Time-course cross-species transcriptomics reveals conserved hepatotoxicity pathways induced by repeated administration of cyclosporine A.

Cyclosporine A (CsA) has shown efficacy against immunity-related diseases despite its toxicity in various organs, including the liver, emphasizing the need to elucidate its underlying hepatotoxicity mechanism. This study aimed to capture the alterations in genome-wide expression over time and the subsequent perturbations of corresponding pathways across species. Six data from humans, mice, and rats, including animal liver tissue, human liver microtissues, and two liver cell lines exposed to CsA toxic dose, were used. The microtissue exposed to CsA for 10 d was analyzed to obtain dynamically differentially expressed genes (DEGs). Single-time points data at 1, 3, 5, 7, and 28 d of different species were used to provide additional evidence. Using liver microtissue-based longitudinal design, DEGs that were consistently up- or down-regulated over time were captured, and the well-known mechanism involved in CsA toxicity was elucidated. Thirty DEGs that consistently changed in longitudinal data were also altered in 28-d rat in-house data with concordant expression. Some genes (e.g. TUBB2A, PLIN2, APOB) showed good concordance with identified DEGs in 1-d and 7-d mouse data. Pathway analysis revealed up-regulations of protein processing, asparagine N-linked glycosylation, and cargo concentration in the endoplasmic reticulum. Furthermore, the down-regulations of pathways related to biological oxidations and metabolite and lipid metabolism were elucidated. These pathways were also enriched in single-time-point data and conserved across species, implying their biological significance and generalizability. Overall, the human organoids-based longitudinal design coupled with cross-species validation provides temporal molecular change tracking, aiding mechanistic elucidation and biologically relevant biomarker discovery.

Omics analysis unveils changes in the metabolome and lipidome of Caenorhabditis elegans upon polydopamine exposure.

Polydopamine (PDA) is an insoluble biopolymer with a dark brown-black color that forms through the autoxidation of dopamine. Because of its outstanding biocompatibility and durability, PDA holds enormous promise for various applications, both in the biomedical and non-medical domains. To ensure human safety, protect health, and minimize environmental impacts, the assessment of PDA toxicity is important. In this study, metabolomics and lipidomics assessed the impact of acute PDA exposure on Caenorhabditis elegans (C. elegans). The findings revealed a pronounced perturbation in the metabolome and lipidome of C. elegans at the L4 stage following 24 hours of exposure to 100 µg/mL PDA. The changes in lipid composition varied based on lipid classes. Increased lipid classes included lysophosphatidylethanolamine, triacylglycerides, and fatty acids, while decreased species involved in several sub-classes of glycerophospholipids and sphingolipids. Besides, we detected 37 significantly affected metabolites in the positive and 8 in the negative ion modes due to exposure to PDA in C. elegans. The metabolites most impacted by PDA exposure were associated with purine metabolism, biosynthesis of valine, leucine, and isoleucine; aminoacyl-tRNA biosynthesis; and cysteine and methionine metabolism, along with pantothenate and CoA biosynthesis; the citrate cycle (TCA cycle); and beta-alanine metabolism. In conclusion, PDA exposure may intricately influence the metabolome and lipidome of C. elegans. The combined application of metabolomics and lipidomics offers additional insights into the metabolic perturbations involved in PDA-induced biological effects and presents potential biomarkers for the assessment of PDA safety.

Cyclosporine A-induced systemic metabolic perturbations in rats: A comprehensive metabolome analysis.

A better understanding of cyclosporine A (CsA)-induced nephro- and hepatotoxicity at the molecular level is necessary for safe and effective use. Utilizing a sophisticated study design, this study explored metabolic alterations after long-term CsA treatment in vivo. Rats were exposed to CsA with 4, 10, and 25 mg/kg for 4 weeks and then sacrificed to obtain liver, kidney, urine, and serum for untargeted metabolomics analysis. Differential network analysis was conducted to explore the biological relevance of metabolites significantly altered by toxicity-induced disturbance. Dose-dependent toxicity was observed in all biospecimens. The toxic effects were characterized by alterations of metabolites related to energy metabolism and cellular membrane composition, which could lead to the cholestasis-induced accumulation of bile acids in the tissues. The unfavorable impacts were also demonstrated in the serum and urine. Intriguingly, phenylacetylglycine was increased in the kidney, urine, and serum treated with high doses versus controls. Differential correlation network analysis revealed the strong correlations of deoxycytidine and guanosine with other metabolites in the network, which highlighted the influence of repeated CsA exposure on DNA synthesis. Overall, prolonged CsA administration had system-level dose-dependent effects on the metabolome in treated rats, suggesting the need for careful usage and dose adjustment.

Antimicrobial sesquiterpenes from the cultured mycobiont Diorygma pruinosum against methicillin-resistant Staphylococcus aureus isolated from Vietnamese street foods.

Traditionally, lichen has been used for many purposes, but there remains a lack of understanding regarding the chemical composition and antimicrobial characteristics of Diorygma pruinosum, a lichen native to Vietnam. In this study, four sesquiterpenes, diorygmones B-E (1-4), one phenolic compound, 3,5-dihydroxy-4-methoxybenzoic acid (5), and one sterol, ß-sitosterol (6), were isolated and structurally elucidated from the cultured mycobiont of the lichen Diorygma pruinosum. Additionally, two compounds, stictic acid (7) and norstictic acid (8), were also isolated from the lichen D. pruinosum. Compounds 2-4 were new compounds. Their chemical structures were established using comprehensive spectroscopic data, and the absolute configurations were confirmed through the analysis of NOESY and electronic circular dichroism (ECD). Moreover, Staphylococcus aureus, a Gram-positive bacterium, has been responsible for various infections, including food poisoning. Herein, we identified and isolated 13 strains of S. aureus from street food sources. Among these strains, one was identified as a multidrug-resistant variant, designated as SAX15, and was subsequently used for further antimicrobial testing. Compounds 1-3 produced zones of inhibition against S. aureus SAX15 (each 5 mm) in comparison to commercial drugs such as penicillin, ciprofloxacin, gentamicin, cefoxitin, and clarithromycin, which displayed inhibitory zones of 7, 5, 10, 9.7, and 7 mm, respectively.

Push forward LC-MS-based therapeutic drug monitoring and pharmacometabolomics for anti-tuberculosis precision dosing and comprehensive clinical management.

The spread of tuberculosis (TB), especially multidrug-resistant TB and extensively drug-resistant TB, has strongly motivated the research and development of new anti-TB drugs. New strategies to facilitate drug combinations, including pharmacokinetics-guided dose optimization and toxicology studies of first- and second-line anti-TB drugs have also been introduced and recommended. Liquid chromatography-mass spectrometry (LC-MS) has arguably become the gold standard in the analysis of both endo- and exo-genous compounds. This technique has been applied successfully not only for therapeutic drug monitoring (TDM) but also for pharmacometabolomics analysis. TDM improves the effectiveness of treatment, reduces adverse drug reactions, and the likelihood of drug resistance development in TB patients by determining dosage regimens that produce concentrations within the therapeutic target window. Based on TDM, the dose would be optimized individually to achieve favorable outcomes. Pharmacometabolomics is essential in generating and validating hypotheses regarding the metabolism of anti-TB drugs, aiding in the discovery of potential biomarkers for TB diagnostics, treatment monitoring, and outcome evaluation. This article highlighted the current progresses in TDM of anti-TB drugs based on LC-MS bioassay in the last two decades. Besides, we discussed the advantages and disadvantages of this technique in practical use. The pressing need for non-invasive sampling approaches and stability studies of anti-TB drugs was highlighted. Lastly, we provided perspectives on the prospects of combining LC-MS-based TDM and pharmacometabolomics with other advanced strategies (pharmacometrics, drug and vaccine developments, machine learning/artificial intelligence, among others) to encapsulate in an all-inclusive approach to improve treatment outcomes of TB patients.

Bio-guided isolation of alpha-glucosidase inhibitory compounds from Vietnamese Garcinia schomburgkiana fruits: in vitro and in silico studies.

Garcinia schomburgkiana is an edible tree widely distributed in the southern region of Vietnam. Little is known about the alpha-glucosidase inhibition of the Vietnamese Garcinia schomburgkiana. The aim of the current study was to explore the anti-diabetic potential of G. schomburgkiana fruits. All the fractions of G. schomburgkiana were evaluated for alpha-glucosidase inhibition, followed by bioassay-guided isolation. A new compound, epi-guttiferone Q (1), together with ten known compounds, guttiferones I-K (2-3), hypersampsone I (4), sampsonione D (5), sampsonione H (6), ß-mangostin (7), α-mangostin (8), 9-hydroxycalabaxanthone (9), and fuscaxanthone (10), were isolated and structurally elucidated. The structure of the new metabolite 1 was confirmed through 1D and 2D NMR spectroscopy, and MS analysis. To the best of our knowledge, the metabolites (except 3) have not been isolated from this plant previously. All isolated compounds were evaluated for their alpha-glucosidase inhibition. Compounds 1-6 showed potent activity with IC50 values ranging from 16.2 to 130.6 µM. Compound 2 was further selected for a kinetic study. The result indicated that it was a competitive type. Additionally, in silico docking was employed to predict the binding mechanism of 1-2 and 4-6 in the active site of alpha-glucosidase, suggesting their potential as promising anti-diabetic compounds. Molecular dynamic simulation was also applied to 1 to better understand its inhibitory mechanism.

Bioactive-Guided Phytochemical Investigations, In Vitro and In Silico Alpha-Glucosidase Inhibition of Two Vietnamese Medicinal Plants Dicranopteris linearis and Psychotria adenophylla.

Little is known about the chemical and biological profiles of Dicranopteris linearis and Psychotria adenophylla. No previous studies have investigated alpha-glucosidase inhibition using extracts from D. linearis and P. adenophylla. In this paper, bioactive-guided isolation procedures were applied to the plants D. linearis and P. adenophylla based on alpha-glucosidase inhibition. From the most active fractions, 20 compounds (DL1-DL13 and PA1-PA7) were isolated. The chemical structures were elucidated using spectroscopic data and compared with those available in the literature. These compounds were evaluated for alpha-glucosidase inhibition, while a molecular docking study was performed to elucidate the mechanisms involved. Consequently, D. linearis and P. adenophylla might serve as a good potential for developing new antidiabetic preparations.

Untargeted Metabolomics Approach for the Differentiation between Panax vietnamensis var. vietnamensis and Panax vietnamensis var. fuscidiscus.

Panax vietnamensis var. vietnamensis (PVV) and Panax vietnamensis var. fuscidiscus (PVF) both belong to Panax vietnamensis species and are chemically and morphologically similar, making it hard to distinguish for the consumer. Herein, 42 PVF and 12 PVV samples were collected in Quang Nam and Lai Chau Province, respectively, and subsequently characterized by ITSr-DNA sequence data to verify their origins. Next, untargeted metabolomics combined with multivariate statistical analysis was developed to differentiate PVV and PVF. The metabolic profiles of PVV and PVF were found to be distinct and classified well using Partial Least-Squares Discriminant Analysis (PLS-DA) in the training set. Among them, seven ginsenosides were of high abundance in PVV, while six were of high abundance in PVF. Next, the test set was used to validate 13 putative differential markers found in the training set, illustrating a complete match with the expression patterns of these ginsenosides in the training set. Finally, PLS-DA and linear Support Vector Machine models both indicated distinct ginsenoside profiles of PVV and PVF without misclassification in the test set. Conclusively, the developed untargeted metabolomics approach might serve as a powerful tool for the authentication of PVV and PVF at the metabolome level.

Systems-level multi-omics characterization provides novel molecular insights into indomethacin toxicity.

The mechanism of indomethacin toxicity at the systemic level is largely unknown. In this study, multi-specimen molecular characterization was conducted in rats treated with three doses of indomethacin (2.5, 5, and 10 mg/kg) for 1 week. Kidney, liver, urine, and serum samples were collected and analyzed using untargeted metabolomics. The kidney and liver transcriptomics data (10 mg indomethacin/kg and control) were subjected to a comprehensive omics-based analysis. Indomethacin exposure at 2.5 and 5 mg/kg doses did not cause significant metabolome changes, whereas considerable alterations in the metabolic profile compared to the control were induced by a dose of 10 mg/kg. Decreased levels of metabolites and an increased creatine level in the urine metabolome indicated injury to the kidney. The integrated omics analysis in both liver and kidney revealed an oxidant-antioxidant imbalance due to an excess of reactive oxygen species, likely originating from dysfunctional mitochondria. Specifically, indomethacin exposure induced changes in metabolites related to the citrate cycle, cell membrane composition, and DNA synthesis in the kidney. The dysregulation of genes related to ferroptosis and suppression of amino acid and fatty acid metabolism were evidence of indomethacin-induced nephrotoxicity. In conclusion, a multi-specimen omics investigation provided important insights into the mechanism of indomethacin toxicity. The identification of targets that ameliorate indomethacin toxicity will enhance the therapeutic utility of this drug.

Parmoferone A, a new depsidone from the lichen Parmotrema cristiferum.

A new depsidone, parmoferone A (1), together with three known compounds, parmosidone K (2), albifolione (3), and 4-chloroorcinol (4) were isolated from the lichen Parmotrema cristiferum (Taylor) Hale (Parmeliaceae). The structures of isolated compounds were identified from its spectroscopic data and by comparison with the literature. Compounds 1-4 were evaluated for alpha-glucosidase inhibition. Compound 1 was determined to be a potent non-competitive inhibitor against alpha-glucosidase with an IC50 value of 18.1 µM.

Sphaeranthone A, a new carvotacetone from the leaves of Sphaeranthus africanus.

A new carvotacetone sphaeranthone A and four known compounds 3-angeloyloxy-5-[2″,3″-epoxy-2″-methylbutanoyloxy]-7-hydroxycarvotacetone (2), 3-angeloyloxy-5-[3″-chloro-2″-hydroxy-2″-methylbutanoyloxy]-7-hydroxycarvotacetone (3), chrysosplenol D (4), and 3-O-methylquercetin (5) were isolated from leaves of Sphaeranthus africanus growing in Vietnam. Their chemical structures were elucidated by extensive 1D and 2D NMR analysis and high-resolution mass spectroscopy as well as comparisons in literature. Compounds 1-3 were evaluated for the alpha-glucosidase inhibition. They showed moderate activity with IC50 values of 103 ± 1.7, 146.8 ± 2.5, 49 ± 0.8 µg/mL, respectively.

Diorygmones A-B, two new guaiane-sesquiterpenes from the cultured lichen mycobiont of Diorygma sp.

Diorygma sp. is a native crustose-lichen in Vietnam. A mycobiont of this lichen was isolated, then cultivated. The present study described the isolation and structural elucidation of two new guaiane-type sesquiterpenes, namely diorygmones A-B. Their absolute chemical structures were elucidated by extensive 1D and 2D NMR analysis, high-resolution mass spectroscopy, electronic circular dichroism (ECD), and comparisons with the literatures. Compounds 1 and 2 were evaluated for cytotoxic activity against HepG2 cell line.

Two new phenolic compounds from Boerhavia erecta collected in Vietnam.

Boerhavia erecta is a tropical plant that is widely used in Asian folk medicine. Little is known about the alpha-glucosidase inhibition and antimicrobial properties of compounds from this plant. In the present study, the phytochemical study of the aerial parts of B. erecta collected in Vietnam was conducted using multiple chromatographic methods. The chemical structures of isolated compounds were identified by comprehensive spectroscopic methods. Two new compounds, berectone C (1) and (E)-tetracosyl 3-(3-hydroxy-4-methoxyphenyl)acrylate (4), together with the known compounds boeravinone C (2), liquiritigenin (3), bis(1H-indol-3-yl)methanone (5), and indole-3-carboxylic acid (6) were isolated and structural elucidated. Compounds 1 and 4 were evaluated for alpha-glucosidase inhibition and antimicrobial activity against antibiotic-resistant, pathogenic bacteria Enterococcus faecium, Staphylococcus aureus, and Acinetobacter baumannii. Compound 1 showed strong inhibition of the alpha-glucosidase enzyme (IC50 43 µg/mL). Only compound 1 exhibited antimicrobial property against A. baumannii, forming an inhibition zone of 11 mm.

Tecomastane, a new megastigmane from the flowers of Tecoma stans.

Tecoma stans is a tropical plant that is widely used in folk medicine. Little is known about the chemical constituents of flowers of this plant. From flowers of the native plant in Vietnam, 12 compounds were isolated and elucidated, including one new compound tecomastane (1) and eleven known compounds, (3S,5R,6S,7E)-5,6-epoxy-3-hydroxy-7-megastigmane-9-one (2), bosciallin (3), chakyunglupulin B (4), (2S,6R)-2,6-dimethyloctane-1,8-diol (5), cleroindicin F (6), rengyoxide (7), 3,4-dihydroxybenzoic acid (8), methyl 3,4-dihydrobenzoate (9), 3,5-dihydroxybenzoic acid (10), luteolin (11), and indole-3-carboxylic acid (12). Compound 5 was a new natural product. The chemical structures of isolated compounds were identified by interpretation of their spectroscopic data (1D, 2D NMR, and HRESIMS) and by comparison with the literature. Compounds 1-7 and 10-12 were evaluated for alpha-glucosidase inhibition and antimicrobial activity against antibiotic-resistant, pathogenic bacteria Enterococcus faecium, Staphylococcus aureus, and Acinetobacter baumannii.

α-Glucosidase inhibitory derivatives of protocetraric acid.

Lichen-derived depsidones have been a successful source for alpha-glucosidase inhibitory agents with numerous advantages. In this article, derivatives of protocetraric acids were designed and synthesised. Diels-Alder reaction, esterification, and Friedel-Crafts alkylation of protocetraric acid with different reagents under Lewis acid were performed. Eleven products were prepared, including 10 new compounds and parmosidone A. Among them, compounds 2-4 and 6 had the novel skeletons. The newly synthetic products were evaluated for alpha-glucosidase inhibition. Among tested compounds, 9 showed the strongest activity, with an IC50 value of 5.9 µM. The molecular docking model indicated the consistency between in vitro and in silico data of alpha-glucosidase inhibition.

In silico and in vitro studies on the anti-cancer activity of artemetin, vitexicarpin and penduletin compounds from Vitex negundo.

Vitex negundo L. (V. negundo) is one of the important medicinal and anticancer enhancer herbs. This plant is commonly used in the preparation of traditional drugs to treat numerous diseases. Inspired by the medicinal properties of this plant, the current study aimed to investigate antiproliferative potential and the primary molecular mechanisms of the apoptotic induction against human HepG2 and MCF-7 cell lines, by pure compounds isolated from targeted fractions of V. negundo which were characterized by NMR, FTIR and HRMS analysis and identified as artemetin (FLV1), vitexicarpin (FLV2), and penduletin (FLV3) compounds. The FLV1, FLV2, and FLV3 compounds were evaluated for the antiproliferative potential against HepG2 and MCF-7 cell lines by cell viability assay and exhibited IC50 values of 2.3, 23.9 and 5.6 µM and 3.9, 25.8, and 6.4 µM, respectively. In addition, those compounds increased the level of reactive oxygen species production, induced cell death occurred via apoptosis, demonstrated by Annexin V-staining cells, contributed significantly to DNA damage, and led to the activation of caspase3/caspase8 pathways.Additionally, molecular docking was also conducted to rationalize the cancer cells inhibitory and to evaluate the ability of the FLV1, FLV2, and FLV3 compounds to be developed as good drug candidates for cancers treatment.

Biological Activities of Lichen-Derived Monoaromatic Compounds.

Lichen-derived monoaromatic compounds are bioactive compounds, associated with various pharmacological properties: antioxidant, antifungal, antiviral, cytotoxicity, and enzyme inhibition. However, little is known about data regarding alpha-glucosidase inhibition and antimicrobial activity. Very few compounds were reported to have these activities. In this paper, a series of monoaromatic compounds from a lichen source were isolated and structurally elucidated. They are 3,5-dihydroxybenzoic acid (1), 3,5-dihydroxybenzoate methyl (2), 3,5-dihydroxy-4-methylbenzoic acid (3), 3,5-dihydroxy-4-methoxylbenzoic acid (4), 3-hydroxyorcinol (5), atranol (6), and methyl hematommate (7). To obtain more derivatives, available compounds from the previous reports such as methyl ß-orsellinate (8), methyl orsellinate (9), and D-montagnetol (10) were selected for bromination. Electrophilic bromination was applied to 8-10 using NaBr/H2O2 reagents to yield products methyl 5-bromo-ß-orsellinate (8a), methyl 3,5-dibromo-orsellinate (9a), 3-bromo-D-montagnetol (10a), and 3,5-dibromo-D-montagnetol (10b). Compounds were evaluated for alpha-glucosidase inhibition and antimicrobial activity against antibiotic-resistant, pathogenic bacteria Enterococcus faecium, Staphylococcus aureus, and Acinetobacter baumannii. Compound 4 showed stronger alpha-glucosidase inhibition than others with an IC50 value of 24.0 µg/mL. Synthetic compound 9a exhibited remarkable activity against Staphylococcus aureus with a MIC value of 4 µg/mL. Molecular docking studies were performed to confirm the consistency between in vitro and in silico studies.

α-Glucosidase Inhibitory and Antimicrobial Benzoylphloroglucinols from Garcinia schomburgakiana Fruits: In Vitro and In Silico Studies.

α-Glucosidase plays a role in hydrolyzing complex carbohydrates into glucose, which is easily absorbed, causing postprandial hyperglycemia. Inhibition of α-glucosidase is therefore an ideal approach to preventing this condition. A novel polyprenylated benzoylphloroglucinol, which we named schomburgkianone I (1), was isolated from the fruit of Garcinia schomburgkiana, along with an already-reported compound, guttiferone K (2). The structures of the two compounds were determined using NMR and HRESIMS analysis, and comparisons were made with previous studies. Compounds 1 and 2 exhibited potent α-glucosidase inhibition (IC50s of 21.2 and 34.8 µM, respectively), outperforming the acarbose positive control. Compound 1 produced wide zones of inhibition against Staphylococcus aureus and Enterococcus faecium (of 21 and 20 mm, respectively), compared with the 19 and 20 mm zones of compound 2, at a concentration of 50 µg/mL. The MIC value of compound 1 against S. aureus was 13.32 µM. An in silico molecular docking model suggested that both compounds are potent inhibitors of enzyme α-glucosidase and are therefore leading candidates as therapies for diabetes mellitus.

Some Antioxidant Properties of Components from the Flower of Ochna integerrima and Their Beneficial Effects on HaCaT Keratinocytes and in Silico Analysis on Tyrosinase.

Four compounds, luteolin (1), 6-γ,γ-dimethylallylquercetin 7-O-ß-D-glucopyranoside (2), 6-γ,γ-dimethylallylkaempferol 7-O-ß-D-glucopyranoside (3), and 6-γ,γ-dimethylallyldihydrokaempferol 7-O-ß-D-glucoside (4), were isolated for the first time from AcOEt extract of the O. integerrima flower. We then evaluated the antioxidant effects of AcOEt, butanol, and MeOH extracts and their effects on H2 O2 against oxidative stress in HaCaT keratinocyte cell lines. Furthermore, 2,2-diphenyl-1-picrylhydrazyl hydrate (DPPH⋅) radical scavenging activities of 1-4 were determined and their mechanisms of action on tyrosinase were predicted by in silico studies. The results revealed that the AcOEt extract and 1-3 exhibited good DPPH⋅ radical scavenging activity. Furthermore, this extract also had a significant protective effect against H2 O2 -induced oxidative stress in HaCaT cells. In silico studies indicated that the activity of 1-3 may be due to tyrosinase inhibition with MM-GBSA free binding energies of -78.9, -70.1, and -71.1 kcal mol-1 , respectively, compared to 4 with an energy -56.9 kcal mol-1 .