Search Results (3,042)

Bacopa monnieri (L.) Wettst. (Family: Scrophulariaceae) is a well-known edible plant used in ethnic and Ayurveda medicine for centuries to improve memory deficit, enhance cognitive function, and treat nervous system disorders. Despite accumulating in vivo evidence for its cognitive benefits, the detailed mechanisms by which its bioactive compounds act on primary neurons remain elusive. In the present study, we dissect the mechanism by which Bacopa monnieri promotes neuronal development by treating primary hippocampal neuronal cultures with its ethanolic extract (BMEE) and integrating insights from in silico network pharmacology. We identified that BMEE at different concentrations promotes neuritogenesis and has a remarkable impact on early neuronal maturation, and axonal and dendritic outgrowth. Also, BMEE regulated synaptic plasticity by increasing the expression of NMDA receptors. Metabolites of BMEE were identified by gas chromatography–mass spectrometry (GC-MS) analysis, from which a network pharmacology model was constructed, in which BMEE metabolites were projected to regulate the neurotrophin signaling pathway. Indeed, the BMEE-mediated neuritogenic effect was abolished by the presence of a TrkA receptor-specific inhibitor, suggesting that the neuritogenic effect of BMEE is TrkA-dependent. Also, molecular docking following MD simulations supported the idea that BMEE metabolites, particularly δ-Tocopherol and O-methyl-, bind with high affinity to the TrkA receptor (NGF-binding domain). This study collectively illuminates the TrkA-mediated pathway through which Bacopa monnieri promotes neuronal development and suggests that bioactive metabolites from BMEE might hold potential as a source for designing therapeutic agents for various cognitive disorders. Full article

Background: Oral squamous cell carcinoma (OSCC) is an aggressive cancer closely associated with smoking and alcohol consumption, with a higher incidence in men. Despite changes in treatment strategies, poor survival persists in most patients, highlighting the need for novel and improved therapeutic options. Naphthoquinone analogs are being investigated because of their active redox structure and broad pharmacological profile; they demonstrate cytotoxic antitumor activity, making them potential candidates for new drug agents. Objective: This study investigated new benzyl-naphthoquinone compounds as potential anticancer agents for various genotypes of oral squamous cell carcinoma (OSCC) and other cancer cells. Methods: This study reports the synthesis and evaluation of a series of eight benzyl-naphthoquinone compounds against oral squamous cell carcinoma. Results: Four compounds 1–4 showed the best cytotoxic profiles, with a selectivity index ≥ 3 for all OSCC cell lines tested. Compound 1 was the most selective compound in all OSCC models, showing a higher selectivity index than both carboplatin and shikonin. Furthermore, compound 1 induced DNA fragmentation, cell-cycle arrest, and caspase-3/7 activation, changes consistent with apoptosis, and time-lapse imaging corroborated the apoptotic phenotype. Hemolysis assays showed minimal toxicity in human erythrocytes, and acute in vivo evaluation in mice revealed no evident adverse effects under the conditions tested, indicating low acute toxicity, although more detailed histopathological and biochemical studies will be required to fully establish the safety profile. Molecular modeling suggested that compound 1 may interact with topoisomerase II, RSK2, and PKM2, which could contribute to the activation of apoptotic pathways, although these interactions remain predictive and require biochemical validation. Finally, in silico analysis of physicochemical and ADMET parameters indicated properties compatible with oral absorption and systemic exposure, together with predicted low toxicity; however, these results are model-based and should be confirmed experimentally. Conclusions: Based on these findings, compound 1 emerges as a promising lead candidate for the development of a novel chemotherapeutic agent against OSCC, with potential therapeutic efficacy against other cancer types. Full article

In response to recent advances in computer-aided drug discovery (CADD) enabled by high-performance computing, computational approaches were employed to support and rationalize the investigation of a VEGFR-2-targeted anticancer candidate, combining molecular-level modeling with experimental validation. Initial in silico ADMET profiling and molecular docking were conducted to support the evaluation of drug-like properties and target engagement within a series of para-toluidine-based derivatives (1–14). The most biologically active compound was further evaluated through 100 ns molecular dynamics simulations and comprehensive DFT calculations to investigate binding stability and electronic characteristics. Based on a rational design strategy and supported by computational analyses, the compounds were synthesized and fully characterized using IR, MS, ¹H/¹³C NMR, and elemental analysis. Biological evaluation was performed against HepG-2, MCF-7, HCT-116, and normal WI-38 cells. Mechanistic studies included VEGFR-2 inhibition, wound-healing migration assays, cell-cycle distribution analysis, apoptosis assessment, and caspase-3 activation. Several derivatives exhibited micromolar cytotoxic activity, with compound 14 emerging as the most active against HepG-2 cells (IC₅₀ = 7.84 ± 0.5 µM), showing cytotoxic activity comparable to that of sorafenib (IC₅₀ = 9.18 ± 0.6 µM) and demonstrating favorable selectivity toward normal WI-38 cells (IC₅₀ = 67.75 ± 3.6 µM). Compound 14 showed moderate VEGFR-2 inhibitory activity (IC₅₀ = 0.55 µM), significant suppression of cell migration, pronounced G₀/G₁ cell-cycle arrest, and robust apoptosis induction supported by caspase-3 activation. Molecular docking and MD simulations supported a stable binding mode within the VEGFR-2 active site. This integrated framework highlights compound 14 as a selectively active VEGFR-2-oriented anticancer candidate scaffold with a favorable selectivity profile, supported by experimental and computational analyses, warranting further lead optimization. Full article

Background/Objectives: Hand, foot, and mouth disease (HFMD) is a major public health concern primarily caused by human enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16), coxsackievirus A6 (CVA6), and certain coxsackievirus B serotypes. Currently available EV-A71 vaccines lack cross-protective efficacy against other serotypes, highlighting the urgent need for multivalent and broadly effective enterovirus vaccines. Methods: Immunoinformatics approaches were used to predict highly immunogenic B-cell and T-cell epitopes, which were assembled to construct a novel multivalent epitope vaccine, rCV-A3V, followed by in silico validation. Recombinant protein expression was confirmed by Western blotting and immunofluorescence assays. The immunogenicity was evaluated in Balb/c mice following intranasal immunization. Results: A preliminary safety evaluation demonstrated that the rCV-A3V vaccine was well tolerated in the mouse model, with no abnormal changes in body weight observed after immunization. In addition, the target protein was successfully expressed. Intranasal immunization induced a strong Th1-biased immune response, robust serum neutralizing and IgG antibody responses, and pronounced mucosal immunity, including elevated sIgA and IgG levels in nasal lavage fluid, sIgA in feces, and substantial sIgA responses in milk. Dominant epitope peptides were also identified. Conclusions: The intranasal live attenuated rCV-A3V vaccine successfully induced humoral, mucosal, and cellular immune responses against EV-A71, CVA16, CVA6, and CVB3, demonstrating broad immunogenicity. These findings provide experimental evidence supporting its potential as a candidate vaccine for HFMD. Full article

Background/Objectives: Severe and recurrent infections due to multidrug-resistant (MDR) Pseudomonas aeruginosa necessitate alternative antimicrobial strategies. Fermented cacao beans represent a niche microbial ecosystem with the potential to harbor beneficial lactic acid bacteria (LAB). This study aimed to isolate and characterize LAB strains from fermented cacao beans in southern Thailand and to evaluate their probiotic potential and antimicrobial activity against MDR P. aeruginosa. Methods and Results: Five Lactiplantibacillus plantarum isolates were identified via MALDI-TOF MS and whole-genome sequencing (WGS). All strains demonstrated antimicrobial activity against 17 clinical MDR P. aeruginosa isolates and CR14 exhibited the largest inhibition zone. The isolates displayed robust probiotic traits, including survival under simulated gastrointestinal conditions. Acid tolerance (pH 2.0) reached 61.15 ± 7.75%, while resistance to pepsin, pancreatin, and bile salts exceeded 88%, 91%, and 92%, respectively. Strong adhesion was confirmed via auto-aggregation (55.02 ± 1.75%), hydrophobicity (45.58 ± 0.96%) and Caco-2 cell attachment (up to 98.11 ± 3.28%). WGS revealed multiple plantaricin-encoding clusters. Coarse-grained molecular dynamic simulations showed that two-peptide plantaricins (plnJ/K and plnNC8-αβ) self-assembled and formed stable pores in bacterial membrane models, confirming a pore-forming antimicrobial mechanism. The strains lacked acquired resistance genes and virulence factors, confirmed by in silico safety assessments. Conclusions: Thus, these L. plantarum strains are promising probiotics for managing MDR P. aeruginosa via functional foods or adjunct therapies. Full article

Background: Tumor cells can reprogram their metabolism, constituting a hallmark of cancer that plays a crucial role in tumor progression. As tumor cells exhibit an increased demand for nutrients, e.g., amino acids, they rely on extracellular sources and show deregulation of transport proteins. Among these, SNAT1 (SLC38A1) is described as the loader for glutamine that is responsible for the main influx of this amino acid. The aim of this study was to assess the molecular function of SNAT1 in melanoma regarding its role in amino acid transport and regulation of cellular metabolism. Methods: siPool-mediated downregulation of SNAT1 expression in melanoma cell lines was used to investigate the molecular function of this protein. Glutamine transport was assessed by measuring the intracellular and extracellular concentrations of glutamine. Regulation of downstream effectors was evaluated with qRT-PCR and Western Blot. Metabolism was investigated by performing Seahorse flux analysis. Mitochondrial staining was examined via flow cytometry. Protein interaction was assessed with Co-IP, and in silico modeling of protein interaction was performed with AlphaFold3. Results: In this study, we uncovered the new finding that SNAT1 is not primarily implicated in glutamine influx into melanoma cells but in signaling in response to extracellular glutamine. We identified P62 and cMYC as downstream effectors of SNAT1. By activating the P62/cMYC-axis and target genes of cMYC, SNAT1 modulates the metabolism of melanoma cells depending on the glutamine level. SNAT1 and P62 are interaction partners. Conclusions: This finding newly suggests that SNAT1 may function as a sensor or receptor (“transceptor”) for glutamine rather than being a direct and primary glutamine transporter, and could open up new therapeutic options targeting melanoma cells. Full article

Complexes of colchicine, colchiceine, and 10-methylthiocolchicine with Li⁺, Na⁺, and K⁺ cations in the form of chlorides were synthesized and then subjected to spectral analysis, DFT theoretical studies, and molecular modeling. The values for water solubility and lipophilicity were also determined using various platforms; both factors are very important for determining the bioavailability of the tested compounds. These compounds were also tested for their fungicidal, herbicidal, insecticidal, and cytotoxic activities. Preliminary in silico studies showed that colchicine, colchiceine, 10-methylthio-colchicine, and their chloride complexes are inactive against selected fungi, weeds, and insects. Colchicine did not show antifungal properties in biological tests and was only active against Aureobasidium pullulans, as were its chloride complexes. The process of complexing colchiceine with metal cations in chloride salts significantly improved the antifungal potency against the selected species A. pullulans and Chaetomium globosum. The highest efficacy of colchiceine complexes was observed only against A. pullulans (MIC = 130 µg/mL) and Ch. globosum (MIC = 65 μg/mL). In contrast to the antifungal activity results, anticancer studies showed that 10-methylthiocolchicine complexes are more active against the SKOV-3 cell line (~IC50 = 2 nM) than colchicine or colchiceine. Molecular-modeling studies confirmed that lithium-coordinated compounds strongly stabilized the active ligand-tubulin complex, which may contribute to the observed cytotoxic activity. Full article

Structure-based strategies are widely used in tuberculosis drug discovery; however, their translational impact remains limited. This review examines how structure-based virtual screening (SBVS) is applied in practice to Mycobacterium tuberculosis targets and explores why docking-derived predictions frequently fail to translate into measurable biological activity. Rather than treating docking scores as quantitative predictors of potency, representative case studies are analyzed to demonstrate that SBVS is most effective when employed as a prioritization framework integrated with appropriate target preparation, physicochemical filtering, and early experimental validation. Across diverse targets, molecular dynamics simulations emerge as a critical discriminator, enabling the identification of binding instability and false-positive hits that persist after static docking. Tuberculosis-specific constraints—including cofactor-dependent catalysis, resistance-associated mutations, membrane-rich environments, and permeability barriers—are discussed as key factors decoupling in silico affinity from whole-cell efficacy. Collectively, these observations support a workflow-oriented view of computational drug discovery in tuberculosis, in which iterative integration of structural modeling and experimental validation is required for meaningful lead identification. Full article

Plant growth regulation is orchestrated by complex hormonal networks involving gibberellin and auxin signaling pathways. In this study, a comprehensive in silico approach was employed to comparatively evaluate the plant growth regulators (PGRs) forchlorfenuron (CPPU) and strigol (STG) against two key proteins from Arabidopsis thaliana: Gibberellin 3-beta-dioxygenase 2 (GA3Ox2), a rate-limiting enzyme in the biosynthesis of bioactive gibberellins, and the auxin signaling repressor IAA7. These targets were specifically selected because they represent critical regulatory nodes in two major hormonal pathways controlling plant growth: GA3Ox2 governs the final steps of gibberellin activation, while IAA7 modulates auxin-responsive gene expression through its interaction with Auxin Response Factors. Therefore, their combined analysis enables the evaluation of potential regulatory effects of PGRs on both gibberellin biosynthesis and auxin-mediated transcriptional control. Molecular docking analyses revealed that both ligands exhibited higher binding affinity toward GA3Ox2 than IAA7, with STG showing slightly more favorable binding energies (−7.91 kcal/mol for GA3Ox2 and −5.43 kcal/mol for IAA7) compared to CPPU (−7.18 and −4.79 kcal/mol, respectively). These results suggest a structural preference of both PGRs toward the gibberellin biosynthetic pathway. To further assess complex stability under near-physiological conditions, 100 ns molecular dynamics (MD) simulations were conducted using the CHARMM36m force field. Despite its slightly lower docking scores, CPPU demonstrated greater conformational stability, lower RMSD fluctuations, and more persistent hydrogen bonding patterns, particularly in complexes with IAA7. In contrast, STG induced more pronounced conformational rearrangements, although it promoted slightly more compact protein conformations in certain systems. Fourier-transform infrared (FTIR) spectroscopy supported the computational findings by confirming the presence of key functional groups responsible for hydrogen bonding and hydrophobic interactions. Collectively, the results indicate that although STG exhibits higher initial binding affinity, CPPU forms more dynamically stable complexes with both proteins. These findings suggest that CPPU may represent a more robust candidate for sustained modulation of auxin and gibberellin signaling pathways in plant growth regulation. Full article

Background: Point mutations to the androgen receptor (AR) ligand-binding domain (LBD) are becoming increasingly recognized as a mechanism of therapeutic resistance in castration resistant prostate cancer (CRPC). The present review explores how point mutations induce molecular changes that contribute to the eventual treatment failure of androgen receptor pathway inhibitors (ARPIs) in CRPC. Methods: The PubMed database was searched for structural studies on the AR LBD. Eligible articles included molecular docking analysis and emphasized changes in ligand–receptor interactions after point mutation. Structural data were obtained from the Protein Data Bank (PDB) using the search parameters “Androgen receptor ligand binding domain”, “Homo sapiens”, and “X-ray diffraction”. PDB files of wild-type and point mutant AR LBDs were accumulated for analysis. Results: A functional shift from inhibiting to activating AR has been documented for multiple ARPIs. Crystallography data and in silico evaluation have deciphered how changes in steric hindrance of the AF-2 domain contribute to ARPI loss of function. To combat therapeutic resistance, discovery efforts have begun to consider combination approaches of orthosteric and allosteric inhibitors, as well as compounds that target other AR domains. Although lead compounds have been identified, none have progressed into the clinic. Conclusions: Questions remain regarding the best approach for rationally designing new AR targeting therapeutics. Understanding how structural changes to the AR LBD lead to the failure of clinical therapeutics is a necessary step that should precede drug discovery campaigns. Moreover, computational modeling is a powerful tool that should be leveraged to streamline therapeutic development. Full article

Background: Forensic DNA phenotyping (FDP) enables the inference of externally visible characteristics (EVCs) and biogeographic ancestry when conventional STR profiling is inconclusive. The ForenSeq™ Imagen kit (107 SNPs) integrates phenotype-, ancestry-, and Y-SNPs markers; however, its performance under partial genotyping conditions has not been systematically evaluated. Methods: Ninety-four samples from a Mexican mestizo population were analyzed using the ForenSeq™ Imagen kit on the MiSeq FGx™ platform. Due to incomplete genotype recovery, 41 samples with >60% locus detection were selected for downstream analyses. Phenotype prediction was performed using the HIrisPlex-S model, and ancestry inference was assessed through principal component analysis. In silico simulations were conducted to evaluate locus-specific dropout effects. Results: Eye color prediction showed both reduced feasibility (68.3%) and lower overall accuracy (56.1%), primarily driven by systematic prediction failure when rs12913832 (HERC2) was absent, although accuracy among successfully predicted samples remained high (82.1%). In contrast, hair and skin color inference remained feasible in >97% and 100% of evaluable samples, respectively; however, classification accuracy was moderate (70% for hair and 61% for skin), improving substantially when allowing adjacent-category concordance (90.2% for skin). Ancestry inference was robust when at least 27 aiSNPs were detected, and Y-SNPs reliably distinguished male and female samples. In silico analyses confirmed the critical contribution of rs12913832 to eye color model operability. Conclusions: FDP performance under partial genotyping reflects a trade-off between prediction feasibility and accuracy and depends on locus-specific integrity rather than overall genotype completeness. The ForenSeq™ Imagen kit shows robustness for ancestry, sex, hair, and skin prediction, although with variable accuracy, whereas eye color inference remains structurally vulnerable to drop out of high-impact variants. Evaluating FDP systems under realistic non-ideal conditions is essential to define their true operational limits and ensure scientifically robust and responsible implementation. Full article

Organophosphorus (OP) nerve agents inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) by phosphylating the catalytic serine. Oxime reactivators can restore enzymatic activity by a nucleophilic attack of the oximate anion on the phosphorus center of the enzyme–OP conjugate; however, clinically used oximes show agent- and enzyme-dependent performance and are particularly challenged by A-series compounds. Here, an in silico strategy is presented to identify candidate antidotes for OP poisoning, including A-series agents. Pharmacophore models are generated from benchmark/template oximes. Pharmacophore-based virtual screening is used to retrieve hit-like scaffolds from the available chemical space, after which selected hits are converted into oxime analogs. Template oximes and newly designed oximes are then docked into the active site of AChE or BChE inhibited by specific nerve agents. The predicted reactivation potential is assessed using mechanistically motivated geometric criteria derived from the accepted reactivation hypothesis, including the distance between the oximate oxygen and the phosphyl phosphorus and the attack angle, relative to the catalytic serine Oγ. This workflow enables a controlled, pairwise comparison of new oximes against their corresponding template oximes for each enzyme–agent combination, providing a rational basis for prioritizing candidates for synthesis and experimental validation. Using the described workflow, we identified a hit compound with the potential to act as an antidote against A-series nerve agent A-230 poisoning. Full article

According to the World Health Organization, antibiotic research remains insufficient, emphasizing the urgent need for new active molecules, particularly against resistant bacteria. Based on known antibacterial scaffolds, new fluoroquinolone derivatives have been synthesized by our research group, including compound 7a, a difluoroboranyl-fluoroquinolone that previously demonstrated activity against sensitive strains. Methods: The minimum inhibitory (MIC) and bactericidal (MBC) concentrations of compound 7a were determined against Staphylococcus aureus, Klebsiella pneumoniae, and Escherichia coli. The selective development of ciprofloxacin-resistant S. aureus was induced by reseeding the isolate on seven consecutive days with an antibiotic concentration that was not capable of inhibiting its development. Pharmacokinetic and toxicological properties were predicted using SwissADME, Way2Drug, and molecular docking (AutoDock Vina). In vivo toxicity was evaluated in BALB/c mice through histopathological liver and kidney analysis and serum biochemical markers. The antibacterial efficacy of 7a (80 mg/kg/day) was assessed in a murine pneumonia model induced by ciprofloxacin-resistant S. aureus. DNA gyrase inhibition was confirmed through plasmid electrophoresis assays in E. coli DH5-α cells. Results: Compound 7a exhibited both MIC and MBC values of 0.25 μg/mL, while ciprofloxacin-resistant S. aureus strains did not exhibit a detectable MIC within the concentration range tested (up to 1024 μg/mL). In silico predictions revealed favorable ADME profiles, low toxicity, and strong interaction with DNA gyrase. In vivo, 7a showed no signs of hepatotoxicity or nephrotoxicity and effectively reduced pneumonic tissue to 1.99% in infected mice. Electrophoretic assays confirmed DNA gyrase inhibition consistent with the mechanism of fluoroquinolones. Conclusions: Compound 7a evidenced activity against ciprofloxacin-resistant S. aureus in vitro and reduced infection progression in vivo. It also displays favorable drug-like properties, low predicted toxicity, and DNA gyrase inhibition. Full article

During infection in vitro with the strain 438/06 of bovine coronavirus (BCoV), a β-coronavirus similar to severe acute respiratory syndrome (SARS) CoV-2, treatment with 6-pentyl-α-pyrone (6PP), a fungal metabolite obtained from Trichoderma atroviride, was recently shown to influence viral load by reducing viral entry. Herein, the ability of 6PP to counteract the BCoV infection was further investigated both in vitro and in silico. Following the BCoV (strain 282/23) infection in bovine (MDBK) cells, the 6PP in co-treatment increased cell viability, reduced morphological signs of cell death, and significantly inhibited viral yield, by lessening the expression of the viral spike (S) protein, as well as the gene transcription of the viral nucleocapsid (NP) protein. In addition, a noticeable down-regulation in the expression of aryl hydrocarbon receptor (AhR) signaling, a strategic modulator of CoVs infection, was found. Molecular docking studies were performed to evaluate the potential interaction between 6PP and AhR involved in the BCoV infection. The docking 3D structural model showed that 6PP fits into a binding pocket positioned between the PASB and TAD domains of bovine AhR (bAhR), where the ligand is stabilized through hydrophobic interactions. In addition, the obtained computational data strongly suggest that the bAhR binding mechanism of 6PP is principally mediated by a well-conserved hydrophobic cavity playing a key role in the modulation of the receptor functions. Overall, our findings showed an antiviral action of 6PP versus BCoV infection in vitro and in silico. Full article

The limited selectivity of most catalytic-site ADAMTS-5 inhibitors and the necessity to preserve aggrecan integrity in early-grade knee osteoarthritis require the development of selective aggrecanase inhibitors. The present study conducted rational in silico screening of flavonoids as potential ADAMTS-5 inhibitors by integrating high-throughput virtual screening, molecular docking, and molecular dynamic simulations targeting the exosite domains of ADAMTS-5 (the Disintegrin-like and spacer domain). The objective was to identify plant-derived flavonoids with favorable drug-like properties and specific interactions towards the ADAMTS-5 exosite as a more targeted alternative to catalytic-site inhibition. In this study, 847 flavonoids were screened using drug-likeness and ADME criteria to identify promising leads. The top 16 selected flavonoids were further subjected to molecular docking and SAR analysis. Of these compounds, Homoeriodictyol satisfied key drug-likeness criteria and exhibited the highest binding affinity to the Disintegrin-like domain, with a binding energy of −23.1 kcal/mol and favorable interactions. Molecular dynamics simulations of the Homoeriodictyol–ADAMTS-5 complex over 100 ns demonstrated stable binding throughout the trajectory. DCCM analysis and PCA further supported the proposed exosite-mediated modulation. To extend exosite mapping beyond the Disintegrin-like domain, this study also examined the spacer domain using a machine-learning-predicted structural model and identified key residues that contribute to ligand binding. Full article