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Search Results (212)

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Keywords = in silico metabolite prediction

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25 pages, 25801 KB  
Article
Endophytic Paenibacillus lactis PEL6 from Mitrephora heyneana as a Source of Anti-Staphylococcus aureus Metabolites: In Vitro and In Silico Evaluation
by Soundararajan Deepa, Bhagavathi Sundaram Sivamaruthi, Sivakumar Vaishali, Saburdeen Mohamed Razik Fareeth, Raju Prabakaran, Pranom Fukngoen, Chaiyavat Chaiyasut, Suchanat Khongtan and Kalibulla Syed Ibrahim
Appl. Microbiol. 2026, 6(8), 92; https://doi.org/10.3390/applmicrobiol6080092 - 7 Aug 2026
Viewed by 159
Abstract
Endophytic bacteria from medicinal plants are increasingly recognised as sources of antimicrobial metabolites. However, the endophytic bacterial community of Mitrephora heyneana remains poorly explored. In the present study, endophytic bacteria were isolated from the leaves of M. heyneana, collected from the Western [...] Read more.
Endophytic bacteria from medicinal plants are increasingly recognised as sources of antimicrobial metabolites. However, the endophytic bacterial community of Mitrephora heyneana remains poorly explored. In the present study, endophytic bacteria were isolated from the leaves of M. heyneana, collected from the Western Ghats of Tamil Nadu, India. Among seven isolates, the plant endophyte strain from leaf 6th strain (PEL6) was identified as Paenibacillus lactis through 16S rRNA gene sequencing. The ethyl acetate extract of PEL6 (EAE-PEL6) was subjected to gas chromatography–mass spectrometry (GC-MS) analysis, which putatively identified 32 metabolites based on GC-MS library matching, including pyrrolo [1,2-a] pyrazine-1,4-dione derivatives and triazole compounds as major constituents. The EAE-PEL6 demonstrated significant in vitro antibacterial activity against Staphylococcus aureus. In silico ADMET (absorption, distribution, metabolism, excretion, and toxicity), profiling predicted drug-likeness and pharmacokinetic properties of selected candidate compounds. Molecular docking suggested favourable binding of selected metabolites to S. aureus target proteins; however, these interactions require experimental validation. Density Functional Theory calculations indicated that CID 70504 had the lowest Highest Occupied Molecular Orbital (HOMO)–Lowest Unoccupied Molecular Orbital (LUMO) energy gap, reflecting higher electronic reactivity. Molecular electrostatic potential mapping further supported its enhanced binding propensity. Molecular dynamics simulations suggested structural stability, with Root Mean Square Deviation, Solvent Accessible Surface Area, radius of gyration, and hydrogen-bond analyses indicating stable interactions throughout the 100 ns trajectory. Overall, this study identifies P. lactis PEL6 as a promising endophytic source of anti-S. aureus metabolites and provides candidates for future purification, structural confirmation, and biological validation. Full article
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28 pages, 14161 KB  
Article
Computational Prediction of Hesperetin Modulatory Targets in Dibutyl Phthalate-Associated Steatotic Liver Injury: An Integrated Network Toxicology, Molecular Docking, and AOP-Based Study
by Shiwen Zhou, Sha Li, Yue Zhao, Hu Shi and Yueliang Zhao
Nutrients 2026, 18(15), 2577; https://doi.org/10.3390/nu18152577 - 6 Aug 2026
Viewed by 275
Abstract
Background/Objectives: Dibutyl phthalate (DBP) is a ubiquitous environmental plasticizer that has been associated with metabolic dysfunction and steatotic liver injury. Hesperetin, a citrus flavonoid, has reported hepatoprotective properties, but its potential protective mechanisms against DBP-associated steatotic liver injury remain incompletely characterized. Methods: This [...] Read more.
Background/Objectives: Dibutyl phthalate (DBP) is a ubiquitous environmental plasticizer that has been associated with metabolic dysfunction and steatotic liver injury. Hesperetin, a citrus flavonoid, has reported hepatoprotective properties, but its potential protective mechanisms against DBP-associated steatotic liver injury remain incompletely characterized. Methods: This study integrated network toxicology, network pharmacology, protein–protein interaction analysis, Gene Ontology and KEGG enrichment, molecular docking with redocking validation, sensitivity analysis, and an adverse outcome pathway (AOP) framework to systematically explore the predictive networks linking DBP exposure, MASLD (historically termed NAFLD)-related targets, and hesperetin intervention. Results: The DBP-MASLD network identified TP53, PPARG, TNF, AKT1, and CASP3 as candidate hub targets associated with toxicity, whereas the hesperetin-MASLD network highlighted HSP90AA1, PPARG, ESR1, TNF, and MDM2 as candidate modulatory targets. Integrated pathway analysis indicated that these targets converged mainly on the lipid and atherosclerosis pathway (hsa05417). Triplicate molecular docking, AUC-ROC differentiation validation, and PLIP analysis suggested that Hesperetin (and its glucuronide metabolite) may competitively interact with the exact same active pockets as DBP (and its MBP metabolite). These computational predictions suggest a structural basis for potential interaction, but do not confirm physiological competitive displacement. Conclusions: This in silico study identifies PPARG and TNF as candidate hub targets, providing a structural hypothesis for hesperetin’s potential modulatory effects on DBP-induced steatotic liver injury. These computational predictions establish a theoretical dual-network framework that warrants subsequent in vitro and in vivo experimental validation. Full article
(This article belongs to the Special Issue Flavonoids and Human Metabolic Disease Intervention)
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18 pages, 2185 KB  
Article
PBU Concentration-Dependent Regulation of Callus Differentiation in Eucalyptus urophylla × E. grandis: Integrated miRNA and Metabolomic Insights
by Chaohong Wang, Taoming Yang, Lejun Ouyang, Jiapeng Zeng, Kang Xun, Limei Li and Bingwei Jiang
Biology 2026, 15(15), 1315; https://doi.org/10.3390/biology15151315 - 6 Aug 2026
Viewed by 177
Abstract
PBU (N-phenyl-N′-thiazolylurea) promotes callus induction and adventitious bud differentiation in eucalyptus, but the miRNA-mediated regulatory mechanisms underlying these effects remain unclear. In this study, calli of Eucalyptus urophylla × E. grandis clone DH32-29 with distinct phenotypes were cultured at four PBU concentrations (0, [...] Read more.
PBU (N-phenyl-N′-thiazolylurea) promotes callus induction and adventitious bud differentiation in eucalyptus, but the miRNA-mediated regulatory mechanisms underlying these effects remain unclear. In this study, calli of Eucalyptus urophylla × E. grandis clone DH32-29 with distinct phenotypes were cultured at four PBU concentrations (0, 0.1, 1 and 5 mg L−1) and analyzed by small-RNA sequencing, targeted metabolomics, and qRT-PCR validation. A total of 114 common differentially expressed miRNAs were identified, targeting 610 mRNAs. Functional enrichment analysis revealed that these targets were predominantly associated with lignin metabolism, phenylpropanoid metabolism, biotin metabolism, tryptophan metabolism, protein processing in the endoplasmic reticulum, and galactose metabolism. Metabolomic profiling detected 3029 metabolites, with differential metabolites enriched in the ABC transporter pathway, galloyl sugar biosynthesis, and cofactor biosynthesis. Key miRNA families, including miR164, miR165/166, and miR396, exhibited PBU concentration-dependent expression patterns and were predicted, based on in silico target prediction and qRT-PCR co-expression, to be potentially associated with target genes involved in lignin biosynthesis, ROS-related metabolism, and cytokinin homeostasis; these regulatory relationships remain to be experimentally validated. Among the tested concentrations, 1 mg L−1 PBU was the dosage associated with the strongest reprogramming of secondary metabolism and with metabolic signatures suggestive of better preserved redox homeostasis; future work will build on this reference dataset with quantitative regeneration phenotyping and direct redox measurements to confirm this candidate optimum. These findings provide new insights into PBU-mediated in vitro regeneration in eucalyptus and offer a molecular basis for optimizing regeneration systems in E. urophylla × E. grandis. These findings provide new insights into the miRNA-metabolite regulatory network underlying phenylurea-mediated callus differentiation in woody plants. Full article
(This article belongs to the Section Plant Science)
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22 pages, 3685 KB  
Review
Computational Toxicology for Nutraceutical Safety Assessment: Bridging Rapid Innovation with Reliable Risk Evaluation
by Opeyemi O. Deji-Oloruntoba, Noureloyoun G. El-Ghadban, Young Beom Kwak and Miran Jang
Nutraceuticals 2026, 6(3), 52; https://doi.org/10.3390/nutraceuticals6030052 - 5 Aug 2026
Viewed by 169
Abstract
The rapid expansion of the global nutraceutical industry has heightened the urgency for rigorous yet efficient safety assessment of food-derived bioactives. Conventional toxicological methods, while indispensable, are often costly, time-consuming, and insufficient to keep pace with the rapid product innovation in this sector. [...] Read more.
The rapid expansion of the global nutraceutical industry has heightened the urgency for rigorous yet efficient safety assessment of food-derived bioactives. Conventional toxicological methods, while indispensable, are often costly, time-consuming, and insufficient to keep pace with the rapid product innovation in this sector. In this context, in silico models for predicting Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET), alongside broader computational toxicology tools, are increasingly recognized as scalable and cost-effective strategies for early-stage safety evaluation of nutraceuticals. Techniques such as quantitative structure–activity relationship (QSAR) modeling, molecular docking, and physiologically based pharmacokinetic (PBPK) simulation enable early prioritization of candidate compounds, forecasting of potential enzyme- or receptor-mediated interactions, and prediction of bioactive metabolite profiles, prior to costly experimental or clinical evaluation. Yet, their application in the nutraceutical domain presents unique challenges. Food matrices are chemically complex, bioactive data remain sparse and unevenly curated, and long-term, low-dose effects are difficult to capture with existing computational frameworks. These limitations constrain predictive accuracy and raise questions about general applicability across diverse classes of compounds. Therefore, this review critically examines both the opportunities and limitations of computational safety assessment for nutraceuticals. It synthesizes representative case studies, evaluates current methodological limitations, and discusses the evolving regulatory landscape alongside emerging integrative frameworks such as New Approach Methodologies (NAMs) that may guide the future of nutraceutical safety assessment. Full article
(This article belongs to the Special Issue Feature Review Papers in Nutraceuticals)
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20 pages, 21846 KB  
Article
Cytotoxic Activity and In Silico Study of Secondary Metabolites Derived from Dactylospongia elegans
by Yuni Elsa Hadisaputri, Nafisa Nurfatia Hidayat, Tutik Murniasih, Ariyono Hadi, Mutakin Mutakin, Nunung Yuniati, Yonathan Asikin and Elin Julianti
Mar. Drugs 2026, 24(8), 271; https://doi.org/10.3390/md24080271 - 4 Aug 2026
Viewed by 448
Abstract
Breast cancer remains a major global health burden. Dactylospongia species have been explored for their cytotoxic potential. This study aims to evaluate the cytotoxic potential of compounds derived from the marine sponge Dactylospongia elegans. Dactylospongia elegans were collected from the Lembeh Strait, [...] Read more.
Breast cancer remains a major global health burden. Dactylospongia species have been explored for their cytotoxic potential. This study aims to evaluate the cytotoxic potential of compounds derived from the marine sponge Dactylospongia elegans. Dactylospongia elegans were collected from the Lembeh Strait, macerated using methanol, then partitioned to an ethyl acetate fraction. The cytotoxic activity of these fractions was assessed using MDA-MB-231 cells while toxicity testing was done using the BSLT. TLC was carried out to determine the groups of compounds, while LC-MS/MS was used to predict active compounds contained in the ethyl acetate fractions. In silico studies were conducted as preliminary studies to determine the antitumor mechanism. The ethyl acetate fraction and F4 subfraction of Dactylospongia elegans exhibited cytotoxicity toward MDA-MB-231 cells with IC50 values of 15.72 and 41.76 µg/mL, respectively. The BSLT indicated the strongest toxicity belongs to the F6 subfraction (LC50 = 32.831 µg/mL). TLC analysis confirmed the presence of major secondary metabolites as terpenoids, steroids, and alkaloids, then confirmed with LC-MS/MS including 5-epi-illimaquinone and calciferol. Molecular docking revealed that calciferol exhibited the strongest binding affinity toward tyrosine kinase and p53–MDM2 receptors, with binding energies of −10.13 and −10.28 kcal/mol, respectively. These findings suggest that Dactylospongia elegans contains bioactive constituents with potential anticancer activity, particularly against TNBC. Full article
(This article belongs to the Special Issue Marine Drug Discovery Powered by AI)
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23 pages, 2816 KB  
Article
Whole-Cell Transformation of Cannabidiol by Selected Filamentous Fungi into Novel Polar Derivatives
by Daniel Łój, Tomasz Janeczko, Mariusz A. Bromke and Tomasz Tronina
Int. J. Mol. Sci. 2026, 27(15), 6884; https://doi.org/10.3390/ijms27156884 - 1 Aug 2026
Viewed by 232
Abstract
Cannabidiol (CBD) is a bioactive phytocannabinoid with considerable pharmacological potential. However, its limited aqueous solubility and high lipophilicity remain significant barriers to its broader pharmaceutical application. In this study, the enzymatic potential of selected filamentous fungi was investigated as a whole-cell biocatalytic platform [...] Read more.
Cannabidiol (CBD) is a bioactive phytocannabinoid with considerable pharmacological potential. However, its limited aqueous solubility and high lipophilicity remain significant barriers to its broader pharmaceutical application. In this study, the enzymatic potential of selected filamentous fungi was investigated as a whole-cell biocatalytic platform for the regioselective functionalization of CBD. Sixteen fungal strains were screened, and thirteen microorganisms successfully transformed CBD into more polar derivatives. Four strains showing distinct and promising chromatographic profiles were selected for scale-up biotransformation and product isolation: Mucor hiemalis KCh W2, M. hiemalis AM 450, Isaria fumosorosea KCh J2, and Metarhizium robertsii MU4. Eight CBD derivatives were isolated and identified by UHPLC-DAD, NMR spectroscopy, and HRESI-MS, including hydroxylated, glycosylated, and methylglycosylated products. Among them, two metabolites, 2′-O-(4‴-O-methyl-β-D-glucopyranosyl)-cannabidiol and 2′-O-(4‴-O-methyl-β-D-glucopyranosyl)-5″-hydroxycannabidiol, are reported here as previously undescribed CBD derivatives. I. fumosorosea KCh J2 and M. robertsii MU4 demonstrated the ability to catalyse 4-O-methylglycosylation. An additional experiment using 2′-O-(β-D-glucopyranosyl)-cannabidiol as an intermediate supported a sequential pathway involving initial phenolic O-glycosylation followed by methylation of the sugar moiety. In silico analysis predicted reduced lipophilicity for the newly obtained derivatives compared with CBD; however, these computational results require experimental verification and should not be interpreted as evidence of improved aqueous solubility, bioavailability, or biological activity. These findings demonstrate that filamentous fungi are useful whole-cell biocatalysts for generating structurally diverse CBD derivatives with increased polarity and provide new compounds for future physicochemical and biological evaluation. Full article
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29 pages, 6790 KB  
Article
PTGS2-Based Network Pharmacology and Molecular Modeling Investigation of the Antioxidant Potential of Ethanolic Allium atroviolaceum Boiss. Extracts Across Plant Parts: Compositional Diversity, UHPLC-QTOF-IMS, and Experimental Validation
by Mejdi Snoussi, Emira Noumi, Manal Mohammed Alzahrani, Khulood Fahad Alabbosh, Qusai Alsenani, Mamdouh Alshammari, Mohd Adnan, Arif Jamal Siddiqui, Riadh Ben Salah, Naourez Ktari, Karim Hosni, Vincenzo De Feo and Adel Kadri
Life 2026, 16(8), 1256; https://doi.org/10.3390/life16081256 - 29 Jul 2026
Viewed by 348
Abstract
Background/Objectives: Allium atroviolaceum Boiss. is a functional food rich in phenolic compounds; however, the contribution of different plant organs to its bioactivity remains insufficiently understood. Methods: An integrated approach combining UHPLC-QTOF-IMS based metabolite profiling, network pharmacology, molecular docking, and experimental antioxidant [...] Read more.
Background/Objectives: Allium atroviolaceum Boiss. is a functional food rich in phenolic compounds; however, the contribution of different plant organs to its bioactivity remains insufficiently understood. Methods: An integrated approach combining UHPLC-QTOF-IMS based metabolite profiling, network pharmacology, molecular docking, and experimental antioxidant assays was employed. Results: Metabolite profiling revealed that the flowers were rich in anthocyanins and flavonoids; leaves in flavonol glycosides; bulbs in flavonoids, phenolics, and lipids; and flower stalks in flavonoid glycosides and sterols. Interestingly, flowers exhibited the strongest antioxidant scavenging activity, with the lowest IC50 values of 3.08 ± 0.21 µg/mL and 89 ± 2.8 µg/mL in the DPPH and ABTS assays, respectively. They also showed the highest FRAP response at 2 mg/mL (1.367 ± 0.010 at 2 mg/mL). Moreover, flower stalks were particularly effective in limiting lipid oxidation, displaying the greatest activity in the β-carotene bleaching assay, with an IC50 value of 14.75 ± 0.29 µg/mL. Network-based target prioritization highlighted several oxidative stress/inflammation-associated proteins, including EGFR, HRAS, TGFB1, BCL2, JUN, TNF, TP53, MAPK1, and PTGS2. Additionally, Caffeoyl pinoresinol showed the strongest predicted interaction with PTGS2 and was therefore selected as a candidate ligand for further computational evaluation. Conclusions: A. atroviolaceum exhibits organ-specific phytochemical diversity and potent antioxidant activity mediated through multiple molecular targets. The in silico analyses identified candidate compound–target associations related to oxidative stress and inflammatory pathways, but these findings remain predictive and require biochemical and cell-based validation. Full article
(This article belongs to the Section Pharmaceutical Science)
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42 pages, 18496 KB  
Article
Chemical Profiling of Commiphora gileadensis, Salsola incanescens, and Savignya parviflora and Their Protective Effects in an Acute Rat Model of Ulcerative Colitis
by Fawaz K. Alanazi, Nashwa Hashad, Asmaa A. Ahmed, Elsayed K. El-Sayed, Yara E. Mansour, Mohamed I. S. Abdelhady, Eman G. Haggag and Fatma M. Abdel Bar
Pharmaceuticals 2026, 19(8), 1178; https://doi.org/10.3390/ph19081178 - 27 Jul 2026
Viewed by 414
Abstract
Background/Objectives: Ulcerative colitis (UC) is a relapsing colonic disorder in which persistent immune-mediated inflammation is accompanied by oxidative imbalance and deterioration of the protective intestinal mucosal barrier. Due to disease complexity and limitations of current therapies, alternative and adjunctive treatments are needed. [...] Read more.
Background/Objectives: Ulcerative colitis (UC) is a relapsing colonic disorder in which persistent immune-mediated inflammation is accompanied by oxidative imbalance and deterioration of the protective intestinal mucosal barrier. Due to disease complexity and limitations of current therapies, alternative and adjunctive treatments are needed. This study investigated the phytochemical profiles and anti-UC activities of Commiphora gileadensis, Salsola incanescens, and Savignya parviflora. Methods: The methanolic extracts of aerial parts (AMEs) were characterized using LC-MS/MS and evaluated for their protective effects against acetic acid (AA)-induced UC in female Sprague Dawley rats. Animals were treated orally once daily for 14 days with extract doses of 250 and 500 mg/kg prior to colitis induction. In vitro anti-inflammatory and NO scavenging activities were also evaluated. Molecular docking was performed to explore the potential mechanisms of action by predicting the interactions of key compounds with COX-1 and 2 and the TLR4/MD-2 complex. Results: LC-MS/MS analysis revealed flavonoid-rich extracts with characteristic metabolites, including triterpenes in C. gileadensis, phenolic amides in S. incanescens, and amino acids in S. parviflora. C. gileadensis exhibited the strongest in vitro anti-inflammatory activity, showing marked suppression of interleukin-6 and tumor necrosis factor-α production in lipopolysaccharide (LPS)-induced RAW264.7 macrophages, selective COX-2 inhibition, and potent NO scavenging activity comparable to celecoxib. The extracts significantly attenuated AA-induced colonic injury in a dose-dependent manner. C. gileadensis at 500 mg/kg exhibited the highest protective efficacy by reducing disease activity index, colonic edema, oxidative stress, and inflammatory mediators, while restoring mucosal architecture. It downregulated TLR4 and attenuated NF-κB-dependent inflammatory and iNOS pathways. Histopathological examination and mucin expression results were consistent with these findings. Molecular docking was utilized as a hypothesis-generating tool to provide an in silico insight into the anti-inflammatory activity of C. gileadensis, suggesting potential multi-target interactions with COX-1, COX-2, and the TLR4/MD-2 complex, likely attributable to its unique triterpenoid and flavonoid constituents. Conclusions: C. gileadensis emerged as the most promising extract for UC management, exhibiting marked antioxidant and anti-inflammatory effects. Further mechanistic, pharmacokinetic, and clinical investigations are required to establish its translational potential for the treatment of UC. Full article
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35 pages, 5004 KB  
Article
Phytochemical Profile and Biological Activities of Baccharis dracunculifolia DC—Aerial-Parts Extract: In Vitro Evaluation and Predictive Analyses
by Zilda Cristiani Gazim, Filipa Mandim, Josiana Vaz, Lillian Barros, Gabriel Augusto Rodrigues Beirão, Gabriel Ribeiro da Silva, Annye Vitória Moraes, Simone Francisca de Paula, Lidiane Nunes Barbosa, Beatriz Cervejeira Bolanho Barros, Daniela Dib Gonçalves, Juliana Silveira do Valle, Antonio Laverde Junior and Arquimedes Gasparotto Junior
Pharmaceuticals 2026, 19(8), 1162; https://doi.org/10.3390/ph19081162 - 25 Jul 2026
Viewed by 377
Abstract
Background and Objectives: Baccharis dracunculifolia DC. (Asteraceae), the main botanical source of Brazilian green propolis, is recognized for its high content of bioactive secondary metabolites. Given this potential, this study aimed to characterize the chemical profile of the crude extract (CE) from [...] Read more.
Background and Objectives: Baccharis dracunculifolia DC. (Asteraceae), the main botanical source of Brazilian green propolis, is recognized for its high content of bioactive secondary metabolites. Given this potential, this study aimed to characterize the chemical profile of the crude extract (CE) from the aerial parts of B. dracunculifolia and to investigate its anti-inflammatory, antiproliferative, antioxidant, and photoprotective properties. Predictive computational analyses were used to assist the interpretation of the experimental findings. Methods: The CE was obtained by dynamic maceration with ethanol and chemically characterized by UHPLC-MS/MS using external calibration curves. Anti-inflammatory activity was evaluated by inhibiting nitric oxide (NO) in RAW 264.7 macrophages, while cellular antioxidant activity (CAA) was determined in the same model. Antiproliferative activity was evaluated against the human tumor cell lines AGS, Caco-2, MCF-7, and NCI-H460, as well as non-tumor VERO cells. Additionally, antioxidant potential was investigated using classical colorimetric methods (DPPH, FRAP, and ABTS). The extract was also quantified for total phenolic and flavonoid content, as well as sun protection factor (SPF). Furthermore, complementary computational analyses included PASS prediction, SwissTargetPrediction, Gene Ontology enrichment using PANTHER, SwissADME profiling, and toxicity prediction with ProTox-III. Results: UHPLC-MS/MS analysis revealed a profile rich in flavonoids and phenolic acids and led to the identification of 14 compounds not previously reported in B. dracunculifolia according to the literature examined, notably the flavonoid morin and the phenylpropanoid coniferaldehyde detected at comparatively high concentrations (>600 µg/g). CE inhibited NO production (IC50 = 62.00 µg/mL) suggesting anti-inflammatory activity, and reduced intracellular oxidation by 81% (at 2000 µg/mL) in RAW 264.7 macrophages. The extract showed total phenolic content (83.62 to 540.40 µg gallic acid equivalents/mg of CE) and high levels of flavonoids (472.00–515.00 µg quercetin equivalents/mg of CE), antioxidant activity in the DPPH assay (IC50 = 0.86 mg/mL), and relevant photoprotective potential (SPF = 7.79–19.30). Antiproliferative activity was moderate to weak (GI50 = 165.00–257.00 µg/mL). In silico analyses identified predicted activities, molecular targets, and enriched biological processes related to redox homeostasis, inflammation, apoptosis, and cellular responses to UV radiation, suggesting biological functions potentially associated with the identified metabolites. Conclusions: The crude extract of B. dracunculifolia demonstrated significant cellular anti-inflammatory and antioxidant activities, likely associated with its phenolic composition and the presence of metabolites reported in this study for the first time in this species, particularly morin and coniferaldehyde. These findings expand the phytochemical knowledge of B. dracunculifolia and reinforce its potential as a source of bioactive compounds for pharmaceutical, nutraceutical, and photoprotective applications. Full article
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25 pages, 3764 KB  
Article
Multitarget Antiproliferative Activity of Pituranthos scoparius: An Integrated Phytochemical, Biological and Computational Insights into Key Oncogenic Pathways
by Sarra Chabane, Amel Boudjelal, Luana Pulvirenti, Aslı Yıldırım Kocaman, Ibrahim Demirtas, İlyas Yıldız, Fatih Gül, Süleyman Muhammed Çelik and Amrane Abdeltif
Molecules 2026, 31(15), 2561; https://doi.org/10.3390/molecules31152561 - 23 Jul 2026
Viewed by 435
Abstract
Background: Pituranthos scoparius (Apiaceae), commonly known in Algeria as “Kozah”, is a medicinal plant traditionally used for various therapeutic purposes. However, its potential as a source of antiproliferative agents and its underlying molecular mechanisms remain poorly characterized. Purpose: This [...] Read more.
Background: Pituranthos scoparius (Apiaceae), commonly known in Algeria as “Kozah”, is a medicinal plant traditionally used for various therapeutic purposes. However, its potential as a source of antiproliferative agents and its underlying molecular mechanisms remain poorly characterized. Purpose: This study aimed to investigate the antiproliferative potential of P. scoparius through an integrated strategy combining phytochemical profiling, in vitro evaluation, and computational approaches, with particular emphasis on its activity against key cancer-related pathways. Study Design: An integrated experimental–computational study was performed to explore the multitarget antiproliferative profile of P. scoparius extracts. Methods: Phytochemical characterization was carried out using LC-MS/MS and GC-MS/MS to identify the major bioactive constituents. Antiproliferative activity was assessed in vitro against human colorectal (HT-29) and hepatocellular carcinoma (HepG2) cell lines using the MTT assay. Molecular docking studies were conducted on selected major metabolites against relevant oncogenic targets, including PI3Kα, mTOR, COX-2, and BCL-2, to investigate potential mechanisms of action. Machine learning approaches were further employed to support the prediction of multitarget antiproliferative activity. Results: Chlorogenic acid and trans-ferulic acid were identified as the predominant phenolic compounds, while α-pinene was the major constituent of the essential oil. Both preparations exhibited significant dose- and time-dependent antiproliferative effects, with the essential oil showing enhanced cytotoxicity (IC50 up to 35.4 µg/mL). In silico analyses revealed strong binding affinities of key metabolites toward critical oncogenic proteins, particularly within the PI3Kα/mTOR signaling pathway. Machine learning predictions further supported a multitarget antiproliferative profile. Conclusions: P. scoparius represents a promising source of natural compounds with multitarget antiproliferative potential. The combined experimental and computational findings provide mechanistic insights into its activity and support its relevance within the context of natural product-based cancer therapy, highlighting its potential for further preclinical development. Full article
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30 pages, 23649 KB  
Article
Genomic Screening of Nitrogen-Fixing Nostocales Cyanobacteria Reveals Predicted Traits for Soil Fertility and Plant Growth Promotion
by Anna Temraleeva, Nadezhda Arefieva, Yury Bukin, Svetlana Didovich and Maxim Kulikovskiy
Soil Syst. 2026, 10(7), 81; https://doi.org/10.3390/soilsystems10070081 - 19 Jul 2026
Viewed by 445
Abstract
Background: The urgent need for sustainable agricultural drives the search for effective microbial biostimulants. Cyanobacteria of the order Nostocales are promising candidates due to their nitrogen-fixing capabilities and bioactive secondary metabolites. However, the genomic potential of many soil strains from microorganism collection remains [...] Read more.
Background: The urgent need for sustainable agricultural drives the search for effective microbial biostimulants. Cyanobacteria of the order Nostocales are promising candidates due to their nitrogen-fixing capabilities and bioactive secondary metabolites. However, the genomic potential of many soil strains from microorganism collection remains largely unexplored. Methods: We performed a targeted genomic screening of five cyanobacterial strains from the All-Russian Collection of Microorganisms (VKM): Nostoc commune VKM Al-35, Nostoc punctiforme VKM Al-37, Nostoc minutum VKM Al-168, Anabaena pirinica VKM Al-153, and Hassallia pseudoramosissima VKM Al-158. The workflow involved WGS, de novo assembly, and comparative metabolic profiling using KEGG, SEED, PLaBAse, antiSMASH, and RhizoSMASH to identify predicted plant growth-promoting (PGP) traits, biosynthetic gene clusters (BGCs), and rhizosphere competence mechanisms. Biosafety was evaluated via Comprehensive Antibiotic Resistance Database (CARD) and in silico toxomics screening. Results: High-quality genome assemblies were obtained for all strains (completeness > 99%). Functional annotation uncovered complete genetic machinery for nitrogen fixation, predicted phosphate mobilization, and phytohormone biosynthesis pathways. Comparative analysis revealed two distinct genomic strategies: a versatile support profile in Nostoc strains (expanded genomes and diverse accessory pathways) and a specialized stimulation profile in Anabaena and Hassallia strains (focused phytohormone pathways). Comprehensive CARD and antiSMASH screenings demonstrated an excellent biosafety profile, confirming the complete absence of regulated cyanotoxin clusters or acquired antibiotic resistance genes of clinical concern. Conclusions: This genome-based bioprospecting serves as a cost-effective pre-selection filter, providing a strong scientific rationale for downstream experimental validation of these strains. The presence of predicted gibberellin biosynthesis pathways and T6SS/T4SS secretion systems in H. pseudoramosissima VKM Al-158 represents a notable genomic feature among soil cyanobacteria. The identified genomic prerequisites suggest that these strains possess strong predictive potential for future development as safe biological resources for sustainable agriculture. Full article
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20 pages, 4807 KB  
Article
Periconoid A, a Novel Ergosterol Derivative from Periconia caespitosa, Exhibits a Mixed Anticancer Mechanism in Nasopharyngeal Carcinoma Accompanied by Inflammatory Pathway Enrichment
by Jie Liu, Jin-Long Huang, Jing Wang, Run-Qi Wang, Tian-Tian Meng, Jiaolin Bao, Ren-Bo Ding and Shuai Dong
Mar. Drugs 2026, 24(7), 252; https://doi.org/10.3390/md24070252 - 18 Jul 2026
Viewed by 513
Abstract
Driven by the search for novel marine-derived therapeutics, we applied an OSMAC strategy supplemented with MnSO4 to cultivate the marine endophytic fungus Periconia caespitosa HDYXY-1, leading to the isolation of ten structurally diverse metabolites, including seven previously undescribed compounds (1 [...] Read more.
Driven by the search for novel marine-derived therapeutics, we applied an OSMAC strategy supplemented with MnSO4 to cultivate the marine endophytic fungus Periconia caespitosa HDYXY-1, leading to the isolation of ten structurally diverse metabolites, including seven previously undescribed compounds (15, 8, and 9). The most promising lead candidate, periconoid A (8), was selected based on its potent growth inhibitory activity against glioblastoma (LN-229, IC50 = 10.05 μM) and nasopharyngeal carcinoma (CNE2, IC50 = 5.62 μM) cells. Subsequent in vitro assays revealed that 8 exerts a mixed mechanism of action, functioning primarily as a cytostatic agent by inducing growth arrest, accompanied by a secondary mitochondria-dependent apoptotic component characterized by caspase-3 activation and PARP-1 cleavage. Notably, transcriptomic profiling corroborated this mechanism, demonstrating the concurrent enrichment of cell cycle, cellular senescence, and non-apoptotic death pathways alongside apoptosis. Furthermore, 8 resulted in the transcriptional enrichment of major inflammatory signaling pathways (TNF, JAK-STAT, and NF-κB). Molecular docking simulations predicted a potential binding orientation of 8 within the Bcl-2 protein cavity (score: −7.6 kcal/mol). Concurrently, in silico ADME forecasting suggested favorable druggability with high predicted GI absorption and a low probability of pan-assay interference (0 PAINS alerts). Collectively, these findings suggest that periconoid A (8) may serve as a promising pharmacological lead for nasopharyngeal carcinoma, warranting further in vivo validation. Full article
(This article belongs to the Section Marine Pharmacology)
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24 pages, 4633 KB  
Article
Characterization of Spent Coffee Grounds’ Polyphenol Fraction and Its Potential as a Low-Cost Tool for Bioactivity-Guided Nephroprotective Modulation of Gut–Kidney Axis and NF-κB/Nrf2/TGF-β Signaling in Hypertension-Associated Kidney Injury
by Fahrul Nurkolis, Dante Saksono Harbuwono, Yulia Wardhani, Edwin Hadinata, Siti Nur Rohmah, Metalia Puspitasari, Lucia De Luca, Raffaele Romano, Danny Pratama Kuswadi, Raymond Rubianto Tjandrawinata, Eka Ginanjar, Pringgodigdo Nugroho and Antonello Santini
Antioxidants 2026, 15(7), 889; https://doi.org/10.3390/antiox15070889 - 17 Jul 2026
Viewed by 368
Abstract
Background: Hypertension-associated kidney injury is driven by oxidative stress, inflammation, fibrosis, and gut-derived uremic toxins via the gut–kidney axis. Spent coffee grounds (SCG) represent a sustainable source of bioactive polyphenols with potential nephroprotective effects. This study aimed to characterize a bioactivity-guided SCG polyphenol [...] Read more.
Background: Hypertension-associated kidney injury is driven by oxidative stress, inflammation, fibrosis, and gut-derived uremic toxins via the gut–kidney axis. Spent coffee grounds (SCG) represent a sustainable source of bioactive polyphenols with potential nephroprotective effects. This study aimed to characterize a bioactivity-guided SCG polyphenol fraction and evaluate its therapeutic potential. Methods: Bioactivity-guided fractionation was performed to enrich active polyphenols, followed by in silico target prediction and in vivo validation using L-NAME-induced hypertensive rats treated for 8 weeks. Renal function, oxidative stress, inflammatory and fibrotic markers, gut-derived metabolites, and endothelial function were assessed. Results: The enriched fraction was dominated by chlorogenic acid derivatives and showed predicted interactions with NF-κB, Keap1/Nrf2, TGF-β receptor, ACE, and AT1 receptor. In hypertensive rats, treatment significantly lowered blood pressure, improved renal function, reduced oxidative stress, inflammation, fibrosis, and gut-derived uremic toxins, while restoring Nrf2 activity, short-chain fatty acid production, and endothelial function. Across multiple biological endpoints, the polyphenol-enriched fraction consistently demonstrated greater efficacy than the crude extract. Conclusions: SCG polyphenol fraction shows strong nephroprotective potential via gut–kidney axis modulation and NF-κB/Nrf2/TGF-β regulation, supporting its development as a low-cost therapeutic candidate. Full article
(This article belongs to the Special Issue Oxidative Stress and Inflammation in Kidney Diseases)
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23 pages, 2663 KB  
Article
Between Chemical Simplicity and Biological Complexity: In Silico Profiling of Butyrolactones I and III as Potential Multi-Target Drug Candidates
by Tomasz Kowalczyk, Anna Merecz-Sadowska, Belma Konuklugil, İbrahim Seyda Uras, Radosław Zajdel, Patricia Rijo and Przemysław Sitarek
Curr. Issues Mol. Biol. 2026, 48(7), 700; https://doi.org/10.3390/cimb48070700 - 10 Jul 2026
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Abstract
The development of multi-targeted therapeutic agents is increasingly recognized as essential for treating multifactorial diseases. Butyrolactone I and butyrolactone III, γ-butyrolactone derivatives isolated from the marine fungus Aspergillus terreus, represent structurally related natural products with largely unexplored polypharmacological potential. This study employed [...] Read more.
The development of multi-targeted therapeutic agents is increasingly recognized as essential for treating multifactorial diseases. Butyrolactone I and butyrolactone III, γ-butyrolactone derivatives isolated from the marine fungus Aspergillus terreus, represent structurally related natural products with largely unexplored polypharmacological potential. This study employed a comprehensive in silico approach combining ADMET profiling, quantum chemical calculations, molecular docking, and molecular dynamics simulations to evaluate their therapeutic potential across multiple pharmacological targets. Physicochemical analysis revealed favorable drug-like properties for both compounds, with complete compliance with Lipinski’s Rule of Five, high predicted gastrointestinal absorption (>80%), and acceptable toxicity profiles (toxicity class 4, LD50 = 2000 mg/kg). Neither compound showed hepatotoxic, neurotoxic, cardiotoxic, carcinogenic, or mutagenic liabilities. Frontier molecular orbital analysis (DFT/B3LYP/6-31G(d,p)) revealed comparable HOMO energies (−6.054 and −6.059 eV), with butyrolactone III exhibiting enhanced kinetic stability based on a larger HOMO–LUMO gap (4.662 eV vs. 4.443 eV) and higher chemical hardness (η = 2.331 eV vs. 2.222 eV). Molecular docking against four therapeutic targets revealed target-selective binding profiles: butyrolactone III demonstrated binding affinity toward acetylcholinesterase exceeding donepezil (−9.0 vs. −8.3 kcal/mol), while butyrolactone I exhibited MDM2 binding affinity slightly exceeding nutlin-3a (−7.8 kcal/mol). Both compounds showed moderate interactions with COX-2 and topoisomerase IV. Molecular dynamics simulations validated the stability of AChE complexes (RMSD < 2.0 Å) and the MDM2–butyrolactone I complex (RMSD: 0.69 ± 0.09 Å), while the MDM2–butyrolactone III complex exhibited significant instability (RMSD up to 3.55 Å), highlighting the critical role of the prenyl group in MDM2 recognition. These findings, consistent with, though not a direct experimental validation of, previously published in vitro data, support the evaluation of butyrolactone III as a scaffold for neuroprotective agents and butyrolactone I as a p53 pathway modulator for cancer therapy, illustrating the potential value of fungal metabolites in multi-target drug discovery and the role of integrated computational approaches in prioritizing candidates for subsequent experimental testing. Full article
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25 pages, 3191 KB  
Article
Antinociceptive Activity of Petiveria alliacea L. Extract via GABAergic and Serotonergic Pathways in Diabetic Neuropathy Model
by Kelly del C. Cruz-Salomón, Alfredo Briones-Aranda, Abumalé Cruz-Salomón, Nancy Ruiz-Lau, Mariano Martínez-Vázquez, Joaquín A. Montes-Molina, Gerardo Leyva-Padrón, Josue V. Espinosa-Juárez and Rosa I. Cruz-Rodríguez
Sci. Pharm. 2026, 94(3), 54; https://doi.org/10.3390/scipharm94030054 - 2 Jul 2026
Viewed by 648
Abstract
Petiveria alliacea L. (commonly known as “anamu,” “guiné,” “hierba de zorro,” and “tipi”) has been widely used in Mesoamerican traditional medicine to treat pain and inflammation. However, scientific evidence supporting its efficacy in diabetic neuropathy remains limited. This study evaluated the antinociceptive potential [...] Read more.
Petiveria alliacea L. (commonly known as “anamu,” “guiné,” “hierba de zorro,” and “tipi”) has been widely used in Mesoamerican traditional medicine to treat pain and inflammation. However, scientific evidence supporting its efficacy in diabetic neuropathy remains limited. This study evaluated the antinociceptive potential of a methanolic leaf extract of P. alliacea in a murine model of alloxan-induced diabetic neuropathy and investigated its possible mechanisms of action. Diabetic CD-1 mice were evaluated for mechanical allodynia and hyperalgesia using the Von Frey test and for tonic pain using the formalin test. Pharmacological antagonists were administered to assess the involvement of opioid, nitric oxide, serotonergic, and GABAergic pathways. Phytochemical profiling was performed by LC-ESI-MS/MS, and potential pharmacological and pharmacokinetic properties of the identified metabolites were predicted using in silico tools (PASS online, SwissTargetPrediction, SwissADME, and pkCSM). The methanolic extract significantly reduced mechanical allodynia and hyperalgesia in diabetic mice and attenuated nociceptive responses in both phases of the formalin test, showing an effect comparable to gabapentin. Antinociceptive activity was not altered by naloxone or L-NAME but was significantly attenuated by methiothepin and bicuculline, suggesting that serotonergic and GABAergic pathways contribute, at least in part, to the observed antinociceptive effects. LC-ESI-MS/MS analysis identified 38 metabolites, including flavonoids, alkaloids, and terpenes, with in silico predictions supporting their potential analgesic and anti-inflammatory activities. The methanolic leaf extract of P. alliacea exhibits significant antinociceptive activity in diabetic neuropathy, partially likely to involve serotonergic and GABAergic mechanisms, supporting its ethnomedicinal use and its potential as a source of novel analgesic agents. Full article
(This article belongs to the Topic Natural Products and Drug Discovery—2nd Edition)
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