Special Issue "New Challenges in Structure Elucidation of Marine Natural Products: NMR Analyses and Other Advanced Methods"

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

Deadline for manuscript submissions: 31 May 2020.

Special Issue Editor

Dr. Marie-Lise Bourguet-Kondracki
E-Mail Website
Guest Editor
Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d’Histoire Naturelle, 57 rue Cuvier (CP54), 75005 Paris, France
Interests: marine natural product chemistry; marine sponges; marine microbiology; marine chemical ecology; bioactivity
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Special Issue Information

Dear Colleagues,

The marine field continues to represent a prolific source of innovative natural products with remarkable biological activities. However, the structure elucidation of these specialized metabolites is often a true challenge due to their small quantity and their complexity. Most of the isolated molecules possess multiple stereocenters, can be halogenated or have peculiar functional groups. Assigning the absolute stereostructure and the conformational properties, which are crucial in biological activities, remains a challenging problem.

X-Ray analyses for crystalline compounds or chemical synthesis approaches including chemical degradation as well as NMR chiral derivatization but also computational studies are the main strategies developed for elucidating the absolute configuration of these molecules. More recently, original approaches of chiroptical methods such as electronic circular dichroism and vibrational circular dichroism have emerged as powerful tools expanding the traditional methods.

This Special Issue proposes to focus on the different challenging strategies, including advanced NMR and innovative stereochemistry determination approaches, for solving the identification of the marine natural products.

Dr. Marie-Lise Bourguet-Kondracki
Guest Editor

Manuscript Submission Information

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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 2000 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

  • NMR analyses
  • X-ray structure analyses
  • partial or total enantioselective synthesis
  • chemical degradation
  • NMR analyses of Mosher esters and related derivatives
  • electronic circular dichroism (ECD or CD)
  • vibrational circular dichroism (VCD)

Published Papers (8 papers)

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Research

Open AccessArticle
Four New Insecticidal Xanthene Derivatives from the Mangrove-Derived Fungus Penicillium sp. JY246
Mar. Drugs 2019, 17(12), 649; https://doi.org/10.3390/md17120649 - 20 Nov 2019
Abstract
Four new xanthene derivatives, penicixanthenes A–D (14), and one known compound 5 were isolated from a marine mangrove endophytic fungus Penicillium sp. JY246 that was obtained from the stem of Ceriops tagal. Their structures were determined by detailed [...] Read more.
Four new xanthene derivatives, penicixanthenes A–D (14), and one known compound 5 were isolated from a marine mangrove endophytic fungus Penicillium sp. JY246 that was obtained from the stem of Ceriops tagal. Their structures were determined by detailed NMR, MS spectroscopic data, modified Mosher’s method, and calculated electronic circular dichroism data. All of the isolated compounds were examined for insecticidal activity. Compounds 2 and 3 showed growth inhibition activity against newly hatched larvae of Helicoverpa armigera Hubner with the IC50 values 100 and 200 μg/mL, respectively, and compounds 1, 3, and 4 showed insecticidal activity against newly hatched larvae of Culex quinquefasciatus with LC50 values of 38.5 (±1.16), 11.6 (±0.58), and 20.5 (±1) μg/mL, respectively. The four xanthene derivatives have the potential to be developed as new biopesticides. Full article
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Open AccessArticle
Novel Microcystins from Planktothrix prolifica NIVA-CYA 544 Identified by LC-MS/MS, Functional Group Derivatization and 15N-labeling
Mar. Drugs 2019, 17(11), 643; https://doi.org/10.3390/md17110643 - 15 Nov 2019
Abstract
Microcystins are cyclic heptapeptides from cyanobacteria that are potent inhibitors of protein phosphatases and are toxic to animals and humans. At present, more than 250 microcystin variants are known, with variants reported for all seven peptide moieties. While d-glutamic acid (d [...] Read more.
Microcystins are cyclic heptapeptides from cyanobacteria that are potent inhibitors of protein phosphatases and are toxic to animals and humans. At present, more than 250 microcystin variants are known, with variants reported for all seven peptide moieties. While d-glutamic acid (d-Glu) is highly-conserved at position-6 of microcystins, there has been only one report of a cyanobacterium (Anabaena) producing microcystins containing l-Glu at the variable 2- and 4-positions. Liquid chromatography–mass spectrometry analyses of extracts from Planktothrix prolifica NIVA-CYA 544 led to the tentative identification of two new Glu-containing microcystins, [d-Asp3]MC-ER (12) and [d-Asp3]MC-EE (13). Structure determination was aided by thiol derivatization of the Mdha7-moiety and esterification of the carboxylic acid groups, while 15N-labeling of the culture and isotopic profile analysis assisted the determination of the number of nitrogen atoms present and the elemental composition of molecular and product-ions. The major microcystin analog in the extracts was [d-Asp3]MC-RR (1). A microcystin with an unprecedented high-molecular-mass (2116 Da) was also detected and tentatively identified as a sulfide-linked conjugate of [d-Asp3]MC-RR (15) by LC–HRMS/MS and sulfide oxidation, together with its sulfoxide (16) produced via autoxidation. Low levels of [d-Asp3]MC-RW (14), [d-Asp3]MC-LR (4), [d-Asp3,Mser7]MC-RR (11), [d-Asp3]MC-RY (17), [d-Asp3]MC-RF (18), [d-Asp3]MC-RR–glutathione conjugate (19), and [d-Asp3]MC-RCit (20), the first reported microcystin containing citrulline, were also identified in the extract, and an oxidized derivative of [d-Asp3]MC-RR and the cysteine conjugate of 1 were partially characterized. Full article
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Open AccessArticle
Prenylated Phenol and Benzofuran Derivatives from Aspergillus terreus EN-539, an Endophytic Fungus Derived from Marine Red Alga Laurencia okamurai
Mar. Drugs 2019, 17(11), 605; https://doi.org/10.3390/md17110605 - 24 Oct 2019
Abstract
Three new prenylated phenol derivatives, terreprenphenols A–C (13), along with four known related compounds (47), were isolated from Aspergillus terreus EN-539, an endophytic fungus obtained from the marine red alga Laurencia okamurai. The structures [...] Read more.
Three new prenylated phenol derivatives, terreprenphenols A–C (13), along with four known related compounds (47), were isolated from Aspergillus terreus EN-539, an endophytic fungus obtained from the marine red alga Laurencia okamurai. The structures of these compounds were established by extensive analysis of 1D/2D NMR data, mass spectrometric data, and optical rotation (OR). The corresponding relationship between absolute configuration and optical rotation for known compounds anodendroic acid (4) and asperterreusine C (5) was ambiguous in literature, and their absolute configurations were therefore discussed and confirmed for the first time by time-dependent density functional (TDDFT) ECD and OR calculations. Compounds 17 inhibited some common aquatic bacteria with MIC values ranging from 2 to 64 μg/mL. Full article
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Open AccessArticle
Bioactive Diketopiperazines and Nucleoside Derivatives from a Sponge-Derived Streptomyces Species
Mar. Drugs 2019, 17(10), 584; https://doi.org/10.3390/md17100584 - 16 Oct 2019
Abstract
Fractionation and purification of the ethyl acetate extract of the culture of a sponge-derived actinomycete, Streptomyces species Call-36, resulted in the isolation and identification of a new diketopiperazine, actinozine A (1), cyclo(2-OH-d-Pro-l-Leu) (2), two new [...] Read more.
Fractionation and purification of the ethyl acetate extract of the culture of a sponge-derived actinomycete, Streptomyces species Call-36, resulted in the isolation and identification of a new diketopiperazine, actinozine A (1), cyclo(2-OH-d-Pro-l-Leu) (2), two new nucleosides, thymidine-3-mercaptocarbamic acid (3) and thymidine-3-thioamine (4), together with cyclo(d-Pro-l-Phe) (5) and cyclo(l-Pro-l-Phe) (6). The structure assignments of the compounds were carried out by interpretation of 1D and 2D NMR data and mass spectral determinations. The absolute configurations of 1 and 2 were determined by Marfey’s method and by comparison of the experimental and TDDFT-calculated ECD spectra. Actinozine A possesses an unprecedented hydroperoxy moiety at C-2 of the proline moiety, while 3 and 4 possess unusual mercaptocarbamic acid and thiohydroxylamine functionalities at N-3 of the thymine moiety. The isolated compounds displayed variable cytotoxic and antimicrobial activities. Full article
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Open AccessArticle
Bathyptilones: Terpenoids from an Antarctic Sea Pen, Anthoptilum grandiflorum (Verrill, 1879)
Mar. Drugs 2019, 17(9), 513; https://doi.org/10.3390/md17090513 - 01 Sep 2019
Abstract
An Antarctic coral belonging to the order Pennatulacea, collected during the 2013 austral autumn by trawl from 662 to 944 m depth, has yielded three new briarane diterpenes, bathyptilone A-C (13) along with a trinorditerpene, enbepeanone A (4 [...] Read more.
An Antarctic coral belonging to the order Pennatulacea, collected during the 2013 austral autumn by trawl from 662 to 944 m depth, has yielded three new briarane diterpenes, bathyptilone A-C (13) along with a trinorditerpene, enbepeanone A (4), which bears a new carbon skeleton. Structure elucidation was facilitated by one- and two-dimensional NMR spectroscopy, mass spectrometry and confirmed by X-ray crystallography. The three compounds were screened in four cancer cell lines. Bathyptilone A displayed selective nanomolar cytotoxicity against the neurogenic mammalian cell line Ntera-2. Full article
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Open AccessArticle
New Peptides from The Marine-Derived Fungi Aspergillus allahabadii and Aspergillus ochraceopetaliformis
Mar. Drugs 2019, 17(9), 488; https://doi.org/10.3390/md17090488 - 21 Aug 2019
Abstract
Four new peptides were isolated from the culture broths of the marine-derived fungi Aspergillus allahabadii and A. ochraceopetaliformis. Based on the results of chemical and spectroscopic analyses, two compounds (1 and 2) from A. allahabadii were determined to be cyclopentapeptides, while [...] Read more.
Four new peptides were isolated from the culture broths of the marine-derived fungi Aspergillus allahabadii and A. ochraceopetaliformis. Based on the results of chemical and spectroscopic analyses, two compounds (1 and 2) from A. allahabadii were determined to be cyclopentapeptides, while those from A. ochraceopetaliformis were a structurally-related cyclodepsihexapeptide (3) and its linear analog (4). In addition to the presence of a D-amino acid residue, the almost reversed sequence of peptides in 3 and 4, relative to those of the 1 and 2, is notable. These new compounds exhibited moderate inhibition against the enzyme sortase A as well as a weak inhibition against isocitrate lyase (2). Full article
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Open AccessArticle
A Collection of Bioactive Nitrogen-Containing Molecules from the Marine Sponge Acanthostrongylophora ingens
Mar. Drugs 2019, 17(8), 472; https://doi.org/10.3390/md17080472 - 15 Aug 2019
Abstract
Thirteen nitrogen-containing molecules (1a/1b and 212) were isolated from the Indonesian sponge Acanthostrongylophora ingens, highlighting the richness of this organism as a source of alkaloids. Their structures were elucidated using one- and two-dimensional NMR spectroscopy and [...] Read more.
Thirteen nitrogen-containing molecules (1a/1b and 212) were isolated from the Indonesian sponge Acanthostrongylophora ingens, highlighting the richness of this organism as a source of alkaloids. Their structures were elucidated using one- and two-dimensional NMR spectroscopy and HR-ESI-MS, while the stereochemistry of the diketopiperazines was established using Marfey’s method. All compounds were screened in our standard bioactivity assays, including antibacterial, antikinases, and amyloid β-42 assays. The most interesting bioactivity result was obtained with the known acanthocyclamine A (3), which revealed for the first time a specific Escherichia coli antimicrobial activity and an inhibitory effect on amyloid β-42 production induced by aftin-5 and no cytotoxicity at the dose of 26 µM. These results highlight the potentiality of a bipiperidine scaffold as a promising skeleton for preventing or reducing the production of amyloid β-42, a key player in the initiation of Alzheimer’s disease. Full article
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Open AccessArticle
The Purification, Characterization, and Biological Activity of New Polyketides from Mangrove-Derived Endophytic Fungus Epicoccum nigrum SCNU-F0002
Mar. Drugs 2019, 17(7), 414; https://doi.org/10.3390/md17070414 - 12 Jul 2019
Abstract
Six new polyketides, including one coumarin (1), two isocoumarins (2 and 3), dihydroradicinin (4), and two benzofuranone derivatives (7 and 8), together with seven known analogues (56 and 913) [...] Read more.
Six new polyketides, including one coumarin (1), two isocoumarins (2 and 3), dihydroradicinin (4), and two benzofuranone derivatives (7 and 8), together with seven known analogues (56 and 913) were isolated from the culture of the mangrove endophytic fungus Epicoccum nigrum SCNU-F0002. The structures were elucidated on the interpretation of spectroscopic data. The absolute configuration of Compounds 2 and 3 were determined by comparison of their ECD spectra with the data of their analogue dihydroisocoumarins described in the literature. The absolute configuration of 4 was determined by single-crystal X-ray diffraction. All the compounds were screened for their antioxidant, antibacterial, anti-phytopathogenic fungi and cytotoxic activities. Using a DPPH radical-scavenging assay, Compounds 1013 showed potent antioxidant activity with IC50 values of 13.6, 12.1, 18.1, and 11.7 μg/mL, respectively. In addition, Compounds 6 and 7 showed antibacterial effects against Bacillus subtilis (ATCC 6538), Escherichia coli (ATCC 8739), and Staphylococcus aureus (ATCC 6538), with MIC values in the range of 25–50 μg/mL. Full article
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