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Marine Drugs
Special Issues
Bioinformatics of Marine Natural Products 3.0
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Bioinformatics of Marine Natural Products 3.0

A special issue of Marine Drugs (ISSN 1660-3397). This special issue belongs to the section "Marine Biotechnology Related to Drug Discovery or Production".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 2778

Special Issue Editor

Dr. Giovanna Romano

E-Mail Website
Guest Editor
Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Naples, Italy
Interests: novel bioactive metabolites from marine microalgae for pharmaceutical; nutraceutical and cosmeceutical applications; novel strategies to enhance industrial production of marine-derived compounds
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are glad to announce the third edition of the Special Issue “Bioinformatics of Marine Natural Products”.

In recent decades, marine natural products (MNPs) and their structural analogs have made a significant contribution to pharmacotherapy, especially for cancer diseases. While marine organisms, especially microbes, are still attracting great attention as promising sources for the sustainable production of novel bioactive compounds and biocatalysts, challenges in drug discovery remain, such as technical barriers to screening, isolation, characterization, and the optimization of production. These challenges may be addressed by using genome-mining-based approaches to explore the biosynthetic capacity of microorganisms relying on DNA extraction, sequencing, and bioinformatics analysis. These approaches make the biosynthetic potential of unculturable microbes accessible, which still represent the vast majority. This is a fast-growing research field, and it is predicted to greatly empower the identification of biosynthetic genes in the genomes of producing organisms, eventually leading to the discovery of novel MNPs.

We thus welcome your contribution to this Special Issue to provide a panorama of the current scenario and information on new approaches to explore the huge amount of big datasets to identify the biosynthetic pathways of natural marine compounds.

Dr. Giovanna Romano
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

  • genome mining
  • biosynthetic genes
  • biosynthetic gene clusters
  • bioinformatics approach
  • cryptic metabolic pathways
  • uncultivable microorganisms
  • polyketide synthase
  • metagenomic approach
  • environmental DNA
  • polyketide synthases (PKSs)
  • non-ribosomal peptides (NRPs)

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Published Papers (2 papers)

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Research

19 pages, 6277 KiB  
Article
TRAF6 Inhibitors from Marine Compound Library: Pharmacophore, Virtual Screening, Fragment Replacement, ADMET, and Molecular Dynamics
by Xuexuan Wu, Saiyi Zhong, Nan Zhou and Lianxiang Luo
Mar. Drugs 2024, 22(6), 260; https://doi.org/10.3390/md22060260 - 5 Jun 2024
Viewed by 1326
Abstract
TRAF6 is an E3 ubiquitin ligase that plays a crucial role in cell signaling. It is known that MMP is involved in tumor metastasis, and TRAF6 induces MMP-9 expression by binding to BSG. However, inhibiting TRAF6’s ubiquitinase activity without disrupting the RING domain [...] Read more.
TRAF6 is an E3 ubiquitin ligase that plays a crucial role in cell signaling. It is known that MMP is involved in tumor metastasis, and TRAF6 induces MMP-9 expression by binding to BSG. However, inhibiting TRAF6’s ubiquitinase activity without disrupting the RING domain is a challenge that requires further research. To address this, we conducted computer-based drug screening to identify potential TRAF6 inhibitors. Using a ligand–receptor complex pharmacophore based on the inhibitor EGCG, known for its anti-tumor properties, we screened 52,765 marine compounds. After the molecular docking of 405 molecules with TRAF6, six compounds were selected for further analysis. By replacing fragments of non-binding compounds and conducting second docking, we identified two promising molecules, CMNPD9212-16 and CMNPD12791-8, with strong binding activity and favorable pharmacological properties. ADME and toxicity predictions confirmed their potential as TRAF6 inhibitors. Molecular dynamics simulations showed that CMNPD12791-8 maintained a stable structure with the target protein, comparable to EGCG. Therefore, CMNPD12791-8 holds promise as a potential inhibitor of TRAF6 for inhibiting tumor growth and metastasis. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products 3.0)
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11 pages, 1768 KiB  
Article
Genomics- and Transcriptomics-Guided Discovery of Clavatols from Arctic Fungi Penicillium sp. MYA5
by Yuan-Yuan Sun, Bo Hu, Hao-Bing Yu, Jing Zhou, Xian-Chao Meng, Zhe Ning, Jin-Feng Ding, Ming-Hui Cui and Xiao-Yu Liu
Mar. Drugs 2024, 22(6), 236; https://doi.org/10.3390/md22060236 - 22 May 2024
Viewed by 1104
Abstract
Clavatols exhibit a wide range of biological activities due to their diverse structures. A genome mining strategy identified an A5cla cluster from Penicillium sp. MYA5, derived from the Arctic plant Dryas octopetala, is responsible for clavatol biosynthesis. Seven clavatols, including one new [...] Read more.
Clavatols exhibit a wide range of biological activities due to their diverse structures. A genome mining strategy identified an A5cla cluster from Penicillium sp. MYA5, derived from the Arctic plant Dryas octopetala, is responsible for clavatol biosynthesis. Seven clavatols, including one new clavatol derivate named penicophenone F (1) and six known clavatols (2–7), were isolated from Penicillium sp. MYA5 using a transcriptome mining strategy. These structures were elucidated by comprehensive spectroscopic analysis. Antibacterial, aldose reductase inhibition, and siderophore-producing ability assays were conducted on compounds 1–7. Compounds 1 and 2 demonstrated inhibitory effects on the ALR2 enzyme with inhibition rates of 75.3% and 71.6% at a concentration of 10 μM, respectively. Compound 6 exhibited antibacterial activity against Staphylococcus aureus and Escherichia coli with MIC values of 4.0 μg/mL and 4.0 μg/mL, respectively. Additionally, compounds 1, 5, and 6 also showed potential iron-binding ability. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products 3.0)
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