Marine Bioactive Compound Discovery by Combining Virtual with Actual Laboratory Experiments

A special issue of Marine Drugs (ISSN 1660-3397). This special issue belongs to the section "Marine Chemoecology for Drug Discovery".

Deadline for manuscript submissions: closed (31 August 2024) | Viewed by 6168

Special Issue Editor

South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
Interests: marine natural product; drug leads; pharmacological mechanism; marine microorganisms; cyanobacteria
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,                

Discovering new marine bioactive compounds is a challenging and time-consuming process that involves multiple intricate steps. One approach to expedite the discovery of these compounds is integrating virtual experiments with actual laboratory experiments. In recent years, there has been an increasing interest in combining computational and experimental methods to accelerate the identification of novel marine bioactive compounds. This innovative strategy, known as "computational experimentation", harnesses the capabilities of advanced computational techniques, including molecular docking, molecular dynamics simulations, and machine learning algorithms, to efficiently and cost-effectively identify and prioritize potential bioactive compounds. Virtual experiments employ mathematical models and algorithms within computer simulations to predict compound properties and activities based on their chemical structures. Actual laboratory experiments involve performing physical tests to measure the effects of these compounds on biological targets, such as cells, enzymes, or organisms.

The integration of virtual and actual laboratory experiments presents a promising approach for the discovery of marine bioactive compounds, thereby enhancing the efficiency and effectiveness of the discovery process. This convergence can ultimately lead to the development of novel products with potential benefits for human health and well-being.

This Special Issue will focus on employing advances in all aspects of marine natural products (MNPs) for drug discovery and development by combining virtual and actual laboratory experiments, including the following aspects:

  • Structurally novel and bioactive MNPs;
  • Predictive models of structure and function of MNPs;
  • Efficacy and pharmacological mechanisms of MNPs;
  • Total synthesis, optimization, or biosynthesis of bioactive or novel MNPs;
  • Research into marine medicinal biological resources.

Dr. Bin Yang
Guest Editor

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Keywords

  • marine natural products
  • biological activity
  • biosynthetic pathway
  • structure–activity relationships
  • molecular docking
  • network pharmacology
  • experimental validation
  • molecular networking
  • molecular dynamics simulations
  • machine learning algorithms

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Published Papers (4 papers)

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Research

11 pages, 2819 KiB  
Article
New Sesquiterpenoids from the Mangrove-Derived Fungus Talaromyces sp. as Modulators of Nuclear Receptors
by Tanwei Gu, Jian Cai, Danni Xie, Jianglian She, Yonghong Liu, Xuefeng Zhou and Lan Tang
Mar. Drugs 2024, 22(9), 403; https://doi.org/10.3390/md22090403 - 3 Sep 2024
Viewed by 1050
Abstract
Four new sesquiterpenoids, talaroterpenes A–D (14), were isolated from the mangrove-derived fungus Talaromyces sp. SCSIO 41412. The structures of compounds 14 were elucidated through comprehensive NMR and MS spectroscopic analyses. The absolute configurations of 14 [...] Read more.
Four new sesquiterpenoids, talaroterpenes A–D (14), were isolated from the mangrove-derived fungus Talaromyces sp. SCSIO 41412. The structures of compounds 14 were elucidated through comprehensive NMR and MS spectroscopic analyses. The absolute configurations of 14 were assigned based on single-crystal X-ray diffraction and calculated electronic circular dichroism analysis. Talaroterpenes A–D (14) were evaluated with their regulatory activities on nuclear receptors in HepG2 cells. Under the concentrations of 200 μM, 1, 3 and 4 exhibited varying degrees of activation on ABCA1 and PPARα, while 4 showed the strongest activities. Furthermore, 4 induced significant alterations in the expression of downstream target genes CLOCK and BMAL1 of RORα, and the in silico molecular docking analysis supported the direct binding interactions of 4 with RORα protein. This study revealed that talaroterpene D (4) was a new potential non-toxic modulator of nuclear receptors. Full article
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15 pages, 6393 KiB  
Article
Novel Metabolites from the Marine-Derived Fungus Peniophora sp. SCSIO41203 Show Promising In Vitro Antitumor Activity as Methuosis Inducers in PC-3 Cells
by Bin Yang, Surun Shao, Mingyi Nie, Qingqing Tie, Xiaoyan Pang, Xiuping Lin, Xuefeng Zhou, Yonghong Liu, Xueni Wang and Yunqiu Li
Mar. Drugs 2024, 22(5), 218; https://doi.org/10.3390/md22050218 - 14 May 2024
Viewed by 1346
Abstract
Two new cytochalasin derivatives, peniotrinins A (1) and B (2), three new citrinin derivatives, peniotrinins C–E (4, 5, 7), and one new tetramic acid derivative, peniotrinin F (12), along with nine structurally related [...] Read more.
Two new cytochalasin derivatives, peniotrinins A (1) and B (2), three new citrinin derivatives, peniotrinins C–E (4, 5, 7), and one new tetramic acid derivative, peniotrinin F (12), along with nine structurally related known compounds, were isolated from the solid culture of Peniophora sp. SCSIO41203. Their structures, including the absolute configurations of their stereogenic carbons, were fully elucidated based on spectroscopic analysis, quantum chemical calculations, and the calculated ECD. Interestingly, 1 is the first example of a rare 6/5/5/5/6/13 hexacyclic cytochalasin. We screened the above compounds for their anti-prostate cancer activity and found that compound 3 had a significant anti-prostate cancer cell proliferation effect, while compounds 1 and 2 showed weak activity at 10 μM. We then confirmed that compound 3 exerts its anti-prostate cancer effect by inducing methuosis through transmission electron microscopy and cellular immunostaining, which suggested that compound 3 might be first reported as a potential anti-prostate methuosis inducer. Full article
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13 pages, 3079 KiB  
Article
Inhibition Effects and Mechanisms of Marine Compound Mycophenolic Acid Methyl Ester against Influenza A Virus
by Zihan Wang, Lishan Sun, Hongwei Zhao, Mamadou Dioulde Sow, Yang Zhang and Wei Wang
Mar. Drugs 2024, 22(5), 190; https://doi.org/10.3390/md22050190 - 23 Apr 2024
Viewed by 1529
Abstract
Influenza A virus (IAV) can cause infection and illness in a wide range of animals, including humans, poultry, and swine, and cause annual epidemics, resulting in thousands of deaths and millions of hospitalizations all over the world. Thus, there is an urgent need [...] Read more.
Influenza A virus (IAV) can cause infection and illness in a wide range of animals, including humans, poultry, and swine, and cause annual epidemics, resulting in thousands of deaths and millions of hospitalizations all over the world. Thus, there is an urgent need to develop novel anti-IAV drugs with high efficiency and low toxicity. In this study, the anti-IAV activity of a marine-derived compound mycophenolic acid methyl ester (MAE) was intensively investigated both in vitro and in vivo. The results showed that MAE inhibited the replication of different influenza A virus strains in vitro with low cytotoxicity. MAE can mainly block some steps of IAV infection post adsorption. MAE may also inhibit viral replication through activating the cellular Akt-mTOR-S6K pathway. Importantly, oral treatment of MAE can significantly ameliorate pneumonia symptoms and reduce pulmonary viral titers, as well as improving the survival rate of mice, and this was superior to the effect of oseltamivir. In summary, the marine compound MAE possesses anti-IAV effects both in vitro and in vivo, which merits further studies for its development into a novel anti-IAV drug in the future. Full article
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11 pages, 2143 KiB  
Article
Pestalotiopols E–J, Six New Polyketide Derivatives from a Marine Derived Fungus Pestalotiopsis sp. SWMU-WZ04-1
by Liyuan Jiang, Baorui Teng, Mengyu Zhang, Siwei Chen, Dan Zhang, Longfei Zhai, Jiafu Lin and Hui Lei
Mar. Drugs 2024, 22(1), 15; https://doi.org/10.3390/md22010015 - 26 Dec 2023
Viewed by 1744
Abstract
Chemical epigenetic cultivation of the sponge-derived fungus Pestalotiopsis sp. SWMU-WZ04-1 contributed to the identification of twelve polyketide derivatives, including six new pestalotiopols E–J (16) and six known analogues (712). Their gross structures were deduced from [...] Read more.
Chemical epigenetic cultivation of the sponge-derived fungus Pestalotiopsis sp. SWMU-WZ04-1 contributed to the identification of twelve polyketide derivatives, including six new pestalotiopols E–J (16) and six known analogues (712). Their gross structures were deduced from 1D/2D NMR and HRESIMS spectroscopic data, and their absolute configurations were further established by circular dichroism (CD) Cotton effects and the modified Mosher’s method. In the bioassay, the cytotoxic and antibacterial activities of all compounds were evaluated. Chlorinated benzophenone derivatives 7 and 8 exhibited inhibitory effects on Staphylococcus aureus and Bacillus subtilis, with MIC values varying from 3.0 to 50 μg/mL. In addition, these two compounds were cytotoxic to four types of human cancer cells, with IC50 values of 16.2~83.6 μM. The result showed that compound 7 had the probability of being developed into a lead drug with antibacterial ability. Full article
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