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Marine Drugs
Special Issues
Discovering Marine Bioactive Compounds by Molecular Networking
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Discovering Marine Bioactive Compounds by Molecular Networking

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 13974

Special Issue Editor

Dr. Roberta Teta

E-Mail Website
Guest Editor
The Blue Chemistry Lab, Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
Interests: bioactive natural products; marine organisms; microorganisms; structure elucidation; biosynthesis; spectroscopic analysis; metabolomics; molecular networking
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, molecular networking has given a significant boost to the exploration and exploitation of the huge chemical potential of marine sources and to the discovery of new drug leads from them. Molecular networking is a computational strategy for automated analysis and mining of MS and LC-MS data. It provides a snapshot of the chemical profile of a sample and allows the early detection of known and new chemical entities in complex mixtures, speeding up the drug discovery pipeline and avoiding compound rediscovery.

The Special Issue “Discovering Marine Bioactive Compounds by Molecular Networking” welcomes contributions focused on the use and implementation of molecular networking for the discovery, characterization, and quantification of bioactive natural products from marine sources.

Dr. Roberta Teta
Guest Editor

Keywords

  • Dereplication
  • Drug discovery
  • Bioactive natural products
  • Mass spectrometry
  • Structure elucidation

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Published Papers (4 papers)

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16 pages, 4086 KiB  
Article
New Pyrroline Isolated from Antarctic Krill-Derived Actinomycetes Nocardiopsis sp. LX-1 Combining with Molecular Networking
by Ting Shi, Yan-Jing Li, Ze-Min Wang, Yi-Fei Wang, Bo Wang and Da-Yong Shi
Mar. Drugs 2023, 21(2), 127; https://doi.org/10.3390/md21020127 - 15 Feb 2023
Cited by 3 | Viewed by 2622
Abstract
Antarctic krill (Euphausia superba) of the Euphausiidae family comprise one of the largest biomasses in the world and play a key role in the Antarctic marine ecosystem. However, the study of E. superba-derived microbes and their secondary metabolites has been [...] Read more.
Antarctic krill (Euphausia superba) of the Euphausiidae family comprise one of the largest biomasses in the world and play a key role in the Antarctic marine ecosystem. However, the study of E. superba-derived microbes and their secondary metabolites has been limited. Chemical investigation of the secondary metabolites of the actinomycetes Nocardiopsis sp. LX-1 (in the family of Nocardiopsaceae), isolated from E. superba, combined with molecular networking, led to the identification of 16 compounds a–p (purple nodes in the molecular network) and the isolation of one new pyrroline, nocarpyrroline A (1), along with 11 known compounds 2–12. The structure of the new compound 1 was elucidated by extensive spectroscopic investigation. Compound 2 exhibited broad-spectrum antibacterial activities against A. hydrophila, D. chrysanthemi, C. terrigena, X. citri pv. malvacearum and antifungal activity against C. albicans in a conventional broth dilution assay. The positive control was ciprofloxacin with the MIC values of <0.024 µM, 0.39 µM, 0.39 µM, 0.39 µM, and 0.20 µM, respectively. Compound 1 and compounds 7, 10, and 11 displayed antifungal activities against F. fujikuroi and D. citri, respectively, in modified agar diffusion test. Prochloraz was used as positive control and showed the inhibition zone radius of 17 mm and 15 mm against F. fujikuroi and D. citri, respectively. All the annotated compounds a–p by molecular networking were first discovered from the genus Nocardiopsis. Nocarpyrroline A (1) features an unprecedented 4,5-dihydro-pyrrole-2-carbonitrile substructure, and it is the first pyrroline isolated from the genus Nocardiopsis. This study further demonstrated the guiding significance of molecular networking in the research of microbial secondary metabolites. Full article
(This article belongs to the Special Issue Discovering Marine Bioactive Compounds by Molecular Networking)
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14 pages, 3607 KiB  
Article
Molecular Networking Revealed Unique UV-Absorbing Phospholipids: Favilipids from the Marine Sponge Clathria faviformis
by Silvia Scarpato, Roberta Teta, Paola De Cicco, Francesca Borrelli, Joseph R. Pawlik, Valeria Costantino and Alfonso Mangoni
Mar. Drugs 2023, 21(2), 58; https://doi.org/10.3390/md21020058 - 18 Jan 2023
Cited by 2 | Viewed by 3315
Abstract
Analysis of extracts of the marine sponge Clathria faviformis by high-resolution LC-MS2 and molecular networking resulted in the discovery of a new family of potentially UV-protecting phospholipids, the favilipids. One of them, favilipid A (1), was isolated and its structure [...] Read more.
Analysis of extracts of the marine sponge Clathria faviformis by high-resolution LC-MS2 and molecular networking resulted in the discovery of a new family of potentially UV-protecting phospholipids, the favilipids. One of them, favilipid A (1), was isolated and its structure determined by mass and tandem mass spectrometry, NMR, electronic circular dichroism (ECD), and computational studies. Favilipid A, which has no close analogues among natural products, possesses an unprecedented structure characterized by a 4-aminodihydropiridinium core, resulting in UV-absorbing properties that are very unusual for a phospholipid. Consequently, favilipid A could inspire the development of a new class of molecules to be used as sunscreen ingredients. In addition, favilipid A inhibited by 58–48% three kinases (JAK3, IKKβ, and SYK) involved in the regulation of the immune system, suggesting a potential use for treatment of autoimmune diseases, hematologic cancers, and other inflammatory states. Full article
(This article belongs to the Special Issue Discovering Marine Bioactive Compounds by Molecular Networking)
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31 pages, 8660 KiB  
Article
Targeted Isolation of Antibiotic Brominated Alkaloids from the Marine Sponge Pseudoceratina durissima Using Virtual Screening and Molecular Networking
by James Lever, Florian Kreuder, Jason Henry, Andrew Hung, Pierre-Marie Allard, Robert Brkljača, Colin Rix, Aya C. Taki, Robin B. Gasser, Jan Kaslin, Donald Wlodkowic, Jean-Luc Wolfender and Sylvia Urban
Mar. Drugs 2022, 20(9), 554; https://doi.org/10.3390/md20090554 - 29 Aug 2022
Cited by 5 | Viewed by 4457
Abstract
Many targeted natural product isolation approaches rely on the use of pre-existing bioactivity information to inform the strategy used for the isolation of new bioactive compounds. Bioactivity information can be available either in the form of prior assay data or via Structure Activity [...] Read more.
Many targeted natural product isolation approaches rely on the use of pre-existing bioactivity information to inform the strategy used for the isolation of new bioactive compounds. Bioactivity information can be available either in the form of prior assay data or via Structure Activity Relationship (SAR) information which can indicate a potential chemotype that exhibits a desired bioactivity. The work described herein utilizes a unique method of targeted isolation using structure-based virtual screening to identify potential antibacterial compounds active against MRSA within the marine sponge order Verongiida. This is coupled with molecular networking-guided, targeted isolation to provide a novel drug discovery procedure. A total of 12 previously reported bromotyrosine-derived alkaloids were isolated from the marine sponge species Pseudoceratina durissima, and the compound, (+)-aeroplysinin-1 (1) displayed activity against the MRSA pathogen (MIC: <32 µg/mL). The compounds (1–3, 6 and 9) were assessed for their central nervous system (CNS) interaction and behavioral toxicity to zebrafish (Danio rerio) larvae, whereby several of the compounds were shown to induce significant hyperactivity. Anthelmintic activity against the parasitic nematode Haemonchus contorutus was also evaluated (2–4, 6–8). Full article
(This article belongs to the Special Issue Discovering Marine Bioactive Compounds by Molecular Networking)
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11 pages, 1482 KiB  
Article
Unveiling the Chemical Diversity of the Deep-Sea Sponge Characella pachastrelloides
by Sam Afoullouss, Anthony R. Sanchez, Laurence K. Jennings, Younghoon Kee, A. Louise Allcock and Olivier P. Thomas
Mar. Drugs 2022, 20(1), 52; https://doi.org/10.3390/md20010052 - 5 Jan 2022
Cited by 2 | Viewed by 5659
Abstract
Sponges are at the forefront of marine natural product research. In the deep sea, extreme conditions have driven secondary metabolite pathway evolution such that we might expect deep-sea sponges to yield a broad range of unique natural products. Here, we investigate the chemodiversity [...] Read more.
Sponges are at the forefront of marine natural product research. In the deep sea, extreme conditions have driven secondary metabolite pathway evolution such that we might expect deep-sea sponges to yield a broad range of unique natural products. Here, we investigate the chemodiversity of a deep-sea tetractinellid sponge, Characella pachastrelloides, collected from ~800 m depth in Irish waters. First, we analyzed the MS/MS data obtained from fractions of this sponge on the GNPS public online platform to guide our exploration of its chemodiversity. Novel glycolipopeptides named characellides were previously isolated from the sponge and herein cyanocobalamin, a manufactured form of vitamin B12, not previously found in nature, was isolated in a large amount. We also identified several poecillastrins from the molecular network, a class of polyketide known to exhibit cytotoxicity. Light sensitivity prevented the isolation and characterization of these polyketides, but their presence was confirmed by characteristic NMR and MS signals. Finally, we isolated the new betaine 6-methylhercynine, which contains a unique methylation at C-2 of the imidazole ring. This compound showed potent cytotoxicity towards against HeLa (cervical cancer) cells. Full article
(This article belongs to the Special Issue Discovering Marine Bioactive Compounds by Molecular Networking)
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