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Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: 31 August 2025 | Viewed by 17813

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Dr. Wing-Leung Wong

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State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Kowloon 999077, Hong Kong
Interests: small-molecule inhibitors; biosensors; chemical biology; G-quadruplex structures; molecular design and synthesis
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Dear Colleagues,

Many naturally occurring bioactive organic compounds, such as polyphenols, carotenoids, phytosterols, organic acids, omega-3 fatty acids, vitamins, nucleosides and nucleotides, and pentacyclic triterpenoids, have attracted attention because of their active biofunctions in the prevention of certain diseases. In recent years, both natural and synthetic or semi-synthetic bioactive organic compounds have been used in modern drug development as the compounds are a prolific source of important lead compounds and pharmacophores. These include anticancer and antimicrobial agents against drug-resistant bacteria, such as superbugs, antivirus agents, cardioprotective agents, and anti-inflammatory agents. To ensure pharmaceutical development to address modern health challenges, the molecular design, synthesis, and semi-synthesis of potentially bioactive compounds and systematic evaluation of their bioactivity, biotoxicity, and potential applications for pre-clinical trials are crucial. These multi-disciplinary investigations may integrate many areas of knowledge and expertise, including, but not limited to, molecular design and organic synthesis, chemical transformation and structure–activity relationship studies, bioactive compound library construction, high-throughput screening, drug-target identification, molecular simulation, in vitro and in vivo evaluations, and so on. Therefore, contributions from cross-disciplinary experts, such as synthetic chemists, medicinal chemists, phytochemists, biochemists, combinatorial chemists, analytical chemists, as well as other practitioners and engineers in related fields, are clearly highly important in supporting pharmaceutical development and advancement. This Special Issue aims to gather individual efforts to support new drug discoveries through the identification, synthesis, and evaluation of novel bioactive organic compounds that may provide positive impacts in various areas of human health.

Dr. Wing-Leung Wong
Guest Editor

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Keywords

bioactive compounds
bioactivity evaluation
drug discovery
medicinal chemistry
chemical biology
natural products
lead compounds and pharmacophores
molecular design and organic synthesis

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Related Special Issue

Exploring Bioactive Organic Compounds for Drug Discovery in Molecules (15 articles)

Published Papers (11 papers)

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Research

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19 pages, 4884 KiB

Open AccessArticle

Selected Polyphenols of Polish Poplar Propolis as a Key Component Shaping Its Antibacterial Properties—In Vitro and In Silico Approaches

by Małgorzata Dżugan, Michał Miłek, Ewa Ciszkowicz, Andrzej Łyskowski and Monika Tomczyk

Molecules 2025, 30(9), 2036; https://doi.org/10.3390/molecules30092036 - 3 May 2025

Viewed by 197

Abstract

Propolis is a natural antibacterial medicine with a varied content of phenolic compounds, which determines the activity of the ethanol extract of propolis (EEP). A new attempt was made to standardize ethanol propolis extract via its conversion into a dry concentrate (dEEP) through a two-step process. Four samples of poplar propolis from the same geographical region were used for the study. Obtained dry concentrates reconstituted in 70% ethanol (500 μg/mL) were analyzed for their antioxidant properties, total phenolic and flavonoid contents, as well as HPLC polyphenol profile. It was shown that dEEP solutions in 70% ethanol, regardless of the diversified quality of the raw material, have equalized antioxidant properties and phenolic and flavonoid contents compared to raw EEPs. However, quantitative differences in the nine individual components were still found by HPLC-DAD. The antibacterial activity of the dEEP solutions (0.03–500 µg/mL) was compared with three individual polyphenols’ effect against Klebsiella pneumoniae and Streptococcus agalactiae. Based on the obtained MIC values and anti-biofilm activity of dEEPs compared to pure polyphenols, it was established that the effectiveness of the extract results from the combined action of flavonoids and phenolic acids. The antibacterial effectiveness of p-coumaric acid, galangin, and pinocembrin was additionally modeled using in silico analyses, suggesting promiscuous binding of all tested polyphenolic ligands to target enzymes. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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17 pages, 5370 KiB

Open AccessArticle

Astaxanthin Mitigates ADHD Symptoms in Spontaneously Hypertensive Rats via Dopaminergic Modulation and Brain–Gut Axis Regulation

by Yueyang Leng, Ning Wu, Jing Wang, Lihua Geng, Yang Yue and Quanbin Zhang

Molecules 2025, 30(7), 1637; https://doi.org/10.3390/molecules30071637 - 7 Apr 2025

Viewed by 576

Abstract

Attention Deficit Hyperactivity Disorder (ADHD) is a prevalent neurodevelopmental disorder that significantly impacts learning, daily functioning, and personal development. Astaxanthin (ASTA), a naturally occurring antioxidant, has garnered interest as a potential therapeutic agent for various diseases, particularly in mitigating oxidative stress. This study explores a novel application of ASTA in the context of ADHD, aiming to investigate its therapeutic effects and underlying mechanisms. Spontaneously hypertensive rats (SHRs), widely used ADHD model animals, were treated with ASTA (50/100 mg/kg/day) for three weeks, 5 mg/kg/day atomoxetine (ATO) as the positive, and Wistar Kyoto (WKY) rats as control. Behavioral improvements were assessed using the open field test (OFT) and the Morris water maze (MWM). Biochemical analyses were conducted to evaluate changes in the levels of various neurotrophic factors, while histological examinations were performed to assess neuroprotective effects. Additionally, the role of ASTA in the brain–gut axis was investigated. The behavioral symptoms of hyperactivity, anxiety, and impaired spatial memory in ADHD animals were mitigated by ASTA. This improvement is primarily attributed to the restoration of neurotransmitter levels, particularly dopamine (DA), achieved through the modulation of several critical components within the dopamine system, including dopamine receptor 1 (DR1), dopamine transporter (DAT), tyrosine hydroxylase (TH), and synaptic-associated protein 25 (SNAP-25). Additionally, regulating the serotonin transporter (SERT) and glial cell-derived neurotrophic factor (GDNF) supports the recovery of serotonin levels and facilitates optimal brain development. Furthermore, cerebellar cells were protected, and the structure of the intestinal microbiota was regulated. ASTA can mitigate ADHD symptoms in SHR through the modulation of the dopaminergic system, multiple neurotransmitters, neurotrophic factors, and the neuro-intestinal environment, which establishes ASTA as a promising nutraceutical candidate for adjunctive therapy in pediatric ADHD. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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20 pages, 3043 KiB

Open AccessArticle

The Counteracting Effect of Chrysin on Dietary Fructose-Induced Metabolic-Associated Fatty Liver Disease (MAFLD) in Rats with a Focus on Glucose and Lipid Metabolism

by Gabriela Campanher, Nelson Andrade, Joanne Lopes, Cláudia Silva, Maria João Pena, Ilda Rodrigues and Fátima Martel

Molecules 2025, 30(2), 380; https://doi.org/10.3390/molecules30020380 - 17 Jan 2025

Viewed by 948

Abstract

The prevalence of metabolic syndrome has been exponentially increasing in recent decades. Thus, there is an increasing need for affordable and natural interventions for this disorder. We explored the effect of chrysin, a dietary polyphenol, on hepatic lipid and glycogen accumulation, metabolic dysfunction-associated fatty liver disease (MAFLD) activity score and oxidative stress and on hepatic and adipose tissue metabolism in rats presenting metabolic syndrome-associated conditions. Rats fed a chow diet were separated into four groups: Control (tap water), Fructose (tap water with 10% fructose), Chrysin (tap water+ chrysin (100 mg/kg body weight/d)), and Fructose + Chrysin (tap water with 10% fructose + chrysin (100 mg/kg body weight/d, daily)) (for 18 weeks). When associated with the chow diet, chrysin reduced hepatic lipid and glycogen storage, increased the hepatic antioxidant potential of glutathione and reduced de novo lipogenesis in the adipose tissue. When associated with the high fructose-diet, chrysin attenuated the increase in lipid and glycogen hepatic storage, improved the MAFLD activity score, decreased hepatic lipid peroxidation, increased the antioxidant potential of glutathione, and improved lipid and glucose metabolic markers in the liver and adipose tissue. In conclusion, our results suggest that chrysin is a beneficial addition to a daily diet for improvement of hepatic metabolic health, particularly for individuals suffering from metabolic syndrome. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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17 pages, 1950 KiB

Open AccessFeature PaperArticle

Exploring Secondary Amine Carnosine Derivatives: Design, Synthesis, and Properties

by Angelica Artasensi, Sarah Mazzotta, Ines Sanz, Licheng Lin, Giulio Vistoli, Laura Fumagalli and Luca Regazzoni

Molecules 2024, 29(21), 5083; https://doi.org/10.3390/molecules29215083 - 28 Oct 2024

Cited by 1 | Viewed by 1106

Abstract

Carnosine is a naturally occurring dipeptide that has been advocated by some authors as an interesting scaffold for the development of potential therapeutic agents in view of the positive outcomes of its supplementation in animal models of human diseases. Its mode of action seems to depend on the quenching of toxic electrophiles, such as 4–hydroxynonenal (HNE). However, carnosine’s bioavailability in humans is lower than that in other mammals. The main reason for such an unfavorable pharmacokinetic profile is the activity of the enzyme human serum carnosinase (E.C. 3.4.13.20), which rapidly hydrolyzes carnosine upon absorption. Therefore, some studies have focused on the design of carnosinase-resistant derivatives that retain binding activity toward toxic electrophiles. Nevertheless, the structural modification of the N-terminus amino group of carnosine has rarely been considered, possibly because of its key role in the electrophile scavenging mechanism. This was proven, since some carnosine N-terminus modification generated inactive compounds, despite some derivatives retaining oral bioavailability and gaining resistance to carnosinase hydrolysis. Herein, we therefore report a study aimed at exploring whether the amino group of carnosine can be conveniently modified to develop carnosinase-resistant derivatives retaining the dipeptide activity toward toxic electrophiles. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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17 pages, 6622 KiB

Open AccessArticle

Preliminary Assessment of the Protective and Antitumor Effects of Several Phytoene-Containing Bacterial and Microalgal Extracts in Colorectal Cancer

by Gloria Perazzoli, Cristina Luque, Antonio León-Vaz, Patricia Gómez-Villegas, Rocío Rengel, Ana Molina-Márquez, Ángeles Morón-Ortiz, Paula Mapelli-Brahm, José Prados, Consolación Melguizo, Antonio Meléndez-Martínez and Rosa León

Molecules 2024, 29(21), 5003; https://doi.org/10.3390/molecules29215003 - 22 Oct 2024

Cited by 1 | Viewed by 1440

Abstract

The identification of new functional food constituents is a priority to improve the prognosis and prevention of colorectal cancer (CRC). In this study, several bacterial and algal phytoene-enriched extracts were obtained, and their potential activity against oxidative damage and their ability to inhibit proliferation and cell migration in several human colon-adenocarcinoma-derived cell lines were assessed. The main conclusions indicate that total extracts of Sphingomonas echinoides and Chlorella sorokiniana exhibited the highest protective effect against oxidative damage. All extracts enhanced the activity of detoxifying enzymes, particularly importantly the increase of NAD(P)H:quinone oxidoreductase activity, which reached a value 40% higher than that of untreated control cells upon exposure to Escherichia coli extracts. Staphylococcus haemolyticus and transgenic E. coli extracts significantly arrested the migration capacity of both cell lines, while S. haemolyticus and C. sorokiniana extracts inhibited cell proliferation by 15 to 20% compared to untreated cells. These results point to these extracts as potential antioxidant complements able to protect cells against oxidative damage and with a moderate ability to inhibit the proliferation and migration of CRC tumor cells, paving the way to design functional foods or probiotic formulations with preventive properties against oxidative stress-related diseases, such as cancer, or as starting point for purifying anticancer compounds. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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18 pages, 3269 KiB

Open AccessArticle

Exploring the Mutated Kinases for Chemoenzymatic Synthesis of N⁴-Modified Cytidine Monophosphates

by Martyna Koplūnaitė, Kamilė Butkutė, Jonita Stankevičiūtė and Rolandas Meškys

Molecules 2024, 29(16), 3767; https://doi.org/10.3390/molecules29163767 - 9 Aug 2024

Viewed by 1104

Abstract

Nucleosides, nucleotides, and their analogues are an important class of molecules that are used as substrates in research of enzymes and nucleic acid, or as antiviral and antineoplastic agents. Nucleoside phosphorylation is usually achieved with chemical methods; however, enzymatic phosphorylation is a viable alternative. Here, we present a chemoenzymatic synthesis of modified cytidine monophosphates, where a chemical synthesis of novel N⁴-modified cytidines is followed by an enzymatic phosphorylation of the nucleosides by nucleoside kinases. To enlarge the substrate scope, multiple mutant variants of Drosophila melanogaster deoxynucleoside kinase (DmdNK) (EC:2.7.1.145) and Bacillus subtilis deoxycytidine kinase (BsdCK) (EC:2.7.1.74) have been created and tested. It has been determined that certain point mutations in the active sites of the kinases alter their substrate specificities noticeably and allow phosphorylation of compounds that had been otherwise not phosphorylated by the wild-type DmdNK or BsdCK. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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14 pages, 2570 KiB

Open AccessArticle

Cytotoxicity and Chemotaxonomic Significance of Saponins from Wild and Cultured Asparagus Shoots

by Tarik Chileh-Chelh, Rosalía López-Ruiz, Ana M. García-Cervantes, Ignacio Rodríguez-García, Miguel A. Rincón-Cervera, Mohamed Ezzaitouni and José L. Guil-Guerrero

Molecules 2024, 29(14), 3367; https://doi.org/10.3390/molecules29143367 - 18 Jul 2024

Viewed by 1677

Abstract

The shoots of Asparagus L. are consumed worldwide, although most species belonging to this genus have a restricted range, and several taxa remain unstudied. In this work, a total of four taxa from different locations were scrutinized and compared with cultivated A. officinalis. All shoots were screened for saponins via LC-MS, and in vitro antiproliferative activities against the HT-29 colorectal cancer cell line were assessed via the MTT assay. The total saponins (TS) contained in the crude extracts ranged from 710.0 (A. officinalis) to 1258.6 mg/100 g dw (A. acutifolius). The richness of the compounds detected in this work stands out; a total of 47 saponins have been detected and quantified in the edible parts (shoots) of five taxa of Asparagus. The structure of all the saponins found present skeletons of the furostane and spirostane type. In turn, the structures with a furostane skeleton are divided into unsaturated and dioxygenated types, both in the 20–22 position. The sum of dioscin and derivatives varied largely among the studied taxa, reaching the following percentages of TS: 27.11 (A. officinalis), 18.96 (A. aphyllus), 5.37 (A. acutifolius), and 0.59 (A. albus); while in A. horridus, this compound remains undetected. Aspachiosde A, D, and M varied largely among samples, while a total of seven aspaspirostanosides were characterized in the analyzed species. The hierarchical cluster analysis of the saponin profiles clearly separated the various taxa and demonstrated that the taxonomic position is more important than the place from which the samples were acquired. Thus, saponin profiles have chemotaxonomic significance in Asparagus taxa. The MTT assay showed dose- and time-dependent inhibitory effects of all saponins extracts on HT-29 cancer cells, and the strongest cell growth inhibition was exercised by A. albus and A. acutifolius (GI₅₀ of 125 and 175 µg/mL). This work constitutes a whole approach to evaluating the saponins from the shoots of different Asparagus taxa and provides arguments for using them as functional foods. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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21 pages, 11265 KiB

Open AccessArticle

Design, Synthesis, and Biological Evaluation of the Quorum-Sensing Inhibitors of Pseudomonas aeruginosa PAO1

by Xinlin Yan, Shi Hou, Cheng Xing, Yuanyuan Zhang, Jiajia Chang, Junhai Xiao and Feng Lin

Molecules 2024, 29(10), 2211; https://doi.org/10.3390/molecules29102211 - 8 May 2024

Cited by 1 | Viewed by 2039

Abstract

Due to the resistance of Gram-negative bacteria Pseudomonas aeruginosa PAO1 to most clinically relevant antimicrobials, the use of traditional antibiotic treatments in hospitals is challenging. The formation of biofilms, which is regulated by the quorum-sensing (QS) system of Pseudomonas aeruginosa (PA), is an important cause of drug resistance. There are three main QS systems in P. aeruginosa: the las system, the rhl system, and the pqs system. The inhibitors of the las system are the most studied. Previously, the compound AOZ-1 was found to have a certain inhibitory effect on the las system when screened. In this study, twenty-four compounds were designed and synthesized by modifying the Linker and Rings of AOZ-1. Using C. violaceum CV026 as a reporter strain, this study first assessed the inhibitory effects of new compounds against QS, and their SAR was investigated. Then, based on the SAR analysis of compound AOZ-1 derivatives, the parent core of AOZ-1 was replaced to explore the structural diversity. Then, nine new compounds were designed and synthesized with a new nucleus core component of 3-amino-tetrahydro-l,3-oxazin-2-one. The compound Y-31 (IC₅₀ = 91.55 ± 3.35 µM) was found to inhibit the QS of C. violaceum CV026. Its inhibitory effect on C. violaceum CV026 was better than that of compound AOZ-1 (IC₅₀ > 200 µM). Furthermore, biofilm formation is one of the important causes of Pseudomonas aeruginosa PAO1 resistance. In this study, it was found that compound Y-31, with a new nucleus core component of 3-amino-tetrahydro-l,3-oxazin-2-one, had the highest biofilm inhibition rate (40.44%). The compound Y-31 has a certain inhibitory effect on the production of PAO1 virulence factors (pyocyanin, rhamnolipid, and elastase) and swarming. When the concentration of compound Y-31 was 162.5 µM, the inhibition rates of pyocyanin, rhamnolipid, and elastase were 22.48%, 6.13%, and 22.67%, respectively. In vivo, the lifetime of wildtype Caenorhabditis elegans N2 infected with P. aeruginosa PAO1 was markedly extended by the new parent nucleus Y-31. This study also performed cytotoxicity experiments and in vivo pharmacokinetics experiments on the compound Y-31. In conclusion, this study identified a compound, Y-31, with a new nucleus core component of 3-amino-tetrahydro-l,3-oxazin-2-one, which is a potential agent for treating P. aeruginosa PAO1 that is resistant to antibiotics and offers a way to discover novel antibacterial medications. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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Review

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30 pages, 3689 KiB

Open AccessReview

Tumor Microenvironment Lactate: Is It a Cancer Progression Marker, Immunosuppressant, and Therapeutic Target?

by Eugene Y. Kim, Joyce Abides, Chandler R. Keller, Steve R. Martinez and Weimin Li

Molecules 2025, 30(8), 1763; https://doi.org/10.3390/molecules30081763 - 15 Apr 2025

Viewed by 712

Abstract

The “Warburg effect” is a term coined a century ago for the preferential use of glycolysis over aerobic respiration in tumor cells for energy production, even under aerobic conditions. Although this is a less efficient mechanism of generating energy from glucose, aerobic glycolysis, in addition to the canonical anaerobic glycolysis, is an effective means of lactate production. The abundant waste product, lactate, yielded by the dual glycolysis in a tumor, has been discovered to be a major biomolecule that drives cancer progression. Lactate is a metabolic energy source that, via cell membrane lactate transporters, shuttles in and out of cancer cells as well as cancer cell-associated stromal cells and immune cells within the tumor microenvironment (TME). Additionally, lactate serves as a pH tuner, signaling ligand and transducer, epigenetic and gene transcription regulator, TME modifier, immune suppressor, chemoresistance modulator, and prognostic marker. With such broad functionalities, the production–consumption–reproduction of TME lactate fuels tumor growth and dissemination. Here, we elaborate on the lactate sources that contribute to the pool of lactate in the TME, the functions of TME lactate, the influence of the TME lactate on immune cell function and local tissue immunity, and anticancer therapeutic approaches adopting lactate manipulations and their efficacies. By scrutinizing these properties of the TME lactate and others that have been well addressed in the field, it is expected that a better weighing of the influence of the TME lactate on cancer development, progression, prognosis, and therapeutic efficacy can be achieved. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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30 pages, 21279 KiB

Open AccessReview

Squirting Cucumber, Ecballium elaterium (L.) A. Ritch: An Update of Its Chemical and Pharmacological Profile

by Attilio Anzano, Bruna de Falco, Laura Grauso and Virginia Lanzotti

Molecules 2024, 29(18), 4377; https://doi.org/10.3390/molecules29184377 - 14 Sep 2024

Viewed by 2690

Abstract

Ecballium elaterium, also known as squirting cucumber, is a plant which is widespread in temperate regions of Europe, Africa and Asia. The plant is considered to be one of the oldest used drugs. In the last decades, E. elaterium has been widely studied as a source of triterpene metabolites named cucurbitacins, often found as glycosylated derivatives, used by the plant as defensive agents. Such metabolites exhibit several biological activities, including cytotoxic, anti-inflammatory, and anti-cancer. Interestingly, the bioactive properties of E. elaterium extracts have been investigated in dozens of studies, especially by testing the apolar fractions, including the essential oils, extracted from leaves and fruits. The purpose of this review is to provide an overview of the chemical profile of different parts of the plants (leaves, flowers, and seeds) analyzing the methods used for structure elucidation and identification of single metabolites. The pharmacological studies on the isolated compounds are also reported, to highlight their potential as good candidates for drug discovery. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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17 pages, 1488 KiB

Open AccessReview

Development of Potential Therapeutic Agents from Black Elderberries (the Fruits of Sambucus nigra L.)

by Yulin Ren, Gunnar Meyer, Andrew T. Anderson, Kaitlyn M. Lauber, Judith C. Gallucci, Gary Gao and Alan Douglas Kinghorn

Molecules 2024, 29(13), 2971; https://doi.org/10.3390/molecules29132971 - 22 Jun 2024

Cited by 2 | Viewed by 4092

Abstract

Elderberry (Sambucus nigra L.) is a widespread deciduous shrub, of which the fruits (elderberries) are used in the food industry to produce different types of dietary supplement products. These berries have been found to show multiple bioactivities, including antidiabetic, anti-infective, antineoplastic, anti-obesity, and antioxidant activities. An elderberry extract product, Sambucol^®, has also been used clinically for the treatment of viral respiratory infections. As the major components, phenolic compounds, such as simple phenolic acids, anthocyanins and other flavonoids, and tannins, show promising pharmacological effects that could account for the bioactivities observed for elderberries. Based on these components, salicylic acid and its acetate derivative, aspirin, have long been used for the treatment of different disorders. Dapagliflozin, an FDA-approved antidiabetic drug, has been developed based on the conclusions obtained from a structure–activity relationship study for a simple hydrolyzable tannin, β-pentagalloylglucoside (β-PGG). Thus, the present review focuses on the development of therapeutic agents from elderberries and their small-molecule secondary metabolites. It is hoped that this contribution will support future investigations on elderberries. Full article

(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)

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