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Special Issue "Deep-Sea Natural Products"

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

Deadline for manuscript submissions: closed (30 June 2016)

Special Issue Editor

Guest Editor
Dr. Danielle Skropeta (Website)

School of Chemistry, University of Wollongong, Wollongong NSW 2522, Australia
Fax: +61 2 42 21 4360
Interests: drug discovery & development; marine natural products; synthesis; structural elucidation; imaging; peptides; carbohydrates; chemical glycobiology; anti-cancer agents

Special Issue Information

Dear Colleagues,

Oceans cover 70% of the world’s surface, with 95% greater than 1000 m deep. Yet of the 30,000 marine natural products reported, less than 2% derive from deep-sea organisms. Today, with improved acoustic technology and greater access to submersibles, deep-sea exploration is uncovering extensive deep-water reefs that are home to a myriad of new species, making the deep sea one of the most biodiverse habitats on the planet.  In the search for sources of new chemical diversity, deep-sea natural products have emerged as a new frontier in drug discovery and development, with over 60% exhibiting significant bioactivity.

Life in the deep sea involves exposure to high hydrostatic pressures, variable temperatures and low oxygen and light, requiring its inhabitants to adapt their biochemical machinery to cope with the extreme conditions. This has the potential to affect both their primary and secondary metabolic pathways, giving rise to structurally unique metabolites.

The deep-sea is a vast and relatively untapped reservoir of unique molecular, structural and biological diversity. As the Guest Editor, I invite scientists to present their recent advances in the field of deep-sea natural products, that is marine natural products obtained from organisms collected at depths of greater than 50 m (164 feet), including the isolation and identification of both deep-sea microbial and invertebrate natural products; biological evaluation, synthesis and biosynthesis; and studies addressing issues challenging the field such as the culturing of deep-sea microbes and deep-sea sponges.

Dr. Danielle Skropeta
Guest Editor

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

  • marine natural products
  • bioactive compounds
  • synthesis; deep-sea
  • deep-water
  • extreme environments
  • trawling
  • dredging
  • manned submersibles
  • remotely operated vehicles

Published Papers (10 papers)

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Research

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Open AccessArticle Biosynthetic Functional Gene Analysis of Bis-Indole Metabolites from 25D7, a Clone Derived from a Deep-Sea Sediment Metagenomic Library
Mar. Drugs 2016, 14(6), 107; doi:10.3390/md14060107
Received: 25 December 2015 / Revised: 10 May 2016 / Accepted: 13 May 2016 / Published: 1 June 2016
PDF Full-text (1494 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
This work investigated the metabolites and their biosynthetic functional hydroxylase genes of the deep-sea sediment metagenomic clone 25D7. 5-Bromoindole was added to the 25D7 clone derived Escherichia coli fermentation broth. The new-generated metabolites and their biosynthetic byproducts were located through LC-MS, in [...] Read more.
This work investigated the metabolites and their biosynthetic functional hydroxylase genes of the deep-sea sediment metagenomic clone 25D7. 5-Bromoindole was added to the 25D7 clone derived Escherichia coli fermentation broth. The new-generated metabolites and their biosynthetic byproducts were located through LC-MS, in which the isotope peaks of brominated products emerged. Two new brominated bis-indole metabolites, 5-bromometagenediindole B (1), and 5-bromometagenediindole C (2) were separated under the guidance of LC-MS. Their structures were elucidated on the basis of 1D and 2D NMR spectra (COSY, HSQC, and HMBC). The biosynthetic functional genes of the two new compounds were revealed through LC-MS and transposon mutagenesis analysis. 5-Bromometagenediindole B (1) also demonstrated moderately cytotoxic activity against MCF7, B16, CNE2, Bel7402, and HT1080 tumor cell lines in vitro. Full article
(This article belongs to the Special Issue Deep-Sea Natural Products)
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Open AccessArticle Deep Sea Water Modulates Blood Pressure and Exhibits Hypolipidemic Effects via the AMPK-ACC Pathway: An in Vivo Study
Mar. Drugs 2013, 11(6), 2183-2202; doi:10.3390/md11062183
Received: 12 April 2013 / Revised: 14 May 2013 / Accepted: 22 May 2013 / Published: 17 June 2013
Cited by 11 | PDF Full-text (1372 KB) | HTML Full-text | XML Full-text
Abstract
Deep sea water (DSW), originally pumped from the Pacific Rim off the coast of Hualien County (Taiwan), and its mineral constituents, were concentrated by a low-temperature vacuum evaporation system to produce a hardness of approximately 400,000 mg/L of seawater mineral concentrate. The [...] Read more.
Deep sea water (DSW), originally pumped from the Pacific Rim off the coast of Hualien County (Taiwan), and its mineral constituents, were concentrated by a low-temperature vacuum evaporation system to produce a hardness of approximately 400,000 mg/L of seawater mineral concentrate. The primary composition of this seawater mineral concentrate was ionic magnesium (Mg2+), which was approximately 96,000 mg/L. Referring to the human recommended daily allowance (RDA) of magnesium, we diluted the mineral concentrate to three different dosages: 0.1 × DSW (equivalent to 3.75 mg Mg2+/kg DSW); 1 × DSW (equivalent to 37.5 mg Mg2+/kg DSW); and 2 × DSW (equivalent to 75 mg Mg2+/kg DSW). Additionally, a magnesium chloride treatment was conducted for comparison with the DSW supplement. The study indicated that 0.1 × DSW, 1 × DSW and 2 × DSW decreased the systolic and diastolic pressures in spontaneous hypertensive rats in an eight-week experiment. DSW has been shown to reduce serum lipids and prevent atherogenesis in a hypercholesterolemic rabbit model. Our results demonstrated that 1 × DSW and 2 × DSW significantly suppressed the serum cholesterol levels, reduced the lipid accumulation in liver tissues, and limited aortic fatty streaks. These findings indicated that the antiatherogenic effects of DSW are associated with 5′-adenosine monophosphate-activated protein kinase (AMPK) stimulation and the consequent inhibition of phosphorylation of acetyl-CoA carboxylase (ACC) in atherosclerotic rabbits. We hypothesize that DSW could potentially be used as drinking water because it modulates blood pressure, reduces lipids, and prevents atherogenesis. Full article
(This article belongs to the Special Issue Deep-Sea Natural Products)
Open AccessArticle Photoprotective Bioactivity Present in a Unique Marine Bacteria Collection from Portuguese Deep Sea Hydrothermal Vents
Mar. Drugs 2013, 11(5), 1506-1523; doi:10.3390/md11051506
Received: 13 March 2013 / Revised: 16 April 2013 / Accepted: 23 April 2013 / Published: 10 May 2013
Cited by 5 | PDF Full-text (876 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Interesting biological activities have been found for numerous marine compounds. In fact, screening of phylogenetically diverse marine microorganisms from extreme environments revealed to be a rational approach for the discovery of novel molecules with relevant bioactivities for industries such as pharmaceutical and [...] Read more.
Interesting biological activities have been found for numerous marine compounds. In fact, screening of phylogenetically diverse marine microorganisms from extreme environments revealed to be a rational approach for the discovery of novel molecules with relevant bioactivities for industries such as pharmaceutical and cosmeceutical. Nevertheless, marine sources deliverables are still far from the expectations and new extreme sources of microbes should be explored. In this work, a marine prokaryotic collection from four Mid-Atlantic Ridge (MAR) deep sea hydrothermal vents near the Azores Islands, Portugal, was created, characterized and tested for its photoprotective capacity. Within 246 isolates, a polyphasic approach, using chemotaxonomic and molecular typing methods, identified 23-related clusters of phenetically similar isolates with high indexes of diversity. Interestingly, 16S rRNA gene sequencing suggested the presence of 43% new prokaryotic species. A sub-set of 139 isolates of the prokaryotic collection was selected for biotechnological exploitation with 484 bacterial extracts prepared in a sustainable upscalling manner. 22% of the extracts showed an industrially relevant photoprotective activity, with two extracts, belonging to new strains of the species Shewanella algae and Vibrio fluvialis, uniquely showing UV-A, UV-B and UV-C protective capacity. This clearly demonstrates the high potential of the bacteria MAR vents collection in natural product synthesis with market applications. Full article
(This article belongs to the Special Issue Deep-Sea Natural Products)
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Open AccessArticle Tetroazolemycins A and B, Two New Oxazole-Thiazole Siderophores from Deep-Sea Streptomyces olivaceus FXJ8.012
Mar. Drugs 2013, 11(5), 1524-1533; doi:10.3390/md11051524
Received: 16 February 2013 / Revised: 18 April 2013 / Accepted: 24 April 2013 / Published: 10 May 2013
Cited by 6 | PDF Full-text (747 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Two new oxazole/thiazole derivatives, named tetroazolemycins A (1) and B (2), have been isolated from the acetone extract of the mycelium of Streptomyces olivaceus FXJ8.012 derived from deep-sea water, together with three known compounds, spoxazomicins A–C (3 [...] Read more.
Two new oxazole/thiazole derivatives, named tetroazolemycins A (1) and B (2), have been isolated from the acetone extract of the mycelium of Streptomyces olivaceus FXJ8.012 derived from deep-sea water, together with three known compounds, spoxazomicins A–C (35), isolated from the fermentation supernatant. The planar structure and relative configuration of tetroazolemycins were elucidated by a combination of spectroscopic analyses, including 1D- and 2D-NMR techniques, and showed to be new pyochelin-type antibiotics. Both compounds showed metal ion-binding activity and their Zn2+ complexes exhibited weak activity against pathogenic bacteria Klebsiella pneumoniae. Full article
(This article belongs to the Special Issue Deep-Sea Natural Products)
Open AccessArticle Four New Chloro-Eremophilane Sesquiterpenes from an Antarctic Deep-Sea Derived Fungus, Penicillium sp. PR19N-1
Mar. Drugs 2013, 11(4), 1399-1408; doi:10.3390/md11041399
Received: 28 January 2013 / Revised: 25 March 2013 / Accepted: 7 April 2013 / Published: 23 April 2013
Cited by 18 | PDF Full-text (944 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A new chloro-trinoreremophilane sesquiterpene 1, three new chlorinated eremophilane sesquiterpenes 24, together with a known compound, eremofortine C (5), were isolated from an Antarctic deep-sea derived fungus, Penicillium sp. PR19N-1. Structures were established using IR, HRMS, [...] Read more.
A new chloro-trinoreremophilane sesquiterpene 1, three new chlorinated eremophilane sesquiterpenes 24, together with a known compound, eremofortine C (5), were isolated from an Antarctic deep-sea derived fungus, Penicillium sp. PR19N-1. Structures were established using IR, HRMS, 1D and 2D NMR techniques. In addition, the plausible metabolic network of these isolated products is proposed. Compound 1 showed moderate cytotoxic activity against HL-60 and A549 cancer cell lines. Full article
(This article belongs to the Special Issue Deep-Sea Natural Products)
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Open AccessArticle Biological Activities of Ethanolic Extracts from Deep-Sea Antarctic Marine Sponges
Mar. Drugs 2013, 11(4), 1126-1139; doi:10.3390/md11041126
Received: 21 February 2013 / Revised: 5 March 2013 / Accepted: 15 March 2013 / Published: 2 April 2013
Cited by 10 | PDF Full-text (430 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We report on the screening of ethanolic extracts from 33 deep-sea Antarctic marine sponges for different biological activities. We monitored hemolysis, inhibition of acetylcholinesterase, cytotoxicity towards normal and transformed cells and growth inhibition of laboratory, commensal and clinically and ecologically relevant bacteria. [...] Read more.
We report on the screening of ethanolic extracts from 33 deep-sea Antarctic marine sponges for different biological activities. We monitored hemolysis, inhibition of acetylcholinesterase, cytotoxicity towards normal and transformed cells and growth inhibition of laboratory, commensal and clinically and ecologically relevant bacteria. The most prominent activities were associated with the extracts from sponges belonging to the genus Latrunculia, which show all of these activities. While most of these activities are associated to already known secondary metabolites, the extremely strong acetylcholinesterase inhibitory potential appears to be related to a compound unknown to date. Extracts from Tetilla leptoderma, Bathydorus cf. spinosus, Xestospongia sp., Rossella sp., Rossella cf. racovitzae and Halichondria osculum were hemolytic, with the last two also showing moderate cytotoxic potential. The antibacterial tests showed significantly greater activities of the extracts of these Antarctic sponges towards ecologically relevant bacteria from sea water and from Arctic ice. This indicates their ecological relevance for inhibition of bacterial microfouling. Full article
(This article belongs to the Special Issue Deep-Sea Natural Products)
Open AccessCommunication Isolation, Characterization, and Bioactivity Evaluation of 3-((6-Methylpyrazin-2-yl)methyl)-1H-indole, a New Alkaloid from a Deep-Sea-Derived Actinomycete Serinicoccus profundi sp. nov.
Mar. Drugs 2013, 11(1), 33-39; doi:10.3390/md11010033
Received: 15 October 2012 / Revised: 7 November 2012 / Accepted: 22 November 2012 / Published: 27 December 2012
Cited by 13 | PDF Full-text (325 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
One new alkaloid, 3-((6-methylpyrazin-2-yl)methyl)-1H-indole (1) was obtained from the deep-sea actinomycete Serinicoccus profundi sp. nov., along with five known compounds (26). Their structures were determined on the basis of detailed analysis of the 1D [...] Read more.
One new alkaloid, 3-((6-methylpyrazin-2-yl)methyl)-1H-indole (1) was obtained from the deep-sea actinomycete Serinicoccus profundi sp. nov., along with five known compounds (26). Their structures were determined on the basis of detailed analysis of the 1D and 2D NMR as well as MS data. The new indole alkaloid displayed weak antimicrobial activity against Staphylococcus aureus ATCC 25923 with an MIC value of 96 μg/mL. It showed no cytotoxicity on a normal human liver cell line (BEL7402) and a human liver tumor cell line (HL-7702). Full article
(This article belongs to the Special Issue Deep-Sea Natural Products)
Open AccessArticle Ammonificins C and D, Hydroxyethylamine Chromene Derivatives from a Cultured Marine Hydrothermal Vent Bacterium, Thermovibrio ammonificans
Mar. Drugs 2012, 10(10), 2300-2311; doi:10.3390/md10102300
Received: 30 July 2012 / Revised: 18 September 2012 / Accepted: 29 September 2012 / Published: 19 October 2012
Cited by 7 | PDF Full-text (431 KB) | HTML Full-text | XML Full-text
Abstract
Chemical and biological investigation of the cultured marine hydrothermal vent bacterium, Thermovibrio ammonifican led to the isolation of two hydroxyethylamine chromene derivatives, ammonificins C and D. Their structures were elucidated using combination of NMR and mass spectrometry. Absolute stereochemistry was ascertained by [...] Read more.
Chemical and biological investigation of the cultured marine hydrothermal vent bacterium, Thermovibrio ammonifican led to the isolation of two hydroxyethylamine chromene derivatives, ammonificins C and D. Their structures were elucidated using combination of NMR and mass spectrometry. Absolute stereochemistry was ascertained by comparison of experimental and calculated CD spectra. Biological evaluation and assessment were determined using the patented ApopScreen cell-based screen for apoptosis-induction. Ammonificins C and D induce apoptosis in micromolar concentrations. To our knowledge, this finding is the first report of chemical compounds that induce apoptosis from the cultured deep-sea marine organism, hydrothermal vent bacterium, Thermovibrio ammonificans. Full article
(This article belongs to the Special Issue Deep-Sea Natural Products)
Open AccessArticle Natural Products from Antarctic Colonial Ascidians of the Genera Aplidium and Synoicum: Variability and Defensive Role
Mar. Drugs 2012, 10(8), 1741-1764; doi:10.3390/md10081741
Received: 29 June 2012 / Revised: 1 August 2012 / Accepted: 8 August 2012 / Published: 20 August 2012
Cited by 14 | PDF Full-text (997 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Ascidians have developed multiple defensive strategies mostly related to physical, nutritional or chemical properties of the tunic. One of such is chemical defense based on secondary metabolites. We analyzed a series of colonial Antarctic ascidians from deep-water collections belonging to the genera [...] Read more.
Ascidians have developed multiple defensive strategies mostly related to physical, nutritional or chemical properties of the tunic. One of such is chemical defense based on secondary metabolites. We analyzed a series of colonial Antarctic ascidians from deep-water collections belonging to the genera Aplidium and Synoicum to evaluate the incidence of organic deterrents and their variability. The ether fractions from 15 samples including specimens of the species A. falklandicum, A. fuegiense, A. meridianum, A. millari and S. adareanum were subjected to feeding assays towards two relevant sympatric predators: the starfish Odontaster validus, and the amphipod Cheirimedon femoratus. All samples revealed repellency. Nonetheless, some colonies concentrated defensive chemicals in internal body-regions rather than in the tunic. Four ascidian-derived meroterpenoids, rossinones B and the three derivatives 2,3-epoxy-rossinone B, 3-epi-rossinone B, 5,6-epoxy-rossinone B, and the indole alkaloids meridianins A–G, along with other minoritary meridianin compounds were isolated from several samples. Some purified metabolites were tested in feeding assays exhibiting potent unpalatabilities, thus revealing their role in predation avoidance. Ascidian extracts and purified compound-fractions were further assessed in antibacterial tests against a marine Antarctic bacterium. Only the meridianins showed inhibition activity, demonstrating a multifunctional defensive role. According to their occurrence in nature and within our colonial specimens, the possible origin of both types of metabolites is discussed. Full article
(This article belongs to the Special Issue Deep-Sea Natural Products)

Review

Jump to: Research

Open AccessReview The Deep-Sea Natural Products, Biogenic Polyphosphate (Bio-PolyP) and Biogenic Silica (Bio-Silica), as Biomimetic Scaffolds for Bone Tissue Engineering: Fabrication of a Morphogenetically-Active Polymer
Mar. Drugs 2013, 11(3), 718-746; doi:10.3390/md11030718
Received: 10 January 2013 / Revised: 4 February 2013 / Accepted: 6 February 2013 / Published: 8 March 2013
Cited by 7 | PDF Full-text (1910 KB) | HTML Full-text | XML Full-text
Abstract
Bone defects in human, caused by fractures/nonunions or trauma, gain increasing impact and have become a medical challenge in the present-day aging population. Frequently, those fractures require surgical intervention which ideally relies on autografts or suboptimally on allografts. Therefore, it is pressing [...] Read more.
Bone defects in human, caused by fractures/nonunions or trauma, gain increasing impact and have become a medical challenge in the present-day aging population. Frequently, those fractures require surgical intervention which ideally relies on autografts or suboptimally on allografts. Therefore, it is pressing and likewise challenging to develop bone substitution materials to heal bone defects. During the differentiation of osteoblasts from their mesenchymal progenitor/stem cells and of osteoclasts from their hemopoietic precursor cells, a lineage-specific release of growth factors and a trans-lineage homeostatic cross-talk via signaling molecules take place. Hence, the major hurdle is to fabricate a template that is functioning in a way mimicking the morphogenetic, inductive role(s) of the native extracellular matrix. In the last few years, two naturally occurring polymers that are produced by deep-sea sponges, the biogenic polyphosphate (bio-polyP) and biogenic silica (bio-silica) have also been identified as promoting morphogenetic on both osteoblasts and osteoclasts. These polymers elicit cytokines that affect bone mineralization (hydroxyapatite formation). In this manner, bio-silica and bio-polyP cause an increased release of BMP-2, the key mediator activating the anabolic arm of the hydroxyapatite forming cells, and of RANKL. In addition, bio-polyP inhibits the progression of the pre-osteoclasts to functionally active osteoclasts. Based on these findings, new bioinspired strategies for the fabrication of bone biomimetic templates have been developed applying 3D-printing techniques. Finally, a strategy is outlined by which these two morphogenetically active polymers might be used to develop a novel functionally active polymer. Full article
(This article belongs to the Special Issue Deep-Sea Natural Products)
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