Search Results (2,014)

Hydroquinine, a cinchona alkaloid, has demonstrated antibacterial activity against multidrug-resistant pathogens, with previous transcriptomic data implicating the arginine deiminase (ADI) pathway. However, its potential molecular target engagement remains to be fully characterized. This study aimed to investigate potential molecular targets of hydroquinine within the ADI pathway utilizing an Escherichia coli BL21 heterologous expression model. We integrated computational molecular docking as a hypothesis-generating tool, in silico-guided site-directed mutagenesis, and continuous broth microdilution growth kinetics profiling. Phenotypic profiling of the ADI-pathway transformants revealed that heterologous expression of the arginine/ornithine antiporter (AOA, encoded by arcD) was associated with growth tolerance under sub-inhibitory hydroquinine pressure. Serving strictly to nominate candidate binding residues, molecular docking predicted that the quinoline and quinuclidine moieties of hydroquinine may interact with residues Trp301 and Glu150 within the predicted AOA binding region. Consistent with these computational predictions, site-directed mutagenesis supported the contribution of these residues to the observed hydroquinine-associated phenotype. E. coli BL21 variants harboring the W301V and E150I arcD mutations lost the observed growth tolerance and exhibited significantly reduced maximum specific growth rates under sub-inhibitory hydroquinine stress. Furthermore, baseline growth defects in untreated mutants indicated potential fitness costs associated with these substitutions. In conclusion, this study provides preliminary insights into AOA as a potential target within a surrogate heterologous host, highlighting bacterial transport systems as candidate targets for future investigation of cinchona alkaloid-based antibacterial development. Full article

The Membrane-Associated Proteins in Eicosanoid and Glutathione metabolism (MAPEG) superfamily comprises integral membrane proteins involved in lipid metabolism, detoxification, and redox regulation. While extensively characterised in eukaryotes, bacterial MAPEG homologs remain poorly understood. In this study, we conducted an in silico analysis of bacterial MAPEG proteins and performed a comparative investigation with selected eukaryotic homologs to assess structural conservation and evolutionary relationships. Sequence alignment and phylogenetic reconstruction showed that the bacterial proteins have the typical MAPEG signature motifs, including residues associated with glutathione binding. Homology modelling and structural prediction analyses indicated conservation of the characteristic trimeric transmembrane architecture typical of the MAPEG family. Comparative structural analysis highlighted a preserved core fold across domains of life, accompanied by variations in loop regions and membrane-embedded segments that may reflect adaptation to distinct cellular environments. Molecular docking simulations suggested a conserved glutathione-binding pocket, although subtle differences in the surrounding residues may influence substrate specificity. Overall, our findings support an evolutionarily conserved structural framework within the MAPEG superfamily and provide insight into the diversification of bacterial members relative to their eukaryotic homologs. This study contributes to a deeper understanding of MAPEG protein evolution and lays the groundwork for future functional and biochemical investigations. Full article

Alkylsulfonic phenyl ester (ASE) is an alternate non-phthalate plasticizer used in PVC and polyurethane manufacture, such as for medical tubing and toys. Plastic-associated endocrine disrupting chemicals have been associated with increased cardiovascular disease risks and have been established as the agonists of a xenobiotic sensor, pregnane X receptor (PXR), which has atherogenic and dyslipidemic effects. However, it is unknown whether ASE activates PXR to adversely affect cardiovascular system. Our objective is to investigate how ASE impacts lipid profiles and cholesterol uptake via PXR signaling. Human hepatic and intestinal cells were used to test activation of PXR by ASE. The computational docking study and site-directed mutagenesis were used to identify key amino acid residues in PXR that interacted with ASE. The natural PXR inhibitor resveratrol was used to prohibit PXR activities. The male C57BL/6 wildtype mice were fed with ASE to evaluate if ASE could alter plasma lipid levels. Our data suggested that ASE was a specific PXR agonist and increased atherogenic cholesterol levels in mice mediated by PXR. Furthermore, ASE treatment increased cholesterol uptake by human intestinal cells through PXR signaling. Our study elucidates the role of PXR as a mediator of xenobiotic-elicited dyslipidemia and provides evidence for the future risk assessment of ASE on cardiovascular diseases. Full article

Ziziphus lotus (L.) Lam (wild jujube) leaves are traditionally used in Moroccan medicine to treat hypertension. The present study evaluated the aqueous extract of Z. lotus leaves (ZLAqExt) for its vasorelaxant effects, mechanisms of action, acute toxicity, antioxidant potential, and phytochemical profile. In phenylephrine-precontracted rat aortic rings, the ZLAqExt induced concentration-dependent relaxation (Emax = 79.25 ± 2.77% at 10⁻¹ mg/mL). The mechanism of action was investigated using specific antagonists and blockers. Complete inhibition by endothelium denudation, and preincubation with L-NAME, hydroxocobalamin, ODQ, and thapsigargin confirmed endothelium-dependent nitric oxide (NO)/cyclic GMP (cGMP)/sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA) pathway involvement. A partial inhibition by BaCl₂, indomethacin, calmidazolium, and KCl indicated cyclooxygenase (COX), endothelium-derived hyperpolarizing factor (EDHF), and inward-rectifier potassium (K_ir) channel contributions. Acute oral toxicity did not show any mortality at 2 g/kg BW in mice. The extract displayed potent antioxidant activity (DPPH IC₅₀: 18.12 ± 1.49 µg/mL; β-carotene bleaching IC₅₀: 8.3 ± 0.014 µg/mL). UHPLC-ESI-MS identified rutin as the major compound, followed by 3′,5′-di-C-β-glucopyranosyl phloretin with high docking affinity for guanylate cyclase and SERCA pump. The presence of flavonoids in the ZLAqExt might have mediated its vasorelaxant effects, supporting its traditional use as an antihypertensive. Our results highlight that Z. lotus is a potential natural therapeutic agent against vascular dysfunction-related cardiovascular disorders. Full article

Aflatoxin contamination remains a critical challenge for food and feed safety, necessitating effective mitigation strategies. This study addresses the challenge of aflatoxin contamination by identifying four novel bacterial candidates capable of degrading four major aflatoxin congeners (B1, B2, G1, and G2). Quantitative HPLC and qualitative LC-HRMS with MS/MS profiling revealed that the isolated bacterial strains achieved high degradation efficiencies of 86–94%, proceeding through distinct demethylation and decarboxylation pathways. Oxford Nanopore whole-genome sequencing identified these potent degraders as Escherichia coli EC_2 and Klebsiella pneumoniae (KP_4, KP_5, and KP_6). To elucidate the genomic basis of this phenotype, we performed a comparative genomic analysis against two non-degrading E. coli strains. Functional annotation revealed complete aromatic degradation modules and intact enzymatic cascades present only in the degrading strains, demonstrating that this biodegradation capability is highly strain specific. Furthermore, molecular docking of key putative enzymes unique to these active cascades demonstrated highly favorable binding affinities (up to −8.70 kcal/mol) with all four aflatoxin congeners, stabilized by robust hydrogen bonding and hydrophobic networks. These findings provide a novel genomic and structural blueprint for aflatoxin biotransformation, highlighting the specific putative candidate enzymes, paaH and mhpB, for future investigations. Full article

DCPMU, a major demethylated metabolite of diuron, is an environmentally persistent contaminant with potential endocrine-disrupting and carcinogenic relevance, yet its mechanistic association with prostate cancer remains unclear. This study investigated DCPMU-related mechanisms in prostate cancer by integrating network toxicology, molecular modeling, bulk transcriptomics, single-cell and spatial transcriptomics, and virtual perturbation analysis. Differentially expressed genes from TCGA-PRAD were intersected with DCPMU-associated and prostate cancer-related targets. Functional enrichment, machine learning screening, and external GEO validation identified seven candidate hub genes: APOBEC3G, SCGB1A1, PTGS1, CA12, CES1, FOLH1, and NOS1. Molecular docking showed favorable DCPMU binding to these proteins, and molecular dynamics simulations further supported stable interactions with PTGS1, CA12, CES1, and FOLH1. Single-cell analysis of GSE141445 revealed cell-type-specific expression, with FOLH1 and CA12 enriched in epithelial cells, CES1 in fibroblasts, and PTGS1 in mast cells. Spatial transcriptomics from GSE181294 showed tumor-enriched FOLH1 expression and increased Core4 module activity in malignant regions. Virtual knockout analysis suggested that FOLH1 perturbation was associated with predicted downstream transcriptional changes, with PTGS1 showing marked perturbation responsiveness. Overall, our integrative analyses suggest that DCPMU exposure is associated with epithelial malignancy, inflammatory metabolism, xenobiotic handling, and tumor-microenvironment remodeling, particularly within malignant epithelial niches. These hypothesis-generating findings require experimental validation to establish any causal role in prostate cancer progression. Full article

Molecular docking is among the most widely used techniques in structure-based drug discovery and has become integral to natural-product research. Despite substantial advances in computational algorithms and artificial intelligence, the methodological quality of published docking studies on natural compounds remains highly variable, and generally accepted methodological guidelines have yet to be established. This review critically evaluates current approaches to molecular docking of natural compounds, examines the specific features of different natural-product classes and protein targets, and offers practical recommendations for the design and validation of docking studies. The review covers the main stages of molecular docking, contemporary search algorithms and scoring functions, protein and ligand preparation, the fundamental limitations of the method, strategies for result validation, and the emerging role of artificial intelligence in computational molecular modeling. A central component is a systematic methodological audit of publications within a prespecified 2025 coverage window, identified by Scopus and PubMed searches executed in August 2026. The audit assessed methodological reporting completeness only and was not intended as a systematic review of biological or pharmacological findings. The audit comprised GPT-assisted structured coding of 1127 publications, detailed full-text assessment of a random sample of 80 studies drawn entirely from the same corpus, and independent human validation of 20 randomly selected Stage 2 publications. In the 80-publication full-text sample, redocking was reported in 7.5% of publications, a qualifying redocking RMSD below 2 Å in 6.2%, positive controls in 87.5%, molecular dynamics in 41.2%, MM/PBSA or MM/GBSA in 12.5%, interaction analysis in 98.8%, and ADMET assessment in 35.0%. Agreement between Stage 1 and Stage 2 was 98.3% across 525 paired criterion decisions. Independent human assessment of the 20-publication validation subsample agreed with Stage 2 in 135 of 140 criterion decisions (96.4%); the five discrepancies all involved AI-coded indeterminate/non-confirmed labels (Unconfirmed or N/A) that the human reviewer classified as No. On the basis of these findings, we propose a practical workflow aimed at improving the reproducibility and methodological rigor of molecular docking studies of natural compounds. A complementary targeted case-enriched validation of redocking and redocking-RMSD classification included 19 publications and two human reviewers. The reviewers reached identical classifications in all 38 criterion decisions; their consensus agreed with Stage 2 in 31 of 38 decisions (81.6%), with seven revisions across four publications. Because this sample was deliberately enriched for informative and ambiguous cases, it was used to examine classification boundaries rather than to estimate prevalence. Because PubMed retrieval was restricted to free full text and the Scopus search used restricted bibliographic fields, these reporting-completeness and validation frequencies primarily characterize an accessibility-enriched corpus and may not fully generalize to subscription-only or otherwise less-accessible journals. By combining a critical appraisal of current methods with a quantitative assessment of published studies and practical recommendations for standardizing the molecular docking of natural compounds, this review offers guidance for researchers in computer-aided drug design. Full article

Background: The rapid emergence of antibiotic resistance in E. coli has outpaced the development of new drugs, creating an urgent demand for novel therapeutic strategies. Methods: We screened ten antibiotics in combination with isochlorogenic acid C (ICAC) against multidrug-resistant (MDR) E. coli. Synergistic effects of antibiotics and ICAC were evaluated by measuring the leakage of alkaline phosphatase (AKP), potassium ions (K⁺), as well as changes in total protein, and ATP levels. The integrity of bacterial membrane and cell wall was visualized by SEM and CLSM. The underlying mechanisms were elucidated via proteomic analysis and molecular docking. Finally, the protective effect of ICAC in vivo was evaluated using an intraperitoneal infection model in SPF female BALB/c mice. Results: ICAC exerted a specific synergistic effect with ciprofloxacin, significantly enhancing its efficacy. The combination disrupted bacterial membrane and cell wall integrity, increased permeability, and inhibited ATP synthesis. Mechanistically, ICAC may target OmpF and inhibit fatty acid biosynthesis. This interference reduced β-oxidation and the influx of acetyl-CoA into the TCA cycle, thereby impairing bacterial energy metabolism and destabilizing the membrane. In vivo validation using a mouse peritonitis model confirmed that the combination treatment effectively alleviated systemic E. coli infection. Conclusion: ICAC may potentiate the antibacterial activity of ciprofloxacin through targeting of OmpF, which disrupts bacterial membrane integrity and energy metabolism, providing a promising candidate strategy for combating infections caused by the tested antibiotic-resistant E. coli. Full article

Mycoplasma synoviae (M. synoviae) is an avian pathogen responsible for respiratory disease and synovitis. The VlhA (variable lipoprotein hemagglutinin) family of surface adhesins plays a critical role in host cell attachment, yet the specific residues and structural determinants governing this interaction remain incompletely understood. In this study, we selected the C-terminal lipid-associated membrane hemagglutinin (LAM HA) domain within the VlhA family as the bait protein, based on its conserved C-terminal region. Yeast two-hybrid screening identified 18 LAM HA-interacting host proteins, and molecular docking pinpointed five residues (S83, R85, Y88, N124, K192) as the most frequent interaction hotspots. To assess their collective functional relevance, we constructed a combined deletion mutant lacking these five candidate residues. At the optimal pH of 6.0–6.5, wild-type LAM HA showed the highest titer (1:2), significantly exceeding that at pH 7.0–7.5 (no activity) and pH 5.0–5.5 (1:1) (p < 0.05), whereas the deletion mutant displayed a reduced titer (from 2 to 1; p = 0.05). Secondary structure analysis at the same pH revealed decreased α-helix content (from 7.90% to 7.57%), along with increased β-sheet (from 38.92% to 38.83%) and random coil (from 10.83% to 10.44%). Molecular dynamics simulations revealed that the deletion mutant exhibited elevated RMSF (from 2.83 ± 1.88 Å to 4.18 ± 2.65 Å) and Rg (from 40.48 ± 1.31 Å to 54.16 ± 4.47 Å) at pH 6.0–6.5, while RMSD showed a slight decrease (11.17 ± 1.33 Å vs. 12.14 ± 0.21 Å), collectively indicating compromised structural stability of the mutant. Collectively, these findings suggest that the LAM HA domain contributes to hemagglutination activity through pH-sensitive conformational stability and specific residue clusters—a property that may be relevant to M. synoviae colonization in the acidic microenvironments of the respiratory tract and synovial fluid during infection. Full article

Symphytum officinale L. is a traditional medicinal plant widely used for wound healing and bone regeneration; however, comparative studies evaluating the biological activities of extracts prepared from different plant organs remain limited. The present study compared the antimicrobial and anti-inflammatory activities of organ-specific S. officinale extracts and investigated their potential molecular mechanisms of bioactivities using molecular docking. Antimicrobial activity was evaluated against six bacterial reference strains by broth serial dilution, whereas anti-inflammatory activity was assessed in a serotonin-induced paw oedema model in rats together with the determination of serum prostaglandin E₂ (PGE₂), tumour necrosis factor-α (TNF-α), and nitrotyrosine levels. Molecular docking was performed against bacterial peptide deformylases, cyclooxygenase-2 (COX-2), and 5-lipoxygenase (5-LOX). The 40% ethanolic leaf extract (S-7) and 70% ethanolic flower extract (S-13) exhibited the broadest antimicrobial spectrum, with pronounced activity against S. aureus, E. faecalis, E. coli, and L. monocytogenes. The 70% ethanolic leaf extract (S-8) demonstrated the strongest early anti-exudative activity (47.50%), whereas the 70% ethanolic flower extract (S-13) most effectively reduced PGE₂, TNF-α, and nitrotyrosine levels. Molecular docking suggested that kaempferol-3-O-glucoside may be the principal contributor to antimicrobial activity through interactions with bacterial peptide deformylases, while hyperoside, isoquercitrin, and rosmarinic acid exhibited favourable interactions with COX-2 and 5-LOX, indicating their key role in exerting anti-inflammatory effects. These findings demonstrate pronounced organ-specific pharmacological differences among S. officinale extracts and identify hydroethanolic leaf, flower, and root extracts as promising candidates for further development as multitarget wound-healing phytopharmaceuticals. Full article

Imidazoles have been proven to be very effective pesticides, especially against phytopathogenic fungi and insects. Due to their negative effects on the environment, only a few imidazoles have been approved for use by the European Commission (EC). There is an urgent need to develop new imidazole derivatives with high efficiency and a wide spectrum of action against numerous pests that are, at the same time, safe for the environment and beneficial for organisms and humans. In order to reduce expensive and time-consuming experiments, an in silico approach based on quantitative structure–activity relationship (QSAR) models is valuable for predicting the toxicity of new or untested chemicals. In this study, we used the Vega and ChemFREE web platforms to evaluate the pesticide similarity, environmental risk properties, and ecotoxicological effects of imidazole derivatives designed for potential synthesis. Adamantane-, alkyl-, and triazole-amide, ester, carbamate, and ketone derivatives were filtered for the evaluated properties, and four alkyl-amides were highlighted as potentially effective and environmentally safe antifungal, herbicidal, and insecticidal agents. Molecular docking studies indicated the possible mechanism of action of the antifungal, herbicidal, insecticidal, and antibacterial activities of the observed compounds and revealed structural features important for binding to specific receptors. Full article

The quinazoline/quinazolinone ring is known as a unique scaffold, and its derivatives possess a broad biological activity profile, including antibacterial, antifungal, anticonvulsant, anti-inflammatory, anti-HIV, and analgesic activity, primarily focusing on anticancer activity. In this study, the synthesis of 2-[[4-oxo-3-(substituted phenyl)-3,4-dihydro-(substituted quinazolin-2-yl)]thio]-N′-(aryl/heteroaryl methylene)acetohydrazide (4a–4x) derivatives and their potential anticancer activities were investigated on the lung cancer A549 cell line, the breast cancer MCF-7 cell line, and healthy fibroblast L929 cell line. Compounds 4c, 4i, 4m, and 4u were identified as the most cytotoxic and selective molecules on the A549 cell line (IC₅₀: 44.75–78.13 µM), while 4i, 4l, 4m, and 4u were identified as the most cytotoxic and selective molecules on the MCF-7 cell line (IC₅₀: 14.43–29.39 µM). The mechanisms of action of their anticancer activities were examined and studied. It was determined that these compounds induced strong apoptosis and significantly activated caspase-3 activation in both cell types and that they interrupted the cell cycle in the pre-G (sub G0) phase. Compounds 4m and 4u exhibited EGFR inhibition (IC₅₀: 4.80 µM, IC₅₀: 5.40 µM, respectively) at a level similar to the standard drug gefitinib (IC₅₀: 1.86 ± 0.43 µM). Based on the results of the biological activity assays, molecular docking, and molecular dynamics simulation studies, the 4-quinazolinone–acetyl hydrazone scaffold can be considered a promising structural framework with potential anticancer activity. More specifically, the findings of this study indicate that the acetyl moiety may function as an important pharmacophoric group, while the trisubstituted quinazolinone core may represent a favorable structural feature for caspase-3 activation. However, the same structural framework appears to be less favorable for EGFR inhibition, possibly due to steric constraints within the EGFR binding pockets. Full article

Plant metabolites are a promising source of new biopesticides, but their chemical diversity exceeds the capacity of experimental screening. Cannabis sativa is a particularly attractive crop for discovering such compounds, although its metabolome has not been systematically evaluated for biopesticidal potential. Here, we computationally analyzed 5211 compounds annotated as C. sativa metabolites in the Cannabis Compound Database (CCD) using an integrated framework combining graph-based molecular prediction and protein–ligand interaction analysis. Initial prioritization employed a directed message passing neural network (DMPNN) trained on molecular graphs augmented with RDKit descriptors. The DMPNN predictions were integrated with a CatBoost-derived docking-consistency score based on residue-level Vina interaction terms, reducing the false-positive rate by about 60% compared with the structural model alone. Informative ligand-residue interactions were identified using a random matrix theory (RMT) framework. The DMPNN identified 1010 compounds as DMPNN-positive (score $\ge 0.70$), indicating structural characteristics more consistent with the DS2 pesticide reference set than with the DS3 AChE-inactive reference set. Then, these compounds were filtered using annotations from the CCD to retain 44 secondary metabolites. Finally, the 44 compounds were ranked by the final ensemble score. Compared with reference pesticides, C. sativa metabolites showed higher predicted median oral LD₅₀ values and fewer organ-specific toxicity alerts at the dataset level, although not for all endpoints. Overall, the combined structural and docking-informed workflow identified a small, chemically diverse set of high-ranking C. sativa compounds that can now be prioritized for experimental validation. Full article

This study investigated the adaptive mechanisms of Shigella sonnei ATCC25931 in response to gamma irradiation stress (0.5 and 1 kGy), with a specific focus on the involvement of fatty acids (FAs) in membrane lipid composition remodeling, adherence, and extracellular proteins. The results demonstrated a notable enhancement in cell hydrophobicity and adherence to KB cells following irradiation, although the invasion rate exhibited a decline from 14% to 2.35% at 1 kGy. Furthermore, gamma irradiation induced notable alterations in fatty acid (FA) composition, characterized by a pronounced reduction in the unsaturated/saturated FA ratio. Additionally, the plasmid profiles revealed the loss of several original plasmids after gamma irradiation. The alterations in extracellular proteins were observed through SDS-PAGE, which demonstrated a reduction in expression at 1 kGy. Furthermore, a molecular docking analysis indicated that fatty acids play a role in inhibiting VirF, a key regulator of Shigella virulence. The least effective inhibitor was capric acid, while linoleic and gamma-linolenic acids formed the most stable inhibitory complexes, which prevented VirF from activating the virulence system. These alterations in fatty acids, plasmids, and extracellular proteins constitute adaptive responses to irradiation-induced stress. Full article

Catechol 2,3-dioxygenase (C23O) is the rate-limiting enzyme in the meta-cleavage pathway of aromatic compound degradation, yet its functional annotation within the structurally conserved VOC superfamily remains challenging due to high sequence homology. Here, we isolated a catechol-degrading strain from bovine feces and identified it as Bacillus thuringiensis HHY919 via whole-genome sequencing. Genome annotation revealed four VOC genes sharing the same COG annotation (“catechol 2,3-dioxygenase”) but divergent KO annotations (two as glyoxalases and two as C23O), suggesting functional divergence. Using homology modeling and molecular docking, we compared their binding affinities toward catechol and 11 derivatives. All four proteins showed typical meta-cleavage binding energies (−4.9 to −5.4 kcal/mol), with slightly more favorable binding than an ortho-cleavage control. Notably, gene4224 exhibited the broadest and strongest predicted affinities in virtual screening against 212 compounds, particularly for trichlorophenol (−6.0 kcal/mol) and complex natural products (qvina_score ≤ −7.6 kcal/mol). Phylogenetic analysis and docking results jointly identified gene3355 and gene4224 as computationally prioritized C23O candidates, with gene4224 recommended as the top candidate for future enzyme engineering and bioremediation studies. This study provides a computational workflow for resolving functional ambiguity in VOC family enzymes and generating testable hypotheses for experimental validation. Full article