A metabolomics guided exploration of marine natural product chemical space

Metabolomics

Volumn 12, Issue 9, 2016, Pages

  Floros, Dimitrios J ^a,c   Jensen, Paul R ^b   Dorrestein, Pieter C ^c   Koyama, Nobuhiro ^c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d KITASATO UNIVERSITY   (Japan)

Author keywords

Marine natural products; Mass spectrometry; Metabolomics; Molecular networking

Indexed keywords

ALTERAMIDE; ANTIPAIN; DACTINOMYCIN; DEFEROXAMINE; ECHINOMYCIN; ETHANOLAOMINE; FERRIOXAMINE; GLUCOPERICIDIN; LOBOPHORIN; MARIDRIC ACID; NATURAL PRODUCT; NODULARIN; NONACTIN; PIERICIDIN A1; STENDOMYCIN; STREPTORUBIN; SURFACTIN; UNCLASSIFIED DRUG; UNDECYLPRODIGININE; VALINOMYCIN; WORTMANNIN;

ARTICLE; MARINE SPECIES; METABOLOMICS; MOLECULAR INTERACTION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; TIME OF FLIGHT MASS SPECTROMETRY; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY;

EID: 84981164648     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-016-1087-5     Document Type: Article

References (57)

1. Allard, P.-M., et al. (2016). Integration of molecular networking and in-silico MS/MS fragmentation for natural products dereplication. Analytical Chemistry. doi:10.1021/acs.analchem.5b04804.
2. Anon. (n.d.). Triphaseco pipeline. Available at: http://triphaseco.com/pipeline/.
3. Baltz, R. H., Miao, V., & Wrigley, S. K. (2005). Natural products to drugs: daptomycin and related lipopeptide antibiotics. Natural Product Reports, 22(6), 717–741.
4. Bérdy, J., & View, A. P. (2005). Bioactive microbial metabolites. The Journal of Antibiotics, 58(1), 1–26.
5. Bischoff, K. M., et al. (2015). Liamocin oil from Aureobasidium pullulans has antibacterial activity with specificity for species of Streptococcus. The Journal of Antibiotics. doi:10.1038/ja.2015.39.
6. Blunt, J. W., et al. (2014). Marine natural products. Natural Product Reports, 31(2), 160–258.
7. Bouslimani, A., et al. (2014). Mass spectrometry of natural products: current, emerging and future technologies. Natural Product Reports, 31(6), 718–729.
8. Burg, R. W., et al. (1979). Avermectins, new family of potent anthelmintic agents: producing organism and fermentation. Antimicrobial Agents and Chemotherapy, 15(3), 361–367.
9. Caboche, S., et al. (2008). NORINE: a database of nonribosomal peptides. Nucleic Acids Research, 36(Database issue), D326–D331.
10. Cheikh-Ali, Z., et al. (2015). Diversity of exophillic acid derivatives in strains of an endophytic Exophiala sp. Phytochemistry, 118, 83–93.
11. Chen, C., et al. (1996). Halymecins, new antimicroalgal substances produced by fungi isolated from marine algae. The Journal of Antibiotics, 49(10), 998–1005.
12. Choi, H., et al. (2012). Honaucins A-C, potent inhibitors of inflammation and bacterial quorum sensing: synthetic derivatives and structure-activity relationships. CHEMISTRY & BIOLOGY, 19(5), 589–598.
13. Dunn, W. B., et al. (2012). Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics, 9(S1), 44–66.
14. Fenical, W., & Jensen, P. R. (2006). Developing a new resource for drug discovery: marine actinomycete bacteria. Nature Chemical Biology, 2(12), 666–673.
15. Fenical, W., et al. (2009). Discovery and development of the anticancer agent salinosporamide A (NPI-0052). Bioorganic & Medicinal Chemistry, 17(6), 2175–2180.
16. Fleming, A. (1929). On the antibacterial action of cultures of a penicillium, with special reference to their use in the isolation of B. influenzæ. British Journal of Experimental Pathology, 10(3), 226.
17. Frank, A. M., et al. (2008). Clustering millions of tandem mass spectra. Journal of Proteome Research, 7(1), 113–122.
18. Gaskins, J. E., & Cheung, P. J. (1986). Exophiala pisciphila. A study of its development. Mycopathologia, 93(3), 173–184.
19. Gerwick, W. H., & Moore, B. S. (2012). Lessons from the past and charting the future of marine natural products drug discovery and chemical biology. Chemistry & Biology, 19(1), 85–98.
20. Guo, A. C., et al. (2013). ECMDB: the E. coli metabolome database. Nucleic Acids Research, 41(Database issue), D625–D630.
21. Horai, H., et al. (2010). MassBank: a public repository for sharing mass spectral data for life sciences. Journal of Mass Spectrometry, 45(7), 703–714.
22. Hou, Y., et al. (2012). Microbial strain prioritization using metabolomics tools for the discovery of natural products. Analytical Chemistry, 84(10), 4277–4283.
23. Hu, Y., et al. (2015). Statistical research on the bioactivity of new marine natural products discovered during the 28 years from 1985 to 2012. Marine Drugs, 13(1), 202–221.
24. Jaccard, P. (1912). The distribution of the flora in the alpine zone.1. New Phytologist, 11(2), 37–50.
25. Kallmeyer, J., et al. (2012). Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences of the United States of America, 109(40), 16213–16216.
26. Kellogg, J. J., et al. (2016). Biochemometrics for natural products research: comparison of data analysis approaches and application to identification of bioactive compounds. Journal of Natural Products. doi:10.1021/acs.jnatprod.5b01014.
27. Kelly, L. W., et al. (2014). Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors. Proceedings of the National Academy of Sciences, 111(28), 10227–10232.
28. Kersten, R. D., et al. (2011). A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nature Chemical Biology, 7(11), 794–802.
29. Kim, J. S., Lee, I. K., & Yun, B. S. (2015). A novel biosurfactant produced by Aureobasidium pullulans L3-GPY from a tiger lily wild flower, Lilium lancifolium Thunb. PloS One, 10(4), e0122917.
30. Kim, J., et al. (2009). LC-MS/MS profiling-based secondary metabolite screening of Myxococcus xanthus. Journal of Microbiology and Biotechnology, 19(1), 51–54.
31. Kinkel, L. L., et al. (2014). Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes. The ISME Journal, 8(2), 249–256.
32. Klitgaard, A., et al. (2015). Combining stable isotope labeling and molecular networking for biosynthetic pathway characterization. Analytical Chemistry, 87(13), 6520–6526.
33. Kurita, K. L., Glassey, E., & Linington, R. G. (2015). Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries. Proceedings of the National Academy of Sciences, 112(39), 11999–12004.
34. Larsson, J., et al. (2007). ChemGPS-NP: tuned for navigation in biologically relevant chemical space. Journal of Natural Products, 70(5), 789–794.
35. Marrone, T. J., & Merz, K. M. J. (1995). Molecular recognition of K+ and Na+ by valinomycin in methanol. Journal of the American Chemical Society, 117(2), 779–791.
36. Mohimani, H., & Pevzner, P. A. (2015). Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks. Natural Product Reports, 33(1), 73–86.
37. Montaser, R., & Luesch, H. (2011). Marine natural products: a new wave of drugs? Future Medicinal Chemistry, 3(12), 1475–1489.
38. Nguyen, D. D., et al. (2013). MS/MS networking guided analysis of molecule and gene cluster families. Proceedings of the National Academy of Sciences of the United States of America, 110(28), E2611–E2620.
39. Nielsen, K. F., et al. (2011). Dereplication of microbial natural products by LC-DAD-TOFMS. Journal of Natural Products, 74(11), 2338–2348.
40. Price, N. P. J., et al. (2013). Structural characterization of novel extracellular liamocins (mannitol oils) produced by Aureobasidium pullulans strain NRRL 50380. Carbohydrate Research, 370, 24–32.
41. Quinn, R. A., & Alexandrov, T. (2014). The community ecology of microbial molecules. Journal of Chemical Ecology, 40(11–12), 1161–1162.
42. Russo, P., et al. (2015). New drugs from marine organisms in Alzheimer’s disease. Marine Drugs, 14(1), 5.
43. Sawada, Y., et al. (2012). RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database. Phytochemistry, 82, 38–45.
44. Sehgal, S. N., Baker, H., & Vézina, C. (1975). Rapamycin (AY-22,989), a new antifungal antibiotic. II. Fermentation, isolation and characterization. The Journal of Antibiotics, 28(10), 727–732.
45. Shannon, P., et al. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498–2504.
46. Smith, D. (2003). Culture collections over the world. International Microbiology, 6(2), 95–100.
47. Subramani, R., & Aalbersberg, W. (2012). Marine actinomycetes: An ongoing source of novel bioactive metabolites. Microbiological Research, 167(10), 571–580.
48. Sumner, L. W., et al. (2007). Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics, 3(3), 211–221.
49. Tautenhahn, R., et al. (2012). XCMS Online: A web-based platform to process untargeted metabolomic data. Analytical Chemistry, 84(11), 5035–5039.
50. Vázquez-Baeza, Y., et al. (2013). EMPeror: A tool for visualizing high-throughput microbial community data. GigaScience, 2(1), 16.
51. Vizcaino, M., et al. (2015). Discovering and deciphering the pathogenic and probiotic activities from the bacterial colibactin pathway. Planta Medica, 81(11), IL40.
52. Watrous, J., et al. (2012). Mass spectral molecular networking of living microbial colonies. Proceedings of the National Academy of Sciences of the United States of America, 109(26), E1743–E1752.
53. Whitman, W. B., Coleman, D. C., & Wiebe, W. J. (1998). Prokaryotes: The unseen majority. Proceedings of the National Academy of Sciences, 95(12), 6578–6583.
54. Wishart, D. S., et al. (2013). HMDB 3.0—the human metabolome database in 2013. Nucleic Acids Research, 41(Database issue), D801–D807.
55. Wang, M., et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology (accepted).
56. Yang, J. Y., et al. (2013). Molecular networking as a dereplication strategy. Journal of Natural Products, 76(9), 1686–1699.
57. Ziemert, N., et al. (2014). Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora. Proceedings of the National Academy of Sciences of the United States of America, 111(12), E1130–E1139.