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Special Issue "Metabolomics - Applications in Marine Natural Products Chemistry"

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A special issue of Marine Drugs (ISSN 1660-3397).

Deadline for manuscript submissions: closed (31 October 2014)

Special Issue Editors

Guest Editor
Dr. Daniel A. Dias (Website)

School of Health and Biomedical Sciences, Laboratory Medicine, RMIT University PO Box 71, Bundoora 3083, Australia
Phone: +61 (0)3 9925 7071
Interests: metabolomics; natural products chemistry; biomarker discovery; analytical chemistry; dereplication; structure elucidation; mass spectrometry; nuclear magnetic resonance spectroscopy
Guest Editor
Dr. Ute Roessner (Website)

School of Botany, University of Melbourne, Victoria 3010, Australia
Fax: +61 3 9347 1072
Interests: metabolomics; analytical biochemistry; metabolism; crop improvement; biomarker discovery

Special Issue Information

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Marine Drugs is an international peer-reviewed Open Access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs).

Keywords

  • metabolomics
  • drug discovery
  • biomarker discovery
  • secondary metabolites
  • endosymbiotic bacteria and fungi
  • fungal and bacterial genomics
  • polyketide synthases
  • dereplication
  • marine origin
  • biological activity

Published Papers (7 papers)

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Research

Open AccessArticle Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins
Mar. Drugs 2015, 13(1), 509-528; doi:10.3390/md13010509
Received: 30 June 2014 / Accepted: 21 November 2014 / Published: 16 January 2015
Cited by 10 | PDF Full-text (1012 KB) | HTML Full-text | XML Full-text
Abstract
Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense [...] Read more.
Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds. Full article
(This article belongs to the Special Issue Metabolomics - Applications in Marine Natural Products Chemistry)
Open AccessArticle LC-MS-Based Metabolomics Study of Marine Bacterial Secondary Metabolite and Antibiotic Production in Salinispora arenicola
Mar. Drugs 2015, 13(1), 249-266; doi:10.3390/md13010249
Received: 26 September 2014 / Accepted: 29 December 2014 / Published: 7 January 2015
Cited by 3 | PDF Full-text (2855 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
An LC-MS-based metabolomics approach was used to characterise the variation in secondary metabolite production due to changes in the salt content of the growth media as well as across different growth periods (incubation times). We used metabolomics as a tool to investigate [...] Read more.
An LC-MS-based metabolomics approach was used to characterise the variation in secondary metabolite production due to changes in the salt content of the growth media as well as across different growth periods (incubation times). We used metabolomics as a tool to investigate the production of rifamycins (antibiotics) and other secondary metabolites in the obligate marine actinobacterial species Salinispora arenicola, isolated from Great Barrier Reef (GBR) sponges, at two defined salt concentrations and over three different incubation periods. The results indicated that a 14 day incubation period is optimal for the maximum production of rifamycin B, whereas rifamycin S and W achieve their maximum concentration at 29 days. A “chemical profile” link between the days of incubation and the salt concentration of the growth medium was shown to exist and reliably represents a critical point for selection of growth medium and harvest time. Full article
(This article belongs to the Special Issue Metabolomics - Applications in Marine Natural Products Chemistry)
Open AccessArticle Accurate Dereplication of Bioactive Secondary Metabolites from Marine-Derived Fungi by UHPLC-DAD-QTOFMS and a MS/HRMS Library
Mar. Drugs 2014, 12(6), 3681-3705; doi:10.3390/md12063681
Received: 28 February 2014 / Revised: 23 May 2014 / Accepted: 11 June 2014 / Published: 20 June 2014
Cited by 25 | PDF Full-text (693 KB) | HTML Full-text | XML Full-text
Abstract
In drug discovery, reliable and fast dereplication of known compounds is essential for identification of novel bioactive compounds. Here, we show an integrated approach using ultra-high performance liquid chromatography-diode array detection-quadrupole time of flight mass spectrometry (UHPLC-DAD-QTOFMS) providing both accurate mass full-scan [...] Read more.
In drug discovery, reliable and fast dereplication of known compounds is essential for identification of novel bioactive compounds. Here, we show an integrated approach using ultra-high performance liquid chromatography-diode array detection-quadrupole time of flight mass spectrometry (UHPLC-DAD-QTOFMS) providing both accurate mass full-scan mass spectrometry (MS) and tandem high resolution MS (MS/HRMS) data. The methodology was demonstrated on compounds from bioactive marine-derived strains of Aspergillus, Penicillium, and Emericellopsis, including small polyketides, non-ribosomal peptides, terpenes, and meroterpenoids. The MS/HRMS data were then searched against an in-house MS/HRMS library of ~1300 compounds for unambiguous identification. The full scan MS data was used for dereplication of compounds not in the MS/HRMS library, combined with ultraviolet/visual (UV/Vis) and MS/HRMS data for faster exclusion of database search results. This led to the identification of four novel isomers of the known anticancer compound, asperphenamate. Except for very low intensity peaks, no false negatives were found using the MS/HRMS approach, which proved to be robust against poor data quality caused by system overload or loss of lock-mass. Only for small polyketides, like patulin, were both retention time and UV/Vis spectra necessary for unambiguous identification. For the ophiobolin family with many structurally similar analogues partly co-eluting, the peaks could be assigned correctly by combining MS/HRMS data and m/z of the [M + Na]+ ions. Full article
(This article belongs to the Special Issue Metabolomics - Applications in Marine Natural Products Chemistry)
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Open AccessArticle Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts
Mar. Drugs 2014, 12(6), 3416-3448; doi:10.3390/md12063416
Received: 6 March 2014 / Revised: 20 May 2014 / Accepted: 20 May 2014 / Published: 5 June 2014
Cited by 11 | PDF Full-text (1484 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Marine invertebrate-associated symbiotic bacteria produce a plethora of novel secondary metabolites which may be structurally unique with interesting pharmacological properties. Selection of strains usually relies on literature searching, genetic screening and bioactivity results, often without considering the chemical novelty and abundance of [...] Read more.
Marine invertebrate-associated symbiotic bacteria produce a plethora of novel secondary metabolites which may be structurally unique with interesting pharmacological properties. Selection of strains usually relies on literature searching, genetic screening and bioactivity results, often without considering the chemical novelty and abundance of secondary metabolites being produced by the microorganism until the time-consuming bioassay-guided isolation stages. To fast track the selection process, metabolomic tools were used to aid strain selection by investigating differences in the chemical profiles of 77 bacterial extracts isolated from cold water marine invertebrates from Orkney, Scotland using liquid chromatography-high resolution mass spectrometry (LC-HRMS) and nuclear magnetic resonance (NMR) spectroscopy. Following mass spectrometric analysis and dereplication using an Excel macro developed in-house, principal component analysis (PCA) was employed to differentiate the bacterial strains based on their chemical profiles. NMR 1H and correlation spectroscopy (COSY) were also employed to obtain a chemical fingerprint of each bacterial strain and to confirm the presence of functional groups and spin systems. These results were then combined with taxonomic identification and bioassay screening data to identify three bacterial strains, namely Bacillus sp. 4117, Rhodococcus sp. ZS402 and Vibrio splendidus strain LGP32, to prioritize for scale-up based on their chemically interesting secondary metabolomes, established through dereplication and interesting bioactivities, determined from bioassay screening. Full article
(This article belongs to the Special Issue Metabolomics - Applications in Marine Natural Products Chemistry)
Figures

Open AccessArticle Metabolomic Profiling and Genomic Study of a Marine Sponge-Associated Streptomyces sp.
Mar. Drugs 2014, 12(6), 3323-3351; doi:10.3390/md12063323
Received: 25 March 2014 / Revised: 7 May 2014 / Accepted: 21 May 2014 / Published: 2 June 2014
Cited by 13 | PDF Full-text (831 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Metabolomics and genomics are two complementary platforms for analyzing an organism as they provide information on the phenotype and genotype, respectively. These two techniques were applied in the dereplication and identification of bioactive compounds from a Streptomyces sp. (SM8) isolated from the [...] Read more.
Metabolomics and genomics are two complementary platforms for analyzing an organism as they provide information on the phenotype and genotype, respectively. These two techniques were applied in the dereplication and identification of bioactive compounds from a Streptomyces sp. (SM8) isolated from the sponge Haliclona simulans from Irish waters. Streptomyces strain SM8 extracts showed antibacterial and antifungal activity. NMR analysis of the active fractions proved that hydroxylated saturated fatty acids were the major components present in the antibacterial fractions. Antimycin compounds were initially putatively identified in the antifungal fractions using LC-Orbitrap. Their presence was later confirmed by comparison to a standard. Genomic analysis of Streptomyces sp. SM8 revealed the presence of multiple secondary metabolism gene clusters, including a gene cluster for the biosynthesis of the antifungal antimycin family of compounds. The antimycin gene cluster of Streptomyces sp. SM8 was inactivated by disruption of the antimycin biosynthesis gene antC. Extracts from this mutant strain showed loss of antimycin production and significantly less antifungal activity than the wild-type strain. Three butenolides, 4,10-dihydroxy-10-methyl-dodec-2-en-1,4-olide (1), 4,11-dihydroxy-10-methyl-dodec-2-en-1,4-olide (2), and 4-hydroxy-10-methyl-11-oxo-dodec-2-en-1,4-olide (3) that had previously been reported from marine Streptomyces species were also isolated from SM8. Comparison of the extracts of Streptomyces strain SM8 and its host sponge, H. simulans, using LC-Orbitrap revealed the presence of metabolites common to both extracts, providing direct evidence linking sponge metabolites to a specific microbial symbiont. Full article
(This article belongs to the Special Issue Metabolomics - Applications in Marine Natural Products Chemistry)
Open AccessArticle NMR-Based Metabolomic Analysis of Spatial Variation in Soft Corals
Mar. Drugs 2014, 12(4), 1876-1890; doi:10.3390/md12041876
Received: 12 December 2013 / Revised: 6 February 2014 / Accepted: 27 February 2014 / Published: 28 March 2014
Cited by 1 | PDF Full-text (1015 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Soft corals are common marine organisms that inhabit tropical and subtropical oceans. They are shown to be rich source of secondary metabolites with biological activities. In this work, soft corals from two geographical locations were investigated using 1H-NMR spectroscopy coupled with [...] Read more.
Soft corals are common marine organisms that inhabit tropical and subtropical oceans. They are shown to be rich source of secondary metabolites with biological activities. In this work, soft corals from two geographical locations were investigated using 1H-NMR spectroscopy coupled with multivariate statistical analysis at the metabolic level. A partial least-squares discriminant analysis showed clear separation among extracts of soft corals grown in Sanya Bay and Weizhou Island. The specific markers that contributed to discrimination between soft corals in two origins belonged to terpenes, sterols and N-containing compounds. The satisfied precision of classification obtained indicates this approach using combined 1H-NMR and chemometrics is effective to discriminate soft corals collected in different geographical locations. The results revealed that metabolites of soft corals evidently depended on living environmental condition, which would provide valuable information for further relevant coastal marine environment evaluation. Full article
(This article belongs to the Special Issue Metabolomics - Applications in Marine Natural Products Chemistry)
Open AccessArticle A Chemoinformatics Approach to the Discovery of Lead-Like Molecules from Marine and Microbial Sources En Route to Antitumor and Antibiotic Drugs
Mar. Drugs 2014, 12(2), 757-778; doi:10.3390/md12020757
Received: 21 November 2013 / Revised: 16 December 2013 / Accepted: 16 January 2014 / Published: 27 January 2014
Cited by 4 | PDF Full-text (2099 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The comprehensive information of small molecules and their biological activities in the PubChem database allows chemoinformatic researchers to access and make use of large-scale biological activity data to improve the precision of drug profiling. A Quantitative Structure–Activity Relationship approach, for classification, was [...] Read more.
The comprehensive information of small molecules and their biological activities in the PubChem database allows chemoinformatic researchers to access and make use of large-scale biological activity data to improve the precision of drug profiling. A Quantitative Structure–Activity Relationship approach, for classification, was used for the prediction of active/inactive compounds relatively to overall biological activity, antitumor and antibiotic activities using a data set of 1804 compounds from PubChem. Using the best classification models for antibiotic and antitumor activities a data set of marine and microbial natural products from the AntiMarin database were screened—57 and 16 new lead compounds for antibiotic and antitumor drug design were proposed, respectively. All compounds proposed by our approach are classified as non-antibiotic and non-antitumor compounds in the AntiMarin database. Recently several of the lead-like compounds proposed by us were reported as being active in the literature. Full article
(This article belongs to the Special Issue Metabolomics - Applications in Marine Natural Products Chemistry)

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