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Marine Drugs
Special Issues
Taking On the Challenges of Marine Natural Products Structure Elucidation
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Taking On the Challenges of Marine Natural Products Structure Elucidation

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

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 20505

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; antifouling, anti-biofilm compounds
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Marine Drugs recently released a successful Special Issue “New Challenges in Structure Elucidation of Marine Natural Products: NMR Analyses and Other Advanced Methods” (https://www.mdpi.com/journal/marinedrugs/special_issues/NMR-advanced), collecting state-of-the-art research outcomes in this field. We are glad to say that in response to readers’ great passion for this research topic, we have decided to launch a second edition of the original Special Issue, which will continue focusing on the different challenging strategies used for solving the identification of marine natural products.

Modern analytical techniques and methods, encompassing mass-spectrometry-based omics strategies, advanced NMR methods, computational chemistry procedures, chiroptical methods, and configurational analysis approaches have emerged as powerful tools for the structure elucidation of marine natural products, expanding upon the traditional methods. These innovative approaches will be at the heart of this second edition Special Issue entitled “Taking on the Challenges of Marine Natural Products Structure Elucidation”.

Dr. Marie-Lise Bourguet-Kondracki
Guest Editor

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

  • Marine Natural Products
  • Structure Elucidation
  • NMR
  • MS
  • Computational Chemistry Procedure
  • Chiroptical Methods
  • Configurational Analysis

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Published Papers (6 papers)

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Research

17 pages, 6186 KiB  
Article
Scalarane-Type Sesterterpenoids from the Marine Sponge Lendenfeldia sp. Alleviate Inflammation in Human Neutrophils
by Bo-Rong Peng, Kuei-Hung Lai, Gene-Hsiang Lee, Steve Sheng-Fa Yu, Chang-Yih Duh, Jui-Hsin Su, Li-Guo Zheng, Tsong-Long Hwang and Ping-Jyun Sung
Mar. Drugs 2021, 19(10), 561; https://doi.org/10.3390/md19100561 - 30 Sep 2021
Cited by 10 | Viewed by 3221
Abstract
Sponge-derived scalaranes are remarkable sesterterpenoids previously found to exhibit profound inhibitory effects against neutrophilic inflammation. In our current work, we constructed the metabolomic profile of marine sponge Lendenfeldia sp. for the first time using a tandem mass spectrometry (MS/MS) molecular networking approach. The [...] Read more.
Sponge-derived scalaranes are remarkable sesterterpenoids previously found to exhibit profound inhibitory effects against neutrophilic inflammation. In our current work, we constructed the metabolomic profile of marine sponge Lendenfeldia sp. for the first time using a tandem mass spectrometry (MS/MS) molecular networking approach. The results highlighted the rich chemical diversity of these scalaranes, motivating us to conduct further research to discover novel scalaranes targeting neutrophilic inflammation. MS- and NMR-assisted isolation and elucidation led to the discovery of seven new homoscalaranes, lendenfeldaranes K–Q (1–7), characterized by methylation at C-24, together with five known derivatives, lendenfeldarane B (8), 25-nor-24-methyl-12,24-dioxoscalar-16-en-22-oic acid (9), 24-methyl-12,24,25-trioxoscalar-16-en-22-oic acid (10), felixin B (11), and 23-hydroxy-20-methyldeoxoscalarin (12). Scalaranes 1–4 and 6–12 were assayed against superoxide anion generation and elastase release, which represented the neutrophilic inflammatory responses of respiratory burst and degranulation, respectively. The results indicated that 1–3 and 6–12 exhibited potential anti-inflammatory activities (IC50 for superoxide anion scavenging: 0.87~6.57 μM; IC50 for elastase release: 1.12~6.97 μM). Full article
(This article belongs to the Special Issue Taking On the Challenges of Marine Natural Products Structure Elucidation)
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14 pages, 10972 KiB  
Article
Structural Characterization and Heparanase Inhibitory Activity of Fucosylated Glycosaminoglycan from Holothuria floridana
by Xiang Shi, Ruowei Guan, Lutan Zhou, Zhichuang Zuo, Xuelin Tao, Pin Wang, Yanrong Zhou, Ronghua Yin, Longyan Zhao, Na Gao and Jinhua Zhao
Mar. Drugs 2021, 19(3), 162; https://doi.org/10.3390/md19030162 - 18 Mar 2021
Cited by 9 | Viewed by 2841
Abstract
Unique fucosylated glycosaminoglycans (FG) have attracted increasing attention for various bioactivities. However, the precise structures of FGs usually vary in a species-specific manner. In this study, HfFG was isolated from Holothuria floridana and purified by anion exchange chromatography with the yield of ~0.9%. [...] Read more.
Unique fucosylated glycosaminoglycans (FG) have attracted increasing attention for various bioactivities. However, the precise structures of FGs usually vary in a species-specific manner. In this study, HfFG was isolated from Holothuria floridana and purified by anion exchange chromatography with the yield of ~0.9%. HfFG was composed of GlcA, GalNAc and Fuc, its molecular weight was 47.3 kDa, and the -OSO3−/-COO− molar ratio was 3.756. HfFG was depolymerized by a partial deacetylation–deaminative cleavage method to obtain the low-molecular-weight HfFG (dHfFG). Three oligosaccharide fragments (Fr-1, Fr-2, Fr-3) with different molecular weights were isolated from the dHfFG, and their structures were revealed by 1D and 2D NMR spectroscopy. HfFG should be composed of repeating trisaccharide units -{(L-FucS-α1,3-)d-GlcA-β1,3-d-GalNAc4S6S-β1,4-}-, in which sulfated fucose (FucS) includes Fuc2S4S, Fuc3S4S and Fuc4S residues linked to O-3 of GlcA in a ratio of 45:35:20. Furthermore, the heparanase inhibitory activities of native HfFG and oligosaccharide fragments (Fr-1, Fr-2, Fr-3) were evaluated. The native HfFG and its oligosaccharides exhibited heparanase inhibitory activities, and the activities increased with the increase of molecular weight. Additionally, structural characteristics such as sulfation patterns, the terminal structure of oligosaccharides and the presence of fucosyl branches may be important factors affecting heparanase inhibiting activity. Full article
(This article belongs to the Special Issue Taking On the Challenges of Marine Natural Products Structure Elucidation)
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12 pages, 1034 KiB  
Article
Density Functional Theory (DFT)-Aided Structure Elucidation of Linear Diterpenes from the Irish Brown Seaweed Bifurcaria bifurcata
by Vangelis Smyrniotopoulos, Daria Firsova, Howard Fearnhead, Laura Grauso, Alfonso Mangoni and Deniz Tasdemir
Mar. Drugs 2021, 19(1), 42; https://doi.org/10.3390/md19010042 - 19 Jan 2021
Cited by 7 | Viewed by 3174
Abstract
Brown alga Bifurcaria bifurcata is an extraordinarily rich source of linear (acylic) diterpenes with enormous structural diversity. As part of our interest into secondary metabolites of the Irish seaweeds, here we report four new acyclic diterpenes (1–4) and seven [...] Read more.
Brown alga Bifurcaria bifurcata is an extraordinarily rich source of linear (acylic) diterpenes with enormous structural diversity. As part of our interest into secondary metabolites of the Irish seaweeds, here we report four new acyclic diterpenes (1–4) and seven known terpenoids (5–11) from the CHCl3 extract of B. bifurcata. The planar structures of the new metabolites were elucidated by means of 1D and 2D NMR, HRMS, and FT-IR spectroscopy. Since linear diterpenes are highly flexible compounds, the assignment of their stereochemistry by conventional methods, e.g., NOESY NMR, is difficult. Therefore, we employed extensive quantum-mechanical prediction of NMR chemical shifts and optical rotation analyses to identify the relative and absolute configurations of the new compounds 1–4. Several compounds moderately inhibited the human breast cancer cell line (MDA-MB-231) with IC50 values ranging from 10.0 to 33.5 μg/mL. This study not only demonstrates the vast capacity of the Irish B. bifurcata to produce highly oxygenated linear diterpenoids, but also highlights the potential of new methodologies for assignment of their stereogenic centers. Full article
(This article belongs to the Special Issue Taking On the Challenges of Marine Natural Products Structure Elucidation)
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9 pages, 418 KiB  
Article
Oxygenated Acyclic Diterpenes with Anticancer Activity from the Irish Brown Seaweed Bifurcaria bifurcata
by Vangelis Smyrniotopoulos, Christian Merten, Daria Firsova, Howard Fearnhead and Deniz Tasdemir
Mar. Drugs 2020, 18(11), 581; https://doi.org/10.3390/md18110581 - 23 Nov 2020
Cited by 12 | Viewed by 3283
Abstract
Brown alga Bifurcaria bifurcata is a prolific source of bioactive acyclic (linear) diterpenes with high structural diversity. In the continuation of our investigations on Irish brown algae, we undertook an in-depth chemical study on the n-hexanes and chloroform subextracts of B. bifurcata [...] Read more.
Brown alga Bifurcaria bifurcata is a prolific source of bioactive acyclic (linear) diterpenes with high structural diversity. In the continuation of our investigations on Irish brown algae, we undertook an in-depth chemical study on the n-hexanes and chloroform subextracts of B. bifurcata that led to isolation of six new (1–6) and two known (7–8) acyclic diterpenes. Chemical structures of the compounds were elucidated by a combination of 1D and 2D NMR, HRMS, FT-IR, [α]D and vibrational circular dichroism (VCD) spectroscopy. Compounds 1–8, as well as three additional linear diterpenes (9–11), which we isolated from the same seaweed before, were tested against the human breast cancer cell line (MDA-MB-231). Several compounds moderately inhibited the growth of the MDA-MB-231 cell line with IC50 values ranging from 11.6 to 32.0 μg/mL. The present study carried out on the lipophilic extracts of the Irish B. bifurcata shows the enormous capacity of this seaweed to produce a large palette of acyclic diterpenes with diverse oxygenation and substitution patterns and promising bioactivities. Full article
(This article belongs to the Special Issue Taking On the Challenges of Marine Natural Products Structure Elucidation)
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21 pages, 3741 KiB  
Article
Mass Spectrometry-Based Characterization of New Spirolides from Alexandrium ostenfeldii (Dinophyceae)
by Joyce A. Nieva, Jan Tebben, Urban Tillmann, Sylke Wohlrab and Bernd Krock
Mar. Drugs 2020, 18(10), 505; https://doi.org/10.3390/md18100505 - 2 Oct 2020
Cited by 6 | Viewed by 2743
Abstract
Spirolides belong to a group of marine phycotoxins produced by the marine planktonic dinophyte Alexandrium ostenfeldii. Composed of an imine moiety and a spiroketal ring system within a macrocylcle, spirolides are highly diverse with toxin types that vary among different strains. This [...] Read more.
Spirolides belong to a group of marine phycotoxins produced by the marine planktonic dinophyte Alexandrium ostenfeldii. Composed of an imine moiety and a spiroketal ring system within a macrocylcle, spirolides are highly diverse with toxin types that vary among different strains. This study aims to characterize the spirolides from clonal A. ostenfeldii strains collected from The Netherlands, Greenland and Norway by mass spectral techniques. The structural characterization of unknown spirolides as inferred from high-resolution mass spectrometry (HR-MS) and collision induced dissociation (CID) spectra revealed the presence of nine novel spirolides that have the pseudo-molecular ions m/z 670 (1), m/z 666 (2), m/z 696 (3), m/z 678 (4), m/z 694 (5), m/z 708 (6), m/z 720 (7), m/z 722 (8) and m/z 738 (9). Of the nine new spirolides proposed in this study, compound 1 was suggested to have a truncated side chain in lieu of the commonly observed butenolide ring in spirolides. Moreover, there is indication that compound 5 might belong to new spirolide subclasses with a trispiroketal ring configuration having a 6:5:6 trispiroketal ring system. On the other hand, the other compounds were proposed as C- and G-type SPX, respectively. Compound 7 is proposed as the first G-type SPX with a 10-hydroxylation as usually observed in C-type SPX. This mass spectrometry-based study thus demonstrates that structural variability of spirolides is larger than previously known and does not only include the presence or absence of certain functional groups but also involves the triketal ring system. Full article
(This article belongs to the Special Issue Taking On the Challenges of Marine Natural Products Structure Elucidation)
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15 pages, 1632 KiB  
Article
Integrating Molecular Networking and 1H NMR Spectroscopy for Isolation of Bioactive Metabolites from the Persian Gulf Sponge Axinella sinoxea
by Reza Mohsenian Kouchaksaraee, Mahdi Moridi Farimani, Fengjie Li, Melika Nazemi and Deniz Tasdemir
Mar. Drugs 2020, 18(7), 366; https://doi.org/10.3390/md18070366 - 16 Jul 2020
Cited by 10 | Viewed by 4303
Abstract
The geographic position, highly fluctuating sea temperatures and hypersalinity make Persian Gulf an extreme environment. Although this unique environment has high biodiversity dominated by invertebrates, its potential in marine biodiscovery has largely remained untapped. Herein, we aimed at a detailed analysis of the [...] Read more.
The geographic position, highly fluctuating sea temperatures and hypersalinity make Persian Gulf an extreme environment. Although this unique environment has high biodiversity dominated by invertebrates, its potential in marine biodiscovery has largely remained untapped. Herein, we aimed at a detailed analysis of the metabolome and bioactivity profiles of the marine sponge Axinella sinoxea collected from the northeast coast of the Persian Gulf in Iran. The crude extract and its Kupchan subextracts were tested in multiple in-house bioassays, and the crude extract and its CHCl3-soluble portion showed in vitro antibacterial activity against Methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium (Efm). A molecular networking (MN)-based dereplication strategy by UPLC-MS/MS revealed the presence of phospholipids and steroids, while 1H NMR spectroscopy indicated the presence of additional metabolites, such as diketopiperazines (DKPs). Integrated MN and 1H NMR analyses on both the crude and CHCl3 extracts combined with an antibacterial activity-guided isolation approach afforded eight metabolites: a new diketopiperazine, (-)-cyclo(L-trans-Hyp-L-Ile) (8); a known diketopiperazine, cyclo(L-trans-Hyp-L-Phe) (7); two known phospholipids, 1-O-hexadecyl-sn-glycero-3-phosphocholine (1) and 1-O-octadecanoyl-sn-glycero-3-phosphocholine (2); two known steroids, 3β-hydroxycholest-5-ene-7,24-dione (3) and (22E)-3β-hydroxycholesta-5,22-diene-7,24-dione (4); two known monoterpenes, loliolide (5) and 5-epi-loliolide (6). The chemical structures of the isolates were elucidated by a combination of NMR spectroscopy, HRMS and [α]D analyses. All compounds were tested against MRSA and Efm, and compound 3 showed moderate antibacterial activity against MRSA (IC50 value 70 μg/mL). This is the first study that has dealt with chemical and bioactivity profiling of A. sinoxea leading to isolation and characterization of pure sponge metabolites. Full article
(This article belongs to the Special Issue Taking On the Challenges of Marine Natural Products Structure Elucidation)
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