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Development of a robust microtiter plate-based assay method for assessment of bioactivity.

A microtiter plate-based assay was developed for the quantitative monitoring of bioactive compound production in Streptomyces hygroscopicus fermentation samples. The method reported demonstrates the successful application of the theories of disk diffusion based methods of bioactivity assessment, to a microtiter assay for high throughput analysis. The assay method facilitates the generation of the dose-response curve of test organisms (Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae) to a bioactive compound. Using this dose-response curve, the method facilitates definition of three distinct Minimum Inhibitory Concentration (MIC) values for use in the characterisation of the bioactive attributes of a sample. The assay uses established standard procedures to facilitate adaptation of the assay for use with a wider range of test microorganisms. Errors due to the assumption of a linear relationship between turbidity and biomass concentration are also reduced, due to incorporation of a step to convert turbidity to biomass concentration, for use in the calculation of bioactivity.

Anti-Bacterial Agents↗

Changes in heartwood chemistry of dead yellow-cedar trees that remain standing for 80 years or more in southeast Alaska.

We measured the concentrations of extractable bioactive compounds in heartwood of live yellow-cedar (Chamaecyparis nootkatensis) trees and five classes of standing snags (1-5, averaging 4, 14, 26, 51, and 81 years-since-death, respectively) to determine how the concentrations changed in the slowly deteriorating snags. Three individuals from each of these six condition classes were sampled at four sites spanning a 260-km distance across southeast Alaska, and the influence of geographic location on heartwood chemistry was evaluated. Cores of heartwood were collected at breast height and cut into consecutive 5-cm segments starting at the pith. Each segment was extracted with ethyl acetate and analyzed by gas chromatography. Concentrations of carvacrol, nootkatene, nootkatol, nootkatone, nootkatin, and total extractives (a sum of 16 compounds) for the inner (0-5 cm from pith), middle (5-10 cm from pith), and surface (outer 1.1-6.0 cm of heartwood) segments from each core were compared within each tree condition class and within segments across condition classes. Heartwood of class 1 and 2 snags had the same chemical composition as live trees. The first concentration changes begin to appear in class 3 snags, which coincides with greater heartwood exposure to the external environment as decaying sapwood sloughs away, after losing the protective outer bark. Within core segments, the concentrations of all compounds, except nootkatene, decrease between snag classes 2 and 5, resulting in the heartwood of class 5 snags having the lowest quantities of bioactive compounds, although not different from the amounts in class 4 snags. This decline in chemical defense is consistent with heartwood of class 5 snags being less decay-resistant than heartwood of live trees, as observed by others. The unique heartwood chemistry of yellow cedar and the slow way it is altered after death allow dead trees to remain standing for up to a century with a profound impact on the ecology of forests in southeast Alaska where these trees are in decline.

Acetates↗

Four new prenylated isoflavonoids in Tadehagi triquetrum.

Investigation on the anthelminthic bioactive compounds of the ethanol extract of Tadehagi triquetrum resulted in the isolation of three new prenylated isoflavones, triquetrumones A (1), B (2), and C (3), and one new prenylated biisoflavanone, (R)-triquetrumone D (4), along with 16 known compounds, cyclokievitone (5), yukovanol (6), aromadendrin (7), kaempferol (8), astragalin (9), 2-O-methyl-l-chiro-inositol (10), galactitol (11), p-hydroxycinnamic acid (12), ursolic acid (13), betulinic acid (14), beta-sitosterol (15), daucosterol (16), stigmasterol (17), stigmasta-5,22-dien-3-O-beta-d-glucopyranoside (18), saccharose (19), and docosanoic acid (20). The structures of 1-4 were elucidated on the basis of spectroscopic and spectrometric methods. Compounds 1-3 displayed mild anthelminthic bioactivity, and compound 3 showed a significant binding ability to the estrogen receptor.

Animals↗

Bioactive aromatic compounds from leaves and stems of Vanilla fragrans.

Alcoholic extracts of leaves and stems of Vanilla fragrans were fractionated with ethyl acetate and aqueous butanol. All three fractions of ethyl acetate, butanol, and water were screened for toxic bioactivity against mosquito larvae. The results of these experiments showed that the fractions from the ethyl acetate and butanol phases were both active in the bioassay. Bioactivity of the ethyl acetate fraction was found to be much greater than that from the butanol fraction in mosquito larvae toxicity. The water phase appeared to contain no substances that impaired mosquito larval growth. Repeated column chromatography of the ethyl acetate fraction on silica gel led to the isolation of 4-ethoxymethylphenol (1), 4-butoxymethylphenol (2), vanillin (3), 4-hydroxy-2-methoxycinnamaldehyde (4), and 3,4-dihydroxyphenylacetic acid (5). Compounds 4 and 5 were isolated from Vanilla species for the first time and 2 has not been reported to have been found in a natural form. 4-Ethoxymethylphenol (1) was the predominant compound, but 4-butoxymethylphenol (2) showed the strongest toxicity to mosquito larvae. The structures of the compounds were determined on the basis of their mass spectra and (1)H or (13)C NMR data.

Animals↗

Antioxidants, low molecular weight carbohydrates, and total antioxidant capacity in strawberries (Fragaria x ananassa): effects of cultivar, ripening, and storage.

Four cultivars of strawberries (Senga Sengana, BFr77111, Elsanta, and Honeoye) were studied for their content of antioxidants, total antioxidant capacity, and low molecular weight carbohydrates in relation to harvest year, ripening stage, and cold storage. For ascorbic acid, chlorogenic acid, ellagic acid, and total antioxidative capacity, measured in both water-soluble and water-insoluble extracts, there was a 2-5-fold variation among cultivars. Unripe berries contained lower concentrations of chlorogenic acid and p-coumaric acid and also quercetin and kaempferol compared with riper berries. During cold storage for up to 3 days, relatively few changes in the concentration of the different antioxidants occurred. The concentrations of several investigated parameters were interrelated, for example, for ascorbic acid and water-soluble antioxidant capacity and for ellagic acid and water-insoluble antioxidant capacity. The dominating sugars in strawberries were fructose and glucose, but considerable amounts of sucrose were also present, and their contents varied among cultivars, giving a predicted glycemic index of approximately 81. Verbascose, raffinose, and stachyose were found in only minor amounts. The study shows that the concentration of a number of bioactive compounds in strawberries varied according to cultivar, ripening stage, and storage. This information should make it possible to select strawberries with an optimal content of bioactive compounds.

Antioxidants↗

On-line coupling of high-performance liquid chromatography to a continuous-flow enzyme assay based on electrospray ionization mass spectrometry.

Liquid chromatography (LC) was coupled on-line to a continuous-flow enzymatic assay using electrospray ionization mass spectrometry (ESI-MS) as readout for the screening of enzyme inhibitors in complex samples. Inhibitors were detected by changes in the concentration of the enzymatic reaction products, indicating the inhibition of enzymatic activity. The molecular masses of the inhibitors were determined with high certainty by using retention time matching and peak shape comparison. Due to the high matching accuracy, baseline separation of coeluting analytes was not necessary in order to identify the correct masses of the bioactive compounds. The continuous-flow system was successfully applied for the screening of complex samples, such as natural extracts. For a red clover extract, detection limits of 0.3-0.8 micromol/L were obtained. System validation was performed by determining the IC(50) values of four inhibitors in the flow-injection mode. The IC(50) values were in the 0.11-5.6 micromol/L range and correspond closely to data obtained by microtiter plate assays. Detection limits were in the range of 0.018-0.35 micromol/L in the flow-injection mode, and 0.075-0.75 micromol/L in the LC mode. These values are well below the typical compound concentrations (1-10 micromol/L) used in high-throughput screening. Together with an interday precision of 12.6%, these results demonstrate the applicability of the system for bioactivity screening of complex mixtures, generating both chemical and biological information on bioactive compounds in a single run.

Animals↗

Crystal structures of a multifunctional triterpene/flavonoid glycosyltransferase from Medicago truncatula.

Glycosylation is a ubiquitous reaction controlling the bioactivity and storage of plant natural products. Glycosylation of small molecules is catalyzed by a superfamily of glycosyltransferases (GTs) in most plant species studied to date. We present crystal structures of the UDP flavonoid/triterpene GT UGT71G1 from Medicago truncatula bound to UDP or UDP-glucose. The structures reveal the key residues involved in the recognition of donor substrate and, by comparison with other GT structures, suggest His-22 as the catalytic base and Asp-121 as a key residue that may assist deprotonation of the acceptor by forming an electron transfer chain with the catalytic base. Mutagenesis confirmed the roles of these key residues in donor substrate binding and enzyme activity. Our results provide an initial structural basis for understanding the complex substrate specificity and regiospecificity underlying the glycosylation of plant natural products and other small molecules. This information will direct future attempts to engineer bioactive compounds in crop plants to improve plant, animal, and human health and to facilitate the rational design of GTs to improve the storage and stability of novel engineered bioactive compounds.

Amino Acids↗

Pharmacological properties of indazole derivatives: recent developments.

The chemistry of indazole and its N-oxide derivatives is very well-known. Indazole derivatives were extensively studied as bioactive compounds, such as anti-aggregatory and vasorelaxant activity by NO release and increase of cGMP levels and anticancer effects, antimicrobial and antiparasitic properties, among others. Recently, the research and development in the medicinal chemistry of these systems have produced compounds with contraceptive activities for men, for the treatment of osteoporosis, inflammatory disorders and neurodegenerative diseases. On the other hand, indazole N-oxide derivatives were poorly studied as bioactive compounds, but recently compounds with antiparasitic properties were produced. In this presentation, recent developments in the chemistry and medicinal chemistry of indazole and its N-oxide derivatives will be reviewed.

Animals↗

Cruciferous vegetables and colo-rectal cancer.

Cruciferous vegetables have been studied extensively for their chemoprotective effects. Although they contain many bioactive compounds, the anti-carcinogenic actions of cruciferous vegetables are commonly attributed to their content of glucosinolates. Glucosinolates are relatively biologically inert but can be hydrolysed to a range of bioactive compounds such as isothiocyanates (ITC) and indoles by the plant-based enzyme myrosinase, or less efficiently by the colonic microflora. A number of mechanisms whereby ITC and indoles may protect against colo-rectal cancer have been identified. In experimental animals cruciferous vegetables have been shown to inhibit chemically-induced colon cancer. However, the results of recent epidemiological cohort studies have been inconsistent and this disparity may reflect a lack of sensitivity of such studies. Possible explanations for the failure of epidemiological studies to detect an effect include: assessment of cruciferous vegetable intake by methods that are subject to large measurement errors; the interaction between diet and genotype has not been considered: the effect that post-harvest treatments may have on biological effects of cruciferous vegetables has not been taken into account.

Anticarcinogenic Agents↗

Virtual screening and rational drug design method using structure generation system based on 3D-QSAR and docking.

An efficient virtual and rational drug design method is presented. It combines virtual bioactive compound generation with 3D-QSAR model and docking. Using this method, it is possible to generate a lot of highly diverse molecules and find virtual active lead compounds. The method was validated by the study of a set of anti-tumor drugs. With the constraints of pharmacophore obtained by DISCO implemented in SYBYL 6.8, 97 virtual bioactive compounds were generated, and their anti-tumor activities were predicted by CoMFA. Eight structures with high activity were selected and screened by the 3D-QSAR model. The most active generated structure was further investigated by modifying its structure in order to increase the activity. A comparative docking study with telomeric receptor was carried out, and the results showed that the generated structures could form more stable complexes with receptor than the reference compound selected from experimental data. This investigation showed that the proposed method was a feasible way for rational drug design with high screening efficiency.

Colchicine↗

Further bioactive acetylenic compounds from the Caribbean sponge Cribrochalina vasculum.

In addition to the known 3-hydroxydocosa-(4E, 15E)-dien-1-yne [1], 3-hydroxy-16-methyleicos-(4E)-en-1-yne [2], and 3-hydroxy-19-methyleicos-(4E)-en-1-yne [3], the lipophilic extract of the Caribbean sponge Cribrochalina vasculum was shown to contain four new bioactive acetylene metabolites, (3R)-hydroxy-14-methyldocos-(4E)-en-1-yne [4], (3R)-hydroxy-16-methyleicos-1-yne [7], (3R)-hydroxy-19-methyleicos-1-yne [8], and docosa-(3E, 15Z)-dien-1-yne [9], whose structures were elucidated on the basis of chemical and spectral studies. The previously unassigned chirality at C-3 of the known compounds 1-3 has been also established as R.

Acetylene↗

Taxonomic study and morphological differentiation of an actinomycete genus, Kitasatospora.

The history and taxonomic criteria of the actinomycete genus, Kitasatospora, are described. The reasons for a change of the position of the genus in the classification system are given and a restriction length polymorphism (RFLP) method for rapid identification is described. Although the bacterial genus, Kitasatospora, resembles the fungal one, Streptomyces, in its morphology, it is clearly different in its cell-wall composition which includes LL- and meso-DAP, glycine and galactose. Following a change in its taxonomic position as a result of insufficient gene analysis, it was re-established by phylogenetic analysis of the entire 16S rRNA gene. Most actinomycetes produce bioactive compounds but the relationship between antibiotic production and morphology has not been studied in detail. Kitasatospora strains may be used as a model because they grow in submerged culture like those actinomycetes strains which produce bioactive compounds. The authors suggest further studies of the correlation between metabolic and morphological differentiation and the mechanism of the production of submerged spores.

Actinomycetales↗

High-temperature liquid chromatography coupled on-line to a continuous-flow biochemical screening assay with electrospray ionization mass spectrometric detection.

The potential of high-temperature liquid chromatography (HTLC) was investigated in an on-line combination with a screening system for bioactive compounds against the enzyme cathepsin B. Samples were separated by HTLC and subsequently analyzed by an on-line continuous-flow enzymatic assay. Detection was performed by electrospray ionization mass spectrometry, revealing both the bioactivity and the molecular mass of the bioactive compounds. Compared to conventional reversed-phase liquid chromatography, the amount of methanol necessary for separation could be decreased to only 10%, which improved the compatibility of LC with a biochemical assay. Sufficient preheating of the mobile phase prior to the separation and postcolumn cooling to prevent deactivation of the enzyme, even at column temperatures as high as 208 degrees C, was achieved as indicated by the reliable peak shapes obtained. The sensitivity was comparable with previously described systems operating at ambient temperatures as similar IC50 values were obtained. Exposing the inhibitors to high temperatures did not lead to thermal decomposition. The separation of inhibitors and the subsequent biochemical assay was performed either isothermally at various temperatures or by applying various temperature gradients as well as at various flow rates. The results obtained clearly show the compatibility of HTLC with an enzymatic screening assay.

Cathepsin B↗

A melanocyte-keratinocyte coculture model to assess regulators of pigmentation in vitro.

Many melanocyte or skin equivalent models have been used to evaluate the potential efficacy of melanogenic compounds to regulate pigmentation, but there has been great variation in results, partially stemming from the use of different cell lines and diverse conditions for the melanogenic assays. In an earlier report, we optimized a microtiter format assay system to screen potential bioactive compounds using immortalized melan-a melanocytes. That assay system, termed the STOPR protocol, allowed effects on melanocyte proliferation and differentiation to be assessed in a highly sensitive, reproducible, and cost-effective manner. However, in the skin and hair, melanocytes interact with keratinocytes, fibroblasts, and other cell types, and testing of putative bioactive compounds on melanocytes alone in culture does not allow one to observe the interactions with those other cell types, such as would occur in vivo. Therefore, we developed a melanocyte-keratinocyte coculture protocol that allows testing of compounds for potential effects on pigmentation in a more physiologically relevant context. It is a sensitive, reproducible, and reliable model for testing melanogenic regulators, and we have standardized it with known melanogenic inhibitors (hydroquinone, arbutin, kojic acid, and niacinamide) and stimulators (alpha-melanocyte-stimulating hormone, 8-methoxypsoralen, and 3,4-dihydroxyphenylalanine). This coculture system allows for large-scale screening of candidate compounds in conjunction with the STOPR protocol and provides a more physiologically relevant system to study melanocyte-keratinocyte interactions and to elucidate the regulatory mechanisms of melanogenic compounds.

Animals↗

Exploring the mechanism of Shengmai San in treating lung adenocarcinoma based on bioinformatics and molecular dynamics simulation.

To investigate the mechanism of Shengmai San (SMS) in the treatment of lung adenocarcinoma (LUAD) based on an integrated strategy combining "network pharmacology, bioinformatics, molecular docking, and molecular dynamics simulation," aiming to provide a precise combination therapy strategy and identify potential bioactive compounds. Differentially expressed genes in LUAD were identified from the Gene Expression Omnibus database using R (originally developed at Bell Laboratories and currently managed by Lucent Technologies). SMS components (ginseng, Ophiopogon japonicus, and Schisandra chinensis) were retrieved from encyclopaedia of traditional Chinese medicine, with Lipinski-compliant compounds selected. Compound targets were predicted via SwissTargetPrediction and Similarity Ensemble Approach. Intersecting targets between differentially expressed genes and compound targets were identified for "herbs-compounds-targets-disease" network construction. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed. Hub targets were identified by analyzing the protein-protein interaction network. High-prognostic relevance targets were screened from The Cancer Genome Atlas. Compounds targeting these were identified through the herbs-compounds-targets-disease network, and absorption, distribution, metabolism, excretion, and toxicity-compliant compounds were selected using SwissADME (a web-based tool provided by the Molecular Modeling Group of the Swiss Institute of Bioinformatics). Core regulatory targets were identified through molecular docking, with complex stability assessed by molecular dynamics simulations. The key bioactive compounds of SMS for treating LUAD were identified as 7-hydroxy-2,5-dimethyl-4H-1-benzopyran-4-one, N-trans-feruloyltyramine, paprazine, and (E)-N-[(2S)-2-hydroxy-2-(4-hydroxyphenyl)ethyl]-3-(4-hydroxyphenyl)prop-2-enamide. Hub targets included AURKA, CCNA2, CCNB1, CDK1, CHEK1, KIF11, NEK2, PLK1, TTK, and TYMS. Among these, CDK1, CHEK1, and PLK1 demonstrated both high-prognostic relevance and strong binding affinity with SMS, emerging as core regulatory targets for SMS in LUAD treatment. Mechanistically, SMS exerts its anticancer effects primarily by modulating the tumor necrosis factor, interleukin-17, cell cycle, and Lipid and atherosclerosis signaling pathways. The active components of SMS, such as paprazine, may exert antitumor effects partly through downregulating CDK1, CHEK1, and PLK1 expression. Although the present study did not examine drug-resistance models or combination regimens, our findings raise the possibility that, in patients with high expression of these genes, combining SMS with standard chemotherapy or targeted therapy could potentially enhance chemosensitivity and mitigate the development of resistance. This hypothesis, however, requires formal testing in appropriate preclinical models and functional validation studies.

Molecular Dynamics Simulation↗

Network pharmacology-based study on the mechanism of Tangfukang formula against type 2 diabetes mellitus.

OBJECTIVE: To explore the mechanism of Tangfukang formula (, TFK) in treating type 2 diabetes mellitus (T2DM). METHODS: We employed network pharmacology combined with experimental validation to explore the potential mechanism of TFK against T2DM. Initially, we filtered bioactive compounds with the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Symptom Mapping (SymMap), and gathered targets of TFK and T2DM. Subsequently, we constructed a protein-protein interaction (PPI) network, enriched core targets through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and adopted molecular docking to study the binding mode of compounds and the signaling pathway. Finally, we employed a KKAy mice model to investigate the effect and mechanism of TFK against T2DM. Biochemical assay, histology assay, and Western blot (WB) were used to assess the mechanism. RESULTS: There were 492 bioactive compounds of TFK screened, and 1226 overlapping targets of TFK against T2DM identified. A compound-T2DM-related target network with 997 nodes and 4439 edges was constructed. KEGG enrichment analysis identified some core pathways related to T2DM, including adenosine 5-monophosphate-activated protein kinase (AMPK) signaling pathway. Molecular docking study revealed that compounds of TFK, including citric acid, could bind to the active pocket of AMPK crystal structure with free binding energy of -4.8, -8 and -7.9, respectively. Animal experiments indicated that TFK decreased body weight, fasting blood glucose, fasting serum insulin, homeostasis model of insulin resistance, glycosylated serum protein, total cholesterol, triglyceride, and low-density lipoprotein cholesterol, and improve oral glucose tolerance test results. TFK reduced steatosis in liver tissue, and infiltration of inflammatory cells, and protected liver cells to a certain extent. WB analysis revealed that, TFK upregulated the phosphorylation of AMPK and branched-chain α-ketoacid dehydrogenase proteins. CONCLUSION: TFK has the potential to effectively manage T2DM, possibly by regulating the AMPK signaling pathway. The present study lays a new foundation for the therapeutic application of TFK in the treatment of T2DM.

Diabetes Mellitus, Type 2↗

Simultaneous determination of ginsenosides and polyacetylenes in American ginseng root (Panax quinquefolium L.) by high-performance liquid chromatography.

A method for simultaneous determination of ginsenosides and polyacetylenes in Panax quinquefolium L. (American ginseng) roots was developed. The ginsenosides Rb1, Rb2, Rc, Rd, Re, Rg1, Ro, malonyl-Rb1, malonyl-Rc, and malonyl-Rd and the polyacetylenes falcarinol and panaxydol were extracted from fresh ginseng roots in a sequential extraction process with 100% methanol followed by 80% aqueous methanol and quantified simultaneously in extracts by high-performance liquid chromatography using diode array detection. Separations were achieved with a phosphate buffer-acetonitrile gradient system using an RP-C18 column. Except for Rd, the present extraction method resulted in similar or significantly higher concentrations of both ginsenosides and polyacetylenes in comparison to commonly used extraction methods for these compounds. The contents of polyacetylenes and ginsenosides were determined in the root hairs, lateral roots, and main roots of 6 year old ginseng plants. The total mean concentrations of ginsenosides and polyacetylenes in root hairs were 31.0 g/kg fresh weight (FW) and 2.6 g/kg FW, respectively, whereas the concentrations of these bioactive compounds in the main roots were significantly lower with total mean concentrations of 17.8 g/kg FW for ginsenosides and 0.6 g/kg FW for polyacetylenes. The concentration of individual and total ginsenosides and polyacetylenes did not differ significantly between main roots of different sizes. Consequently, it is possible to do quantitative screening for ginsenosides and polyacetylenes to breed ginseng roots with higher levels of bioactive compounds.

Chromatography, High Pressure Liquid↗

Integrated data mining and network pharmacology to explore the prescription patterns from a senior TCM oncologist's clinical practice in treating chemotherapy-induced hand-foot syndrome.

Hand-foot syndrome (HFS) is a common and refractory adverse effect of chemotherapy lacking specific therapeutic strategies currently. Traditional Chinese medicine (TCM) has shown empirical efficacy in clinical HFS management. This study integrated data mining and network pharmacology to systematically elucidate the medication principles and molecular mechanisms underlying Professor Gang Xie's prescriptions for HFS. All medical records from Professor Xie's specialist clinic (January 2020 to March 2025) were retrospectively collected and standardized in Excel. Prescriptions were analyzed through frequency statistics, association and clustering. Active ingredients of core herb pairs and their disease-related targets were identified using TCMSP, HERB, GeneCards, PharmGKB and GEO databases. Protein-protein interaction (PPI) networks, gene ontology (GO), and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed. Molecular docking validated interactions between key bioactive compounds and targets. This study involved 217 prescriptions containing 150 herbs. Core herb combinations comprised Radix Astragali (Huangqi), Poria (Fuling), and Radix Pseudostellariae (Taizishen), predominantly classified as spleen-tonifying agents with warm properties, targeting lung, spleen, and stomach meridians. Network analysis identified 67 bioactive compounds and 899 disease targets. Quercetin, kaempferol, acacetin and luteolin were identified the key ingredients. The core targets (TP53, STAT3, PIK3CA, HSP90AA1, AKT1, CTNNB1, PI3KR1, MAPK1) were enriched in MAPK and PI3K-Akt signaling pathways. Molecular docking confirmed strong binding affinity between key compounds and targets. Professor Xie's therapeutic strategy for HFS emphasizes "spleen fortification, phlegm elimination, and stasis resolution." The core herb combination likely exerts anti-HFS effects via modulation of MAPK and PI3K-Akt pathways, providing a pharmacological basis for TCM-driven HFS management.

Network Pharmacology↗