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Discovery, Isolation, and Mechanisms of Bioactive Natural Products

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Natural Products Chemistry".

Deadline for manuscript submissions: closed (28 February 2025) | Viewed by 18458

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Dr. Qiang Zhang

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Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
Interests: omics; natural product; anti-diabetes; neural protection; plant growth regulation; natural product repurposing; alkaloids; limonoids
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Special Issue Information

Dear Colleagues,

We are pleased to announce the opening of a Special Issue on the Discovery, Isolation and Mechanisms of Bioactive Natural Products. This Special Issue aims to publish research and advances in the field of natural product discovery, particularly in the identification and characterization of bioactive compounds from natural sources and the investigation of their mechanisms of action.

The scope of this Special Issue includes, but is not limited to, the following areas: the isolation, purification, and structural elucidation of natural products, bioassay-guided fractionation, biological evaluation and the active mechanism of natural products, and natural -product-based drug discovery and development.

We welcome contributions from researchers with diverse backgrounds and perspectives and encourage the submission of high-quality manuscripts that advance our understanding of the discovery and mechanistic studies of bioactive natural products. We believe this Special Issue will serve as a valuable resource for the scientific community, and we look forward to receiving your submissions.

Dr. Qiang Zhang
Guest Editor

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Keywords

natural product
bioactivity
structural elucidation
mechanism

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Related Special Issue

Discovery, Isolation, and Mechanisms of Bioactive Natural Products (2nd Edition) in Molecules

Published Papers (9 papers)

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Research

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18 pages, 3225 KiB

Open AccessArticle

Phytochemical Characterization and Anti-Biofilm Activity of Primula veris L. Roots

by Antoaneta Trendafilova, Desislava Raykova, Viktoria Ivanova, Miroslav Novakovic, Paraskev Nedialkov, Tsvetelina Paunova-Krasteva, Ralitsa Veleva and Tanya Topouzova-Hristova

Molecules 2025, 30(8), 1702; https://doi.org/10.3390/molecules30081702 - 10 Apr 2025

Viewed by 200

Abstract

In this study, three new undescribed triterpene saponins named primulasaponin III–V (19–21) were isolated from the roots of Primula veris L. of Bulgarian origin together with the known primulasaponin I. Their structures were elucidated via 1D and 2D NMR spectroscopy and HR-ESI-MS. In addition, 17 known phenolic compounds (six flavones, three acetophenones, four bisbibenzyls, and four phenolic glycosides) were identified in the chloroform and methanol extracts. Among them, flavone, 2′-methoxyflavone, 3′-methoxyflavone, 3′-hydroxy-4′,5′-dimethoxyflavone, 2′,5′-dimethoxyflavone, 3′-methoxy-4′,5′-methylendioxyflavone, paeonol, 2-primeverosyl-5-methoxy-acetophenone, and paeonolide were detected for the first time in the roots of P. veris. The minimum inhibitory and minimum bactericidal concentrations of the chloroform and methanol extracts of P. veris roots and the saponin-enriched fraction were determined, with MIC values ranging between 0.5 and 1 mg/mL. Additionally, the tested samples were evaluated for their ability to inhibit biofilm formation in the presence of sub-MICs. All tested samples showed better biofilm inhibition of Gram-negative strains compared to Gram-positive strains. The strongest effect was observed for the chloroform extract against the biofilm formation of Pseudomonas aeruginosa, while the saponin-enriched fraction showed the highest percentage of biofilm inhibition of Escherichia coli, Staphylococcus aureus, and Staphylococcus mutans. At the same time, chloroform extract showed lower cytotoxicity against human keranocyte cell line HaCaT, as compared with methanol extract and the saponin-enriched fraction. Full article

(This article belongs to the Special Issue Discovery, Isolation, and Mechanisms of Bioactive Natural Products)

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28 pages, 3363 KiB

Open AccessArticle

Influence of Season, Hive Position, Extraction Method and Storage Temperature on Polyphenols and Antioxidant Activity of Croatian Honey

by Ivana Šola, Valerija Vujčić Bok, Ivana Fabijanić, Jasna Jablan, Laura Borgese, Andrea Humski, Marina Mikulić, Krešimir Sanković, Zdenko Franić and Gordana Rusak

Molecules 2025, 30(4), 919; https://doi.org/10.3390/molecules30040919 - 17 Feb 2025

Viewed by 537

Abstract

The aim of our study was to compare the composition of polyphenolic compounds between the Croatian acacia (Robinia pseudoacacia L.) and chestnut (Castanea sativa Mill.) honey from several aspects: production season, hive position (on the edge and in the middle of a series of hives), part of the hive (small or normal extension), and honey extraction method (centrifuging or draining honey combs). Additionally, in acacia honey, we also monitored the influence of different storage temperatures (room temperature (RT) and 4 °C) on the content of phenolic compounds. To separate, identify and quantify individual flavonoids and phenolic acids from the honey, we used the HPLC method. The total polyphenols and antioxidant activity of the samples, their antimicrobial activity and their elemental content were also measured. The significant influence of the season, hive position, and extraction method on the total identified phenolic compounds, phenolic acids, flavonoids, total phenols and antioxidant activity was detected in almost all the acacia and chestnut honey samples. Chestnut honey from 2013 had more total phenolics (TPs) and antioxidant capacity (FRAP) than chestnut from 2014 and 2015. Honey collected from smaller extensions of hives had significantly higher TPs and FRAP compared to normal hive extensions. Centrifugation reduced the TPs and FRAP in most cases, but not always uniformly. Storage at RT led to the predominance of gallic, p-coumaric and benzoic acid in acacia honey, while storage at 4 °C maintained p-coumaric acid as the dominant phenolic acid. Flavonoids, particularly pinobanksin in acacia honey and hesperetin/pinobanksin in chestnut honey, were less affected by the storage conditions compared to phenolic acids. The non-centrifuged chestnut sample from 2015 showed the lowest MIC values against the most tested pathogenic bacteria. All the honey samples showed an extremely low concentration of heavy metals and relatively high concentrations of potassium and calcium. Full article

(This article belongs to the Special Issue Discovery, Isolation, and Mechanisms of Bioactive Natural Products)

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23 pages, 8659 KiB

Open AccessArticle

iTRAQ-Based Proteomic Profiling of Skin Aging Protective Effects of Tremella fuciformis-Derived Polysaccharides on D-Galactose-Induced Aging Mice

by Yuanyuan Xu, Xiaofei Liu, Jingjing Guan, Jin Chen and Xiaofei Xu

Molecules 2024, 29(21), 5191; https://doi.org/10.3390/molecules29215191 - 2 Nov 2024

Cited by 1 | Viewed by 1206

Abstract

In the present study, a heteromannan primarily composed of mannose, fucose, xylose, glucose, and arabinose at a molar ratio of 4.78:1.18:1:0.82:0.11 containing a low proportion of glucuronic acid with weight-average molecular weights of 3.6 × 10⁶ Da, named NTP, was prepared from the fruiting body of Tremella fuciformis. The anti-skin-aging effects of NTP on d-Galactose-induced aging mice and the biological mechanisms were investigated by an iTRAQ-based proteomics approach. NTP substantially mitigated skin aging characterized by a decreased loss of hydroxyproline and hyaluronic acid and reduced oxidative stress in the skin. Moreover, 43 differentially expressed proteins (DEPs) were identified in response to NTP, of which 23 were up-regulated and 20 were down-regulated. Bioinformatics analysis revealed that these DEPs were mainly involved in the biological functions of cellular and metabolic regulations, immune system responses, and structural components. The findings provided new insights into the biological mechanisms underlying the anti-skin-aging actions of T. fuciformis-derived polysaccharides and facilitated NTP applications in naturally functional foods. Full article

(This article belongs to the Special Issue Discovery, Isolation, and Mechanisms of Bioactive Natural Products)

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16 pages, 2254 KiB

Open AccessArticle

Synthesis and Cheminformatics-Directed Antibacterial Evaluation of Echinosulfonic Acid-Inspired Bis-Indole Alkaloids

by Darren C. Holland, Joshua B. Hayton, Milton J. Kiefel and Anthony R. Carroll

Molecules 2024, 29(12), 2806; https://doi.org/10.3390/molecules29122806 - 12 Jun 2024

Cited by 2 | Viewed by 1890

Abstract

Synthetic efforts toward complex natural product (NP) scaffolds are useful ones, particularly those aimed at expanding their bioactive chemical space. Here, we utilised an orthogonal cheminformatics-based approach to predict the potential biological activities for a series of synthetic bis-indole alkaloids inspired by elusive sponge-derived NPs, echinosulfone A (1) and echinosulfonic acids A–D (2–5). Our work includes the first synthesis of desulfato-echinosulfonic acid C, an α-hydroxy bis(3′-indolyl) alkaloid (17), and its full NMR characterisation. This synthesis provides corroborating evidence for the structure revision of echinosulfonic acids A-C. Additionally, we demonstrate a robust synthetic strategy toward a diverse range of α-methine bis(3′-indolyl) acids and acetates (11–16) without the need for silica-based purification in either one or two steps. By integrating our synthetic library of bis-indoles with bioactivity data for 2048 marine indole alkaloids (reported up to the end of 2021), we analyzed their overlap with marine natural product chemical diversity. Notably, the C-6 dibrominated α-hydroxy bis(3′-indolyl) and α-methine bis(3′-indolyl) analogues (11, 14, and 17) were found to contain significant overlap with antibacterial C-6 dibrominated marine bis-indoles, guiding our biological evaluation. Validating the results of our cheminformatics analyses, the dibrominated α-methine bis(3′-indolyl) alkaloids (11, 12, 14, and 15) were found to exhibit antibacterial activities against methicillin-sensitive and -resistant Staphylococcus aureus. Further, while investigating other synthetic approaches toward bis-indole alkaloids, 16 incorrectly assigned synthetic α-hydroxy bis(3′-indolyl) alkaloids were identified. After careful analysis of their reported NMR data, and comparison with those obtained for the synthetic bis-indoles reported herein, all of the structures have been revised to α-methine bis(3′-indolyl) alkaloids. Full article

(This article belongs to the Special Issue Discovery, Isolation, and Mechanisms of Bioactive Natural Products)

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11 pages, 4126 KiB

Open AccessArticle

Three New Ionone Glycosides from Rhododendron capitatum Maxim

by Jun-Ren Yang, Yue-Tong Zhu, Yi-Qin Zeng, Hong-Quan Li, Chun-Huan Li and Jin-Ming Gao

Molecules 2024, 29(11), 2462; https://doi.org/10.3390/molecules29112462 - 23 May 2024

Cited by 2 | Viewed by 1320

Abstract

Six ionone glycosides (1–3 and 5–7), including three new ones, named capitsesqsides A−C (1–3), together with an eudesmane sesquiterpenoid glycoside (4) and three known triterpenoid saponins (8–10) were isolated from Rhododendron capitatum. The structures of these compounds were determined by extensive spectroscopic techniques (MS, UV, 1D-NMR, and 2D-NMR) and comparison with data reported in the literature. The absolute configurations were determined by comparison of the experimental and theoretically calculated ECD curves and LC-MS analyses after acid hydrolysis and derivatization. The anti-inflammatory activities of these compounds were evaluated in the LPS-induced RAW264.7 cells. Molecular docking demonstrated that 2 has a favorable affinity for NLRP3 and iNOS. Full article

(This article belongs to the Special Issue Discovery, Isolation, and Mechanisms of Bioactive Natural Products)

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23 pages, 7146 KiB

Open AccessArticle

Network Pharmacology Analysis of Liquid-Cultured Armillaria ostoyae Mycelial Metabolites and Their Molecular Mechanism of Action against Gastric Cancer

by Zhishuo Wang, Ruiqi Wang, Zhiguo Na, Shanshan Liang, Fan Wu, Hongyao Xie, Xue Zhang, Wei Xu and Xin Wang

Molecules 2024, 29(7), 1668; https://doi.org/10.3390/molecules29071668 - 8 Apr 2024

Cited by 2 | Viewed by 2082

Abstract

Armillaria sp. are traditional edible medicinal mushrooms with various health functions; however, the relationship between their composition and efficacy has not yet been determined. Here, the ethanol extract of liquid-cultured Armillaria ostoyae mycelia (AOME), a pure wild Armillaria sp. strain, was analyzed using UHPLC-QTOF/MS, network pharmacology, and molecular docking techniques. The obtained extract affects various metabolic pathways, such as JAK/STAT and PI3K/AKT. The extract also contains important compounds such as 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl] benzamide, isoliquiritigenin, and 7-hydroxycoumarin. Moreover, the extract targets key proteins, including EGFR, SCR, and IL6, to suppress the progression of gastric cancer, thereby synergistically inhibiting cancer development. The molecular docking analyses indicated that the main compounds stably bind to the target proteins. The final cell culture experimental data showed that the ethanol extract inhibited MGC-803 gastric cancer cells. In summary, our research revealed the beneficial components of AOME for treating gastric cancer and its associated molecular pathways. However, further research is needed to confirm its effectiveness and safety in gastric cancer patients. Full article

(This article belongs to the Special Issue Discovery, Isolation, and Mechanisms of Bioactive Natural Products)

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16 pages, 1220 KiB

Open AccessArticle

Untargeted Phytochemical Profiling, Antioxidant, and Antimicrobial Activities of a Tunisian Capsicum annuum Cultivar

by Yossri Grojja, Hafedh Hajlaoui, Simon Vlad Luca, Jouda Abidi, Krystyna Skalicka-Woźniak, Sami Zouari and Mohamed Bouaziz

Molecules 2023, 28(17), 6346; https://doi.org/10.3390/molecules28176346 - 30 Aug 2023

Cited by 5 | Viewed by 2121

Abstract

Peppers are among the spices possessing a wide plethora of biological properties due to their excellent supply of health-related metabolites. Capsicum annuum L. (Solanaceae) is cultivated throughout Tunisia, and there is a shortage of information on the identification of the secondary metabolites in the seeds of this species as well as on their biological activities. In the present work, we intended to undertake a chemical characterization of the bioactive compounds from the hydro-methanolic seed extract of C. annuum as well as an evaluation of its broad spectrum of antimicrobial and antioxidant activities. The chemical profile was evaluated by RP-HPLC-DAD-QTOF-MS/MS, whereas the total phenol and flavonoid content, antioxidant, and antimicrobial activities were determined in in vitro assays. In this work, 45 compounds belonging to various phytochemical classes, such as organic acids (2), phenolic compounds (4 phenolic acids and 5 flavonoids), capsaicinoids (3), capsianosides (5), fatty acids (13), amino acids (1), sphingolipids (10), and steroids (2) were identified in the hydro-methanolic seed extract of C. annuum. The phenolic and flavonoid content (193.7 mg GAE/g DW and 25.1 mg QE/g DW, respectively) of the C. annuum extract correlated with the high antiradical activity (IC₅₀ = 45.0 µg/mL), reducing power (EC₅₀ = 61.3 µg/mL) and chelating power (IC₅₀ = 79.0 µg/mL) activities. The hydro-methanolic seed extract showed an important antimicrobial activity against seven bacterial and four fungal strains. In fact, the inhibition zones (IZs) for bacteria ranged from 9.00 ± 1.00 mm to 12.00 ± 0.00 mm; for fungi, the IZs ranged from 12.66 ± 0.57 mm to 13.66 ± 0.57 mm. The minimal inhibition concentration and minimal bactericidal concentration values showed that the extract was more effective against fungi than bacteria. Full article

(This article belongs to the Special Issue Discovery, Isolation, and Mechanisms of Bioactive Natural Products)

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11 pages, 1045 KiB

Open AccessArticle

Polyoxygenated Stigmastane-Type Steroids from Vernonia kotschyana Sch. Bip. ex Walp. and Their Chemophenetic Significance

by Nadine Tseme Wandji, Gabin Thierry M. Bitchagno, Isabelle Mawabo Kamga, Joseph Tchamgoue, Celine Nguefeu Nkenfou, Bruno Ndjakou Lenta, Norbert Sewald and Simeon Fogue Kouam

Molecules 2023, 28(13), 5278; https://doi.org/10.3390/molecules28135278 - 7 Jul 2023

Cited by 2 | Viewed by 1575

Abstract

Four polyoxygenated stigmastanes (1–4) alongside known analogues (7–8) and flavonoids (5–6) were isolated from a dichloromethane/methanol (1:1, v/v) extract of the whole plant of Vernonia kotschyana Sch. Bip. ex Walp. (Asteraceae). Their structures were determined by means of spectroscopic and spectrometric analysis. The relative stereochemistry of the new compounds was established and confirmed via biosynthesis evidence and cyclization of 1 under acidic conditions. A plausible biosynthetic pathway to the new compounds and the chemophenetic significance of the isolated constituents were also discussed. The crude extract, fractions, and compounds (1–3) were assessed for their antibacterial activity against five highly prevalent bacterial strains. The fractions and compounds showed low to moderate activity with minimal inhibitory concentrations (MICs) > 125 µg/mL. Full article

(This article belongs to the Special Issue Discovery, Isolation, and Mechanisms of Bioactive Natural Products)

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Review

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29 pages, 4390 KiB

Open AccessReview

Research Advances in Clinical Applications, Anticancer Mechanism, Total Chemical Synthesis, Semi-Synthesis and Biosynthesis of Paclitaxel

by Shengnan Zhang, Taiqiang Ye, Yibin Liu, Guige Hou, Qibao Wang, Fenglan Zhao, Feng Li and Qingguo Meng

Molecules 2023, 28(22), 7517; https://doi.org/10.3390/molecules28227517 - 10 Nov 2023

Cited by 23 | Viewed by 6305

Abstract

Paclitaxel, a natural secondary metabolite isolated and purified from the bark of the Taxus tree, is considered one of the most successful natural anticancer drugs due to its low toxicity, high potency and broad-spectrum anticancer activity. Taxus trees are scarce and slow-growing, and with extremely low paclitaxel content, the contradiction between supply and demand in the market is becoming more and more intense. Therefore, researchers have tried to obtain paclitaxel by various methods such as chemical synthesis, artificial culture, microbial fermentation and tissue cell culture to meet the clinical demand for this drug. This paper provides a comprehensive overview of paclitaxel extraction, combination therapy, total synthesis, semi-synthesis and biosynthesis in recent years and provides an outlook, aiming to provide a theoretical basis and reference for further research on the production and application of paclitaxel in the future. Full article

(This article belongs to the Special Issue Discovery, Isolation, and Mechanisms of Bioactive Natural Products)

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