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Marine Drugs
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Metabolomics - Applications in Marine Natural Products Chemistry
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Metabolomics - Applications in Marine Natural Products Chemistry

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

Deadline for manuscript submissions: closed (31 October 2014) | Viewed by 84052

Special Issue Editors

Dr. Daniel A. Dias

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Guest Editor
School of Health and Biomedical Sciences, Laboratory Medicine, RMIT University, P.O. Box 71, Bundoora 3083, Australia
Interests: metabolomics; natural products chemistry; biomarker discovery; analytical chemistry; dereplication; structure elucidation; mass spectrometry; nuclear magnetic resonance spectroscopy
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Ute Roessner

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Guest Editor
Metabolomics Australia, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
Interests: metabolomics; analytical biochemistry; metabolism; crop improvement; biomarker discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Manuscript Submission Information

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. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short 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 thoroughly refereed through a single-blind 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 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

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Related Special Issue

Published Papers (7 papers)

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Research

1012 KiB  
Article
Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins
by Natalie Heffernan, Nigel P. Brunton, Richard J. FitzGerald and Thomas J. Smyth
Mar. Drugs 2015, 13(1), 509-528; https://doi.org/10.3390/md13010509 - 16 Jan 2015
Cited by 137 | Viewed by 11830
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 against [...] 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)
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2855 KiB  
Article
LC-MS-Based Metabolomics Study of Marine Bacterial Secondary Metabolite and Antibiotic Production in Salinispora arenicola
by Utpal Bose, Amitha K. Hewavitharana, Yi Kai Ng, Paul Nicholas Shaw, John A. Fuerst and Mark P. Hodson
Mar. Drugs 2015, 13(1), 249-266; https://doi.org/10.3390/md13010249 - 7 Jan 2015
Cited by 47 | Viewed by 11813
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 the [...] 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)
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693 KiB  
Article
Accurate Dereplication of Bioactive Secondary Metabolites from Marine-Derived Fungi by UHPLC-DAD-QTOFMS and a MS/HRMS Library
by Sara Kildgaard, Maria Mansson, Ina Dosen, Andreas Klitgaard, Jens C. Frisvad, Thomas O. Larsen and Kristian F. Nielsen
Mar. Drugs 2014, 12(6), 3681-3705; https://doi.org/10.3390/md12063681 - 20 Jun 2014
Cited by 120 | Viewed by 14147
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 mass [...] 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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1484 KiB  
Article
Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts
by Lynsey Macintyre, Tong Zhang, Christina Viegelmann, Ignacio Juarez Martinez, Cheng Cheng, Catherine Dowdells, Usama Ramadan Abdelmohsen, Christine Gernert, Ute Hentschel and RuAngelie Edrada-Ebel
Mar. Drugs 2014, 12(6), 3416-3448; https://doi.org/10.3390/md12063416 - 5 Jun 2014
Cited by 111 | Viewed by 15644
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 secondary [...] 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)
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831 KiB  
Article
Metabolomic Profiling and Genomic Study of a Marine Sponge-Associated Streptomyces sp.
by Christina Viegelmann, Lekha Menon Margassery, Jonathan Kennedy, Tong Zhang, Ciarán O'Brien, Fergal O'Gara, John P. Morrissey, Alan D. W. Dobson and RuAngelie Edrada-Ebel
Mar. Drugs 2014, 12(6), 3323-3351; https://doi.org/10.3390/md12063323 - 2 Jun 2014
Cited by 47 | Viewed by 11849
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 sponge [...] 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)
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1015 KiB  
Article
NMR-Based Metabolomic Analysis of Spatial Variation in Soft Corals
by Qing He, Ruiqi Sun, Huijuan Liu, Zhufeng Geng, Dawei Chen, Yinping Li, Jiao Han, Wenhan Lin, Shushan Du and Zhiwei Deng
Mar. Drugs 2014, 12(4), 1876-1890; https://doi.org/10.3390/md12041876 - 28 Mar 2014
Cited by 14 | Viewed by 7664
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 multivariate [...] 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)
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2099 KiB  
Article
A Chemoinformatics Approach to the Discovery of Lead-Like Molecules from Marine and Microbial Sources En Route to Antitumor and Antibiotic Drugs
by Florbela Pereira, Diogo A. R. S. Latino and Susana P. Gaudêncio
Mar. Drugs 2014, 12(2), 757-778; https://doi.org/10.3390/md12020757 - 27 Jan 2014
Cited by 31 | Viewed by 10086
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 used [...] 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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