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Marine Drugs
Special Issues
Challenges on Structural Determination of Marine Natural Products
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Challenges on Structural Determination of Marine Natural Products

A special issue of Marine Drugs (ISSN 1660-3397). This special issue belongs to the section "Structural Studies on Marine Natural Products".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 7065

Special Issue Editors

Dr. Bae Munhyung

E-Mail Website
Guest Editor
College of Pharmacy, Gachon University, 191, Hambangmoe-ro, Rm. 303, Yeonsu-gu, Incheon 21936, Republic of Korea
Interests: marine natural products; structure determination; molecular networking; computational analysis; biosynthetic pathway
Dr. Jae-hyuk Jang

E-Mail Website
Guest Editor
Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology/KRIBB School, University of Science and Technology, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si 28116, Chungbuk, Republic of Korea
Interests: marine natural products; structure determination; marine-derived fungus; biosynthesis

Special Issue Information

Dear Colleagues,                

Marine ecosystems, covering 70% of the surface of the earth, possess great biological diversity, providing interests for researchers over past decades. Due to their characteristic envrionments, marine natural products have been regarded as a highlighted source for the discovery of structurally and biologically novel drug candidates.

To overcome challenges in structure elucidation due to their diversity, marine natural products scientists have developed various chemical methodologies and recent advances in chemoinformatics tools, genome sequencing, and quantum-based computational analysis now provide combinatorial approches for the structure determination.

In this Special Issue, we invite academic and industry scientists to submit articles from marine-natural-products-driven studies, highlighting challenges in structural determination with biological activities.

Dr. Bae Munhyung
Dr. Jae-hyuk Jang
Guest Editors

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
  • chemical derivatization
  • computational analysis
  • biosynthesis
  • structure elucidation
  • methodology development

Published Papers (5 papers)

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Research

28 pages, 2175 KiB  
Article
Sulfated Triterpene Glycosides from the Far Eastern Sea Cucumber Cucumaria djakonovi: Djakonoviosides C1, D1, E1, and F1; Cytotoxicity against Human Breast Cancer Cell Lines; Quantitative Structure–Activity Relationships
by Alexandra S. Silchenko, Anatoly I. Kalinovsky, Sergey A. Avilov, Roman S. Popov, Ekaterina A. Chingizova, Ekaterina S. Menchinskaya, Elena A. Zelepuga, Elena G. Panina, Vadim G. Stepanov, Vladimir I. Kalinin and Pavel S. Dmitrenok
Mar. Drugs 2023, 21(12), 602; https://doi.org/10.3390/md21120602 - 22 Nov 2023
Viewed by 1349
Abstract
Four new mono- and trisulfated triterpene penta- and tetraosides, djakonoviosides C1 (1), D1 (2), E1 (3), and F1 (4) were isolated from the Far Eastern sea cucumber Cucumaria djakonovi (Cucumariidae, Dendrochirotida), [...] Read more.
Four new mono- and trisulfated triterpene penta- and tetraosides, djakonoviosides C1 (1), D1 (2), E1 (3), and F1 (4) were isolated from the Far Eastern sea cucumber Cucumaria djakonovi (Cucumariidae, Dendrochirotida), along with six known glycosides found earlier in other Cucumaria species. The structures of unreported compounds were established on the basis of extensive analysis of 1D and 2D NMR spectra as well as by HR-ESI-MS data. The set of compounds contains six different types of carbohydrate chains including two new ones. Thus, djakonovioside C1 (1) is characterized by xylose as the second residue, that was a branchpoint in the pentasaccharide chain. Meanwhile, only quinovose and rarely glucose have been found earlier in pentasaccharide chains branched at C-2 of the second sugar unit. Djakonovioside E1 (3) is characterized by a tetrasaccharide trisulfated chain, with glucose as the second residue. So, in the series of isolated glycosides, three types of sugars in the second position were presented: the most common, quinovose—in six compounds; glucose—in three substances; and the rare xylose—in one glycoside. The set of aglycones was composed of holostane- and non-holostane-type polycyclic systems; the latter comprised normal and reduced side chains. Noticeably, isokoreoside A (9), isolated from C. djakonovi, was a single glycoside having a 9(11)-double bond, indicating two oxidosqualenecyclases are operating in the process of the biosynthesis of aglycones. Some of the glycosides from C. djakonovi, which were characterized by pentasaccharide branched chains containing one to three sulfate groups, are chemotaxonomic features of the representatives of the genus Cucumaria. The assortment of sugar parts of Cucumaria’s glycosides was broadened with previously undescribed penta- and tetrasaccharide moieties. The metabolic network of sugar parts and aglycones is constructed based on biogenetic relationships. The cytotoxic action of compounds 1–10, isolated from C. djakonovi, against human breast cancer cell lines was investigated along with the hemolytic activity. Erythrocytes were, as usual, more sensitive to the membranolytic action of the glycosides than cancer cells. The triple-negative breast cancer MDA-MB-231 cell line was more vulnerable to the action of glycosides in comparison with the other tested cancer cells, while the MCF-7 cell line was less susceptible to cytotoxic action. Djakonovioside E1 (3) demonstrated selective action against ER-positive MCF-7 and triple-negative MDA-MB-231 cell lines, while the toxic effect in relation to normal mammary epithelial cells (MCF-10A) was absent. Cucumarioside A2-5 (6) inhibited the formation and growth of colonies of cancer cells to 44% and tumor cell migration to 85% of the control. Quantitative structure–activity relationships (QSAR) were calculated on the basis of the correlational analysis of the physicochemical properties and structural features of the glycosidic molecules and their membranolytic activity. QSAR revealed the extremely complex nature of such relationships, but these calculations correlated well with the observed SAR. Full article
(This article belongs to the Special Issue Challenges on Structural Determination of Marine Natural Products)
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13 pages, 3374 KiB  
Article
A Comprehensive Computational NMR Analysis of Organic Polyarsenicals including the Marine Sponge-Derived Arsenicins A–D and Their Synthetic Analogs
by Andrea Defant and Ines Mancini
Mar. Drugs 2023, 21(10), 511; https://doi.org/10.3390/md21100511 - 27 Sep 2023
Viewed by 982
Abstract
The adamantane structure of arsenicin A and nor-adamantane structures of arsenicins B–D have gained attention as unique natural polyarsenicals, as well as hits showing promising anticancer activity. The purpose of this study is to apply the predictive power of NMR DFT calculations in [...] Read more.
The adamantane structure of arsenicin A and nor-adamantane structures of arsenicins B–D have gained attention as unique natural polyarsenicals, as well as hits showing promising anticancer activity. The purpose of this study is to apply the predictive power of NMR DFT calculations in order to identify a valid tool to be used in the structural elucidation of similar molecules. 1H- and 13C-NMR chemical shifts of twelve natural and synthetic polyarsenical analogs were calculated and validated by comparison with experimental data acquired in CDCl3 solutions, in regard to mean absolute error (MAE) values under various combinations of two methods (GIAO and CSGT), four functionals and five basis sets, also considering relativistic effects. The best computational approaches are highlighted for predicting the chemical shifts of 1H and 13C nuclei and J(1H,1H) coupling constants in the series of O- and S-polyarsenicals. This comprehensive analysis contributes to making NMR spectroscopy appealing for the structural elucidation of such molecules, contrary to the first structural elucidation of natural arsenicin A, in which the experimental NMR analysis was limited by the poor presence of proton and carbon atoms in its structure and by the shortage of reference data. Full article
(This article belongs to the Special Issue Challenges on Structural Determination of Marine Natural Products)
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13 pages, 1580 KiB  
Article
Xinghamide A, a New Cyclic Nonapeptide Found in Streptomyces xinghaiensis
by Soohyun Um, Jaeyoun Lee, Sung Jin Kim, Kyung A Cho, Ki Sung Kang and Seung Hyun Kim
Mar. Drugs 2023, 21(10), 509; https://doi.org/10.3390/md21100509 - 26 Sep 2023
Cited by 1 | Viewed by 1251
Abstract
Xinghamide A (1), a new nonapeptide, was discovered in Streptomyces xinghaiensis isolated from a halophyte, Suaeda maritima (L.) Dumort. Based on high-resolution mass and NMR spectroscopic data, the planar structure of 1 was established, and, in particular, the sequence of nine [...] Read more.
Xinghamide A (1), a new nonapeptide, was discovered in Streptomyces xinghaiensis isolated from a halophyte, Suaeda maritima (L.) Dumort. Based on high-resolution mass and NMR spectroscopic data, the planar structure of 1 was established, and, in particular, the sequence of nine amino acids was determined with ROESY and HMBC NMR spectra. The absolute configurations of the α-carbon of each amino acid residue were determined with 1-fluoro-2,4-dinitrophenyl-l-and -d-leucine amide (Marfey’s reagents) and 2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl isothiocyanate, followed by LC-MS analysis. The anti-inflammatory activity of xinghamide A (1) was evaluated by inhibitory abilities against the nitric oxide (NO) secretion and cyclooxygenase-2 (COX-2) expression in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Full article
(This article belongs to the Special Issue Challenges on Structural Determination of Marine Natural Products)
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15 pages, 1603 KiB  
Article
Tandocyclinones A and B, Ether Bridged C-Glycosyl Benz[a]anthracenes from an Intertidal Zone Streptomyces sp.
by Thanh-Hau Huynh, Eun Seo Bae, Bo Eun Heo, Jayho Lee, Joon Soo An, Yun Kwon, Sang-Jip Nam, Ki-Bong Oh, Jichan Jang, Sang Kook Lee and Dong-Chan Oh
Mar. Drugs 2023, 21(9), 500; https://doi.org/10.3390/md21090500 - 21 Sep 2023
Viewed by 1332
Abstract
Two new proton-deficient metabolites, tandocyclinones A and B (1 and 2), were discovered via the chemical profiling of the Streptomyces sp. strain TDH03, which was isolated from a marine sediment sample collected from the intertidal mudflat in Tando Port, the Republic [...] Read more.
Two new proton-deficient metabolites, tandocyclinones A and B (1 and 2), were discovered via the chemical profiling of the Streptomyces sp. strain TDH03, which was isolated from a marine sediment sample collected from the intertidal mudflat in Tando Port, the Republic of Korea. The structures of 1 and 2 were elucidated as new ether-bridged C-glycosyl benz[a]anthracenes by using a combination of spectroscopic analyses of ultraviolet (UV) and mass spectrometry (MS) data, along with nuclear magnetic resonance (NMR) spectra, which were acquired in tetrahydrofuran (THF)-d8 selected after an extensive search for a solvent, resulting in mostly observable exchangeable protons in the 1H NMR spectrum. Their configurations were successfully assigned by applying a J-based configuration analysis, rotating-frame Overhauser enhancement spectroscopy (ROESY) NMR correlations, chemical derivatization methods based on NMR (a modified version of Mosher’s method) and circular dichroism (CD) (Snatzke’s method using Mo2(OAc)4-induced CD), as well as quantum-mechanics-based computational methods, to calculate the electronic circular dichroism (ECD). Tandocyclinones A and B (1 and 2) were found to have weak antifungal activity against Trichophyton mentagrophytes IFM40996 with an MIC value of 128 μg/mL (244 and 265 μM for 1 and 2, respectively). A further biological evaluation revealed that tandocyclinone A (1) displayed inhibitory activity against Mycobacterium avium (MIC50 = 40.8 μM) and antiproliferative activity against SNU638 and HCT116 cancer cells, with IC50 values of 31.9 µM and 49.4 µM, respectively. Full article
(This article belongs to the Special Issue Challenges on Structural Determination of Marine Natural Products)
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12 pages, 3388 KiB  
Communication
Briavioids E–G, Newly Isolated Briarane-Diterpenoids from a Cultured Octocoral Briareum violaceum
by Thanh Hao Huynh, Chia-Jung Liu, Yi-Hung Liu, Su-Ying Chien, Zhi-Hong Wen, Lee-Shing Fang, Jih-Jung Chen, Yang-Chang Wu, Jui-Hsin Su and Ping-Jyun Sung
Mar. Drugs 2023, 21(2), 124; https://doi.org/10.3390/md21020124 - 14 Feb 2023
Cited by 1 | Viewed by 1613
Abstract
The chemical screening of a cultured soft coral, Briareum violaceum, led to the isolation of eight natural, briarane-related diterpenoids, including three unreported metabolites, briavioids E–G (1–3), and five known briaranes, briacavatolides B (4) and C ( [...] Read more.
The chemical screening of a cultured soft coral, Briareum violaceum, led to the isolation of eight natural, briarane-related diterpenoids, including three unreported metabolites, briavioids E–G (1–3), and five known briaranes, briacavatolides B (4) and C (5), briaexcavatin L (6), briaexcavatolide U (7) and briarenol K (8). The structures of briaranes 1–8 were established using spectroscopic methods. The absolute configuration of briavioid A (9), obtained in a previous study, was reported for the first time in this study by a single-crystal X-ray diffraction analysis using a copper radiation source. The anti-inflammatory activity of briaranes 1 and 2 and briaranes 4–8 was evaluated by screening their inhibitory ability against the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) proteins in lipopolysaccharide (LPS)-induced RAW 264.7 macrophage cells. Full article
(This article belongs to the Special Issue Challenges on Structural Determination of Marine Natural Products)
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