CRYSTALLOGRAPHY;

ANTI-BACTERIAL AGENTS; BACTERIA; BIOLOGICAL PRODUCTS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DNA REPLICATION; FERMENTATION; FUNGI; GENE LIBRARY; HIGH-THROUGHPUT SCREENING ASSAYS; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY;

EID: 84901500239     PISSN: 00218820     EISSN: 18811469     Source Type: Journal    
DOI: 10.1038/ja.2014.12     Document Type: Review

References (74)

1. Demain, A. L. & Sanchez, S. Microbial drug discovery: 80 years of progress. J. Antibiot. 62, 5-16 (2009
2. Liu, X. et al. Bioprospecting microbial natural product libraries from the marine environment for drug discovery. J. Antibiot. 63, 415-422 (2010
3. O mura, S. Microbial metabolites: 45 years of wandering, wondering and discovering. Tetrahedron 67, 6420-6459 (2011
4. Newman, D. J. & Cragg, G. M. Natural products as sources of new drugs over the 30 years from 1981 to 2010. J. Nat. Prod. 75, 311-335 (2012
5. Cragg, G. M. & Newman, D. J. Natural products: A continuing source of novel drug leads. Biochim. Biophys. Acta 1830, 3670-3695 (2013
6. Bérdy, J. Thoughts and facts about antibiotics: Where we are now and where we are heading. J. Antibiot. 65, 385-395 (2012
7. Henrich, C. J. & Beutler, J. Matching the power of high throughput screening to the chemical diversity of natural products. Nat. Prod. Rep. 30, 1284-1298 (2013
8. Takagi, M. & Shin-Ya, K. Construction of a natural product library containing secondary metabolites produced by actinomycetes. J. Antibiot. 65, 443-447 (2012
9. Langlykke, A. CRC Handbook of Antibiotic Compounds (Bardy, J. et al.) (CRC, Boca Raton, FL, 1980
10. Vanmiddlesworth, F. & Cannell, R. J. P. Dereplication and partial identification of natural products. Nat. Prod. Isolation 4, 279-327 (1998
11. Hook, D. J., More, C. F., Yacoucci, J. J., Dubay, G. & O'Connor, S. Integrated biologicalphysicochemical system for the identification of antitumor compounds in fermentation broths. J. Chromatogr. 385, 99-108 (1987
12. Hook, D. J. Approaches to automating the dereplication of bioactive natural products- The key step in high throughput screening of bioactive materials from natural sources. J. Biomol. Screen. 2, 145-152 (1997
13. Ibrahim, A., Yang, L. & Johnston, C. Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery. Proc. Natl Acad. Sci. USA 109, 19196-19210 (2012
14. Harris, G. A., Galhena, A. S. & Fernández, F. M. Ambient sampling/ionization mass spectrometry: Applications and current trends. Anal. Chem. 83, 4508-4538 (2011
15. Monge, M. E., Harris, G. A., Dwivedi, P. & Fernández, F. M. Mass spectrometry: Recent advances in direct open air surface sampling/ionization. Chem. Rev. 113, 2269-2308 (2013
16. Roach, P. J., Laskin, J. & Laskin, A. Nanospray desorption electrospray ionization: An ambient method for liquid-extraction surface sampling in mass spectrometry. Analyst 135, 2233-2236 (2010
17. Watrous, J. et al. Mass spectral molecular networking of living microbial colonies. Proc. Natl Acad. Sci. USA 109, E1743-E1752 (2012
18. Hsu, C-C. et al. Real-time metabolomics on living microorganisms using ambient electrospray ionization flow-probe. Anal. Chem. 85, 7014-7018 (2013
19. Van Berkel, G. J., Kertesz, V. & King, R. C. High-throughput mode liquid microjunction surface sampling probe. Anal. Chem. 81, 7096-7101 (2009
20. Kai, M., Gonzá lez, I., Genilloud, O., Singh, S. B. & Svatoš, A. Direct mass spectrometric screening of antibiotics from bacterial surfaces using liquid extraction surface analysis. Rapid Commun. Mass Spectrom. 26, 2477-2482 (2012
21. Zachariasova, M. et al. Analysis of multiple mycotoxins in beer employing (ultra) -highresolution mass spectrometry. Rapid Commun. Mass Spectrom. 24, 3357-3367 (2010
22. Vaclavik, L., Zachariasova, M., Hrbek, V. & Hajslova, J. Analysis of multiple mycotoxins in cereals under ambient conditions using direct analysis in real time (DART) ionization coupled to high resolution mass spectrometry. Talanta 82, 1950-1957 (2010
23. Watrous, J. D. & Dorrestein, P. C. Imaging mass spectrometry in microbiology. Nat. Rev. Microbiol. 9, 683-694 (2011
24. Kersten, R. D. et al. A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat. Chem. Biol. 7, 794-802 (2011
25. Mazzeo, J. R., Neue, U. D., Kele, M., Plumb, R. S. & Corp, W. A new separation technique takes advantage of sub-2-mm HPLC. Anal. Chem. 77, 460A-467A (2005
26. Chan, E., Yap, S. & Lau, A. Ultra-performance liquid chromatography/time-of-flight mass spectrometry based metabolomics of raw and steamed Panax notoginseng. Mass Spectrom. 21, 519-528 (2007
27. Dan, M. et al. Metabolite profiling of Panax notoginseng using UPLC-ESI-MS. Phytochemistry 69, 2237-2244 (2008
28. Tchoumtchoua, J., Njamen, D., Mbanya, J. C., Skaltsounis, A-L. & Halabalaki, M. Structure-oriented UHPLC-LTQ Orbitrap-based approach as a dereplication strategy for the identification of isoflavonoids from Amphimas pterocarpoides crude extract. J. Mass Spectrom. 48, 561-575 (2013
29. Bertrand, S. et al. Detection of metabolite induction in fungal co-cultures on solid media by high-throughput differential ultra-high pressure liquid chromatography-timeof- flight mass spectrometry fingerprinting. J. Chromatogr. A 1292, 219-228 (2013
30. Wolfender, J-L. HPLC in natural product analysis: The detection issue. Planta Med. 75, 719-734 (2009
31. Wolfender, J., Marti, G. & Queiroz, E. F. Advances in techniques for profiling crude extracts and for the rapid identification of natural products: Dereplication, Quality control and metabolomics. Curr. Org. Chem. 1808-1832 (2010
32. Nordström, A., Want, E., Northen, T., Lehtiö, J. & Siuzdak, G. Multiple ionization mass spectrometry strategy used to reveal the complexity of metabolomics. Anal. Chem. 80, 421-429 (2008
33. Moco, S. et al. A liquid chromatography-mass spectrometry-based metabolome database for tomato. Plant Physiol. 141, 1205-1218 (2006
34. Wishart, D. S. Current progress in computational metabolomics. Brief. Bioinform. 8, 279-293 (2007
35. De Vos, R. C. H. et al. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat. Protoc. 2, 778-791 (2007
36. Suits, F., Lepre, J., Du, P., Bischoff, R. & Horvatovich, P. Two-dimensional method for time aligning liquid chromatography-mass spectrometry data. Anal. Chem. 80, 3095-3104 (2008
37. Ito, T., Odake, T., Katoh, H., Yamaguchi, Y. & Aoki, M. High-throughput profiling of microbial extracts. J. Nat. Prod. 74, 983-988 (2011
38. Kato, N., Takahashi, S., Nogawa, T., Saito, T. & Osada, H. Construction of a microbial natural product library for chemical biology studies. Curr. Opin. Chem. Biol. 16, 101-108 (2012
39. Cuthbertson, D. J. et al. Accurate mass-time tag library for LC/MS-based metabolite profiling of medicinal plants. Phytochemistry 91, 187-197 (2013
40. Potterat, O. & Hamburger, M. Concepts and technologies for tracking bioactive compounds in natural product extracts: Generation of libraries, and hyphenation of analytical processes with bioassays. Nat. Prod. Rep. 30, 546-564 (2013
41. Michel, T., Halabalaki, M. & Skaltsounis, A-L. New concepts, experimental approaches, and dereplication strategies for the discovery of novel phytoestrogens from natural sources. Planta Med. 79, 514-532 (2013
42. Lang, G. et al. Bioactivity profiling using HPLC/microtiter-plate analysis: Application to a New Zealand marine alga-derived fungus, Gliocladium sp. J. Nat. Prod. 69, 621-624 (2006
43. Johnson, T. A. et al. Natural product libraries to accelerate the high-throughput discovery of therapeutic leads. J. Nat. Prod. 74, 2545-2555 (2011
44. Johansen, K. T., Wubshet, S. G. & Nyberg, N. T. HPLC-NMR revisited: Using time-slice high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance with database-Assisted dereplication. Anal. Chem. 85, 3183-3189 (2013
45. Wagenaar, M. M. Pre-fractionated microbial samples - The second generation natural products library at Wyeth. Molecules 13, 1406-1426 (2008
46. Strege, M. A. High-performance liquid chromatographic-electrospray ionization mass spectrometric analyses for the integration of natural products with modern highthroughput screening. J. Chromatogr. B Biomed. Sci. Appl. 725, 67-78 (1999
47. Bohni, N. et al. Integration of microfractionation, qNMR and zebrafish screening for the in vivo bioassay-guided isolation and quantitative bioactivity analysis of natural products. PLoS One 8, e64006 (2013
48. Nielsen, K. Fungal metabolite screening: Database of 474 mycotoxins and fungal metabolites for dereplication by standardised liquid chromatography-UV- mass spectrometry methodology. J. Chromatogr. A 1002, 111-136 (2003
49. Nielsen, K. F., Mansson, M., Rank, C., Frisvad, J. C. & Larsen, T. O. Dereplication of microbial natural products by LC-DAD-TOFMS. J. Nat. Prod. 74, 2338-2348 (2011
50. Boswell, P. G., Schellenberg, J. R., Carr, P. W., Cohen, J. D. & Hegeman, A. D. A study on retention 'projection' as a supplementary means for compound identification by liquid chromatography-mass spectrometry capable of predicting retention with different gradients, flow rates, and instruments. J. Chromatogr. A 1218, 6732-6741 (2011
51. Ridder, L. et al. Automatic chemical structure annotation of an LC-MS(n) based metabolic profile from green tea. Anal. Chem. 85, 6033-6040 (2013
52. Konishi, Y. et al. Molecular formula analysis by an MS/MS/MS technique to expedite dereplication of natural products. Anal. Chem. 79, 1187-1197 (2007
53. Horai, H. et al. MassBank: A public repository for sharing mass spectral data for life sciences. J. Mass Spectrom. 45, 703-714 (2010
54. López-Pérez, J. L., Therón, R., del Olmo, E. & Díaz, D. NAPROC-13: A database for the dereplication of natural product mixtures in bioassay-guided protocols. Bioinformatics 23, 3256-3257 (2007
55. Holt, T. G. The design and development of an integrated natural products screening database. J. Biomol. Screen. 5, 421-433 (2000
56. Mansson, M. et al. Explorative solid-phase extraction (E-SPE) for accelerated microbial natural product discovery, dereplication, and purification. J. Nat. Prod. 73, 1126-1132 (2010
57. Singh, S. B. et al. Occurrence, distribution, dereplication and efficient discovery of thiazolyl peptides by sensitive-resistant pair screening. J. Antibiot. (Tokyo) 66, 599-607 (2013
58. Kim, H. J., Jee, E. H., Ahn, K. S., Choi, H. S. & Jang, Y. P. Identification of marker compounds in herbal drugs on TLC with DART-MS. Arch. Pharm. Res. 33, 1355-1359 (2010
59. Lane, S. et al. Toward single-calibrant quantification in HPLC. A comparison of three detection strategies: Evaporative light scattering, chemiluminescent nitrogen, and proton NMR. Anal. Chem. 77, 4354-4365 (2005
60. Cremin, P. A & Zeng, L. High-throughput analysis of natural product compound libraries by parallel LC-MS evaporative light scattering detection. Anal. Chem. 74, 5492-5500 (2002
61. Hutchinson, J. P. et al. Comparison of the response of four aerosol detectors used with ultra high pressure liquid chromatography. J. Chromatogr. A 1218, 1646-1655 (2011
62. Adnani, N., Michel, C. R. & Bugni, T. S. Universal quantification of structurally diverse natural products using an evaporative light scattering detector. J. Nat. Prod. 75, 802-806 (2012
63. Vervoort, N., Daemen, D. & Török, G. Performance evaluation of evaporative light scattering detection and charged aerosol detection in reversed phase liquid chromatography. J. Chromatogr. A 1189, 92-100 (2008
64. Hasada, K. et al. Quantitative determination of atractylon in Atractylodis Rhizoma and Atractylodis Lanceae Rhizoma by 1H-NMR spectroscopy. J. Nat. Med. 64, 161-166 (2010
65. Pauli, G. F., Jaki, B. U. & Lankin, D. C. A routine experimental protocol for qHNMR illustrated with Taxol. J. Nat. Prod. 70, 589-595 (2007
66. Farrant, R. D. et al. NMR quantification using an artificial signal. Magn. Reson. Chem. 48, 753-762 (2010
67. Lang, G. et al. Evolving trends in the dereplication of natural product extracts: New methodology for rapid, small-scale investigation of natural product extracts. J. Nat. Prod. 71, 1595-1599 (2008
68. Wolfender, J., Queiroz, E. F. & Hostettmann, K. The importance of hyphenated techniques in the discovery of new lead compounds from nature. Expert Opin. Drug Discov. 1, 237-260 (2006
69. Jaroszewski, J. W. Hyphenated NMR methods in natural products research, part 1: Direct hyphenation. Planta Med. 71, 691-700 (2005
70. Jaroszewski, J. W. Hyphenated NMR methods in natural products research, Part 2: HPLC-SPE-NMR and other new trends in NMR hyphenation. Planta Med. 71, 795-802 (2005
71. Williamson, R. T. et al. New diffusion-edited NMR experiments to expedite the dereplication of known compounds from natural product mixtures. Org. Lett. 2, 289-292 (2000
72. Cassani, J., Nilsson, M. & Morris, G. A. Flavonoid mixture analysis by matrix-Assisted diffusion-ordered spectroscopy. J. Nat. Prod. 75, 131-134 (2012
73. Inokuma, Y. et al. X-ray analysis on the nanogram to microgram scale using porous complexes. Nature 495, 461-466 (2013
74. Genilloud, O. et al. Current approaches to exploit actinomycetes as a source of novel natural products. J. Ind. Microbiol. Biotechnol. 38, 375-389 (2011