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Marine Drugs
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Molecular Networking as a Strategy in Discovery of Marine Bioactive...
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Molecular Networking as a Strategy in Discovery of Marine Bioactive Compounds

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

Deadline for manuscript submissions: closed (28 August 2020) | Viewed by 27461

Special Issue Editor

Prof. Dr. Mehdi A. Beniddir

E-Mail Website
Guest Editor
Équipe “Pharmacognosie-Chimie des Substances Naturelles” BioCIS, CNRS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
Interests: natural products; chemoinformatics; metabolomics pipelines
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Landmark advances in bioinformatics tools and analytical chemistry, particularly in mass spectrometry (MS), have recently enhanced the field of natural product (NP) research, putting today’s practicing chemists in the enviable position of being able to efficiently speed up the NP discovery process. In this context, molecular networking has proven to be a very efficient tool to rapidly identify new NPs within complex mixtures. Since its introduction in 2012, this emerging computer-based approach has totally revolutionized the “art of NP isolation”, enabling the transition from the traditional “grind and find” model to the streamlined hypothesis-driven targeting of NPs.

In this Special Issue of Marine Drugs, you are kindly invited to submit articles that describe creative endeavors that have led to the discovery of unprecedented bioactive marine natural products using molecular networking.

Dr. Mehdi A. Beniddir
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

  • Bioactive marine natural products
  • Dereplication
  • Structure elucidation
  • Targeted isolation

Published Papers (5 papers)

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Research

18 pages, 2954 KiB  
Article
Genome Mining, Microbial Interactions, and Molecular Networking Reveals New Dibromoalterochromides from Strains of Pseudoalteromonas of Coiba National Park-Panama
by Librada A. Atencio, Cristopher A. Boya P., Christian Martin H., Luis C. Mejía, Pieter C. Dorrestein and Marcelino Gutiérrez
Mar. Drugs 2020, 18(9), 456; https://doi.org/10.3390/md18090456 - 03 Sep 2020
Cited by 11 | Viewed by 3995
Abstract
The marine bacterial genus Pseudoalteromonas is known for their ability to produce antimicrobial compounds. The metabolite-producing capacity of Pseudoalteromonas has been associated with strain pigmentation; however, the genomic basis of their antimicrobial capacity remains to be explained. In this study, we sequenced the [...] Read more.
The marine bacterial genus Pseudoalteromonas is known for their ability to produce antimicrobial compounds. The metabolite-producing capacity of Pseudoalteromonas has been associated with strain pigmentation; however, the genomic basis of their antimicrobial capacity remains to be explained. In this study, we sequenced the whole genome of six Pseudoalteromonas strains (three pigmented and three non-pigmented), with the purpose of identifying biosynthetic gene clusters (BGCs) associated to compounds we detected via microbial interactions along through MS-based molecular networking. The genomes were assembled and annotated using the SPAdes and RAST pipelines and mined for the identification of gene clusters involved in secondary metabolism using the antiSMASH database. Nineteen BGCs were detected for each non-pigmented strain, while more than thirty BGCs were found for two of the pigmented strains. Among these, the groups of genes of nonribosomal peptide synthetases (NRPS) that code for bromoalterochromides stand out the most. Our results show that all strains possess BGCs for the production of secondary metabolites, and a considerable number of distinct polyketide synthases (PKS) and NRPS clusters are present in pigmented strains. Furthermore, the molecular networking analyses revealed two new molecules produced during microbial interactions: the dibromoalterochromides D/D’ (11–12). Full article
(This article belongs to the Special Issue Molecular Networking as a Strategy in Discovery of Marine Bioactive Compounds)
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21 pages, 2024 KiB  
Article
Bioactive Molecular Networking for Mapping the Antimicrobial Constituents of the Baltic Brown Alga Fucus vesiculosus
by Larissa Buedenbender, Francesca Anna Astone and Deniz Tasdemir
Mar. Drugs 2020, 18(6), 311; https://doi.org/10.3390/md18060311 - 13 Jun 2020
Cited by 21 | Viewed by 8751
Abstract
The brown alga Fucus vesiculosus is common to the intertidal zones of the Baltic Sea, where it is exposed to high fouling pressures by microorganisms. Our previous studies showed, repeatedly, the consistent antimicrobial activity of F. vesiculosus crude extracts against human pathogens, while [...] Read more.
The brown alga Fucus vesiculosus is common to the intertidal zones of the Baltic Sea, where it is exposed to high fouling pressures by microorganisms. Our previous studies showed, repeatedly, the consistent antimicrobial activity of F. vesiculosus crude extracts against human pathogens, while untargeted metabolomics analyses have revealed a variety of metabolites. In this study, we applied the UPLC-QToF-MS/MS-based “bioactive molecular networking” (BMN) concept on the most bioactive n-hexane and n-butanol subextracts of Baltic F. vesiculosus coupled with in silico dereplication tools to identify the compounds responsible for antimicrobial activity. The first antimicrobial cluster identified by BMN was galactolipids. Our targeted isolation efforts for this class led to the isolation of six monogalactosyldiacylglycerol (MGDG) derivatives (1–6) and one digalactosyldiacylglycerol (DGDG, 7). The MGDGs 5 and 6 and the DGDG 7 exhibited activity against Staphylococcus aureus. The second compound class with high bioactivity was phlorotannins. In particular, phlorethol-type phlorotannins showed high correlations with antimicrobial activity based on the BMN approach, and two phlorotannins (8–9) were isolated. This study shows that antimicrobial components of F. vesiculosus reside in the algal cell walls and membranes and that BMN provides a complementary tool for the targeted isolation of bioactive metabolites. Full article
(This article belongs to the Special Issue Molecular Networking as a Strategy in Discovery of Marine Bioactive Compounds)
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21 pages, 4749 KiB  
Article
Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors
by Ipsita Mohanty, Sheila Podell, Jason S. Biggs, Neha Garg, Eric E. Allen and Vinayak Agarwal
Mar. Drugs 2020, 18(2), 124; https://doi.org/10.3390/md18020124 - 19 Feb 2020
Cited by 22 | Viewed by 5541
Abstract
Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor [...] Read more.
Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor a far greater diversity of low-abundance natural products that have evaded discovery. While these low-abundance natural products may not be feasible to isolate, insights into their chemical structures can be gleaned by careful curation of mass fragmentation spectra. Sponges are also some of the most complex, multi-organismal holobiont communities in the oceans. We overlay sponge metabolomes with their microbiome structures and detailed metagenomic characterization to discover candidate gene clusters that encode production of sponge-derived natural products. The multi-omic profiling strategy for sponges that we describe here enables quantitative comparison of sponge metabolomes and microbiomes to address, among other questions, the ecological relevance of sponge natural products and for the phylochemical assignment of previously undescribed sponge identities. Full article
(This article belongs to the Special Issue Molecular Networking as a Strategy in Discovery of Marine Bioactive Compounds)
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16 pages, 3643 KiB  
Article
Marine Bacteria from Rocas Atoll as a Rich Source of Pharmacologically Active Compounds
by Karen Y. Velasco-Alzate, Anelize Bauermeister, Marcelo M. P. Tangerina, Tito M. C. Lotufo, Marcelo J. P. Ferreira, Paula C. Jimenez, Gabriel Padilla, Norberto P. Lopes and Letícia V. Costa-Lotufo
Mar. Drugs 2019, 17(12), 671; https://doi.org/10.3390/md17120671 - 28 Nov 2019
Cited by 12 | Viewed by 3376
Abstract
Rocas Atoll is a unique environment in the equatorial Atlantic Ocean, hosting a large number of endemic species, however, studies on the chemical diversity emerging from this biota are rather scarce. Therefore, the present work aims to assess the metabolomic diversity and pharmacological [...] Read more.
Rocas Atoll is a unique environment in the equatorial Atlantic Ocean, hosting a large number of endemic species, however, studies on the chemical diversity emerging from this biota are rather scarce. Therefore, the present work aims to assess the metabolomic diversity and pharmacological potential of the microbiota from Rocas Atoll. A total of 76 bacteria were isolated and cultured in liquid culture media to obtain crude extracts. About one third (34%) of these extracts were recognized as cytotoxic against human colon adenocarcinoma HCT-116 cell line. 16S rRNA gene sequencing analyses revealed that the bacteria producing cytotoxic extracts were mainly from the Actinobacteria phylum, including Streptomyces, Salinispora, Nocardiopsis, and Brevibacterium genera, and in a smaller proportion from Firmicutes phylum (Bacillus). The search in the spectral library in GNPS (Global Natural Products Social Molecular Networking) unveiled a high chemodiversity being produced by these bacteria, including rifamycins, antimycins, desferrioxamines, ferrioxamines, surfactins, surugamides, staurosporines, and saliniketals, along with several unidentified compounds. Using an original approach, molecular networking successfully highlighted groups of compounds responsible for the cytotoxicity of crude extracts. Application of DEREPLICATOR+ (GNPS) allowed the annotation of macrolide novonestimycin derivatives as the cytotoxic compounds existing in the extracts produced by Streptomyces BRB-298 and BRB-302. Overall, these results highlighted the pharmacological potential of bacteria from this singular atoll. Full article
(This article belongs to the Special Issue Molecular Networking as a Strategy in Discovery of Marine Bioactive Compounds)
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17 pages, 5087 KiB  
Article
Scopularides Revisited: Molecular Networking Guided Exploration of Lipodepsipeptides in Australian Marine Fish Gastrointestinal Tract-Derived Fungi
by Ahmed H. Elbanna, Zeinab G. Khalil, Paul V. Bernhardt and Robert J. Capon
Mar. Drugs 2019, 17(8), 475; https://doi.org/10.3390/md17080475 - 16 Aug 2019
Cited by 22 | Viewed by 4900
Abstract
Chemical analysis of a cultivation of an Australian Mugil mullet gastrointestinal tract (GIT) derived fungus, Scopulariopsis sp. CMB-F458, yielded the known lipodepsipeptides scopularides A (1) and B (2). A comparative global natural product social (GNPS) molecular networking analysis of [...] Read more.
Chemical analysis of a cultivation of an Australian Mugil mullet gastrointestinal tract (GIT) derived fungus, Scopulariopsis sp. CMB-F458, yielded the known lipodepsipeptides scopularides A (1) and B (2). A comparative global natural product social (GNPS) molecular networking analysis of ×63 co-isolated fungi, detected two additional fungi producing new scopularides, with Beauveria sp. CMB-F585 yielding scopularides C–G (3–7) and Scopulariopsis sp. CMB-F115 yielding scopularide H (8). Structures inclusive of absolute configurations were assigned by detailed spectroscopic and C3 Marfey’s analysis, together with X-ray analyses of 3 and 8, and biosynthetic considerations. Scopularides A–H (1–8) did not exhibit significant growth inhibitory activity against a selection of Gram positive (+ve) and negative (−ve) bacteria, a fungus, or a panel of three human carcinoma cell lines. Full article
(This article belongs to the Special Issue Molecular Networking as a Strategy in Discovery of Marine Bioactive Compounds)
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