Search Results (613)

Monoacylglycerols (MAGs) are significant intermediate byproducts in the hydrolysis of oils and fats. The accumulation of MAGs not only reduces the quality and purity of the final products in biodiesel production and edible oil refining but also poses challenges for downstream separation processes. Therefore, the development of efficient biocatalysts for the specific MAG conversion is of great industrial importance. The lipase from Aspergillus oryzae (AOL) has shown potential for lipid modification; however, the wild-type enzyme (WT) suffers from poor solubility, tendency to aggregate, and low specific activity towards MAGs in aqueous systems, which severely restricts its practical application. In this study, a combinatorial protein engineering strategy was employed to overcome these limitations. We integrated fusion protein technology with rational design to enhance both the functional expression and catalytic efficiency of AOL. Firstly, the superfolder green fluorescent protein (sfGFP) was fused to the N-terminus of AOL. The results indicated that the sfGFP fusion tag significantly improved the solubility and stability of the enzyme, preventing the formation of inclusion bodies. The fusion protein sfGFP-AOL exhibited a MAG conversion rate of approximately 65%, confirming the positive impact of the fusion tag on enzyme developability. To further boost catalytic performance, site-directed mutagenesis was performed based on structural analysis. Among the variants, the mutant sfGFP-Y92Q emerged as the most potent candidate. In the MAG conversion, sfGFP-Y92Q achieved a conversion rate of 98%, which was not only significantly higher than that of sfGFP-AOL but also outperformed the widely used commercial immobilized lipase, Novozym 435 (~54%). Structural modeling and docking analysis revealed that the Y92Q mutation optimized the geometry of the active site. The substitution of Tyrosine with Glutamine at position 92 likely enlarged the substrate-binding pocket and altered the local electrostatic environment, thereby relieving steric hindrance and facilitating the access of the bulky MAG substrate to the catalytic center. In conclusion, this work demonstrates that the synergistic application of sfGFP fusion and rational point mutation (Y92Q) can dramatically transform the catalytic properties of AOL. The engineered sfGFP-Y92Q variant serves as a robust and highly efficient biocatalyst for MAG degradation. Its superior performance compared to commercial standards suggests immense potential for cost-effective applications in the bio-manufacturing of high-purity fatty acids and biodiesel, offering a greener alternative to traditional chemical processes. Full article

Per- and polyfluoroalkyl substances (PFASs), as a class of “permanent chemicals” with high environmental persistence and bioaccumulation, have attracted much attention. In this study, we focused on the molecular mechanism of the interaction between perfluoroalkyl acids (PFAAs) and peroxisome proliferator-activated receptor δ (PPARδ). Using molecular docking, binding free energy calculation, and structural analysis, we systematically investigated the binding modes, key amino acid residues, and binding energies of 20 structurally diverse PFAAs with PPARδ. The results showed that the binding energies of PFAAs with PPARδ were significantly affected by the molecular weight, the number of hydrogen bond donors, and the melting point of PFAAs. PFAAs with smaller molecular weights and fewer hydrogen bond donors showed stronger binding affinity. The binding sites were concentrated in high-frequency amino acid residues such as TRP-256, ASN-269, and GLY-270, and the interaction forces were dominated by hydrogen and halogen bonds. PFAAs with branched structure of larger molecular weight (e.g., 3m-PFOA, binding energy of −2.92 kcal·mol⁻¹; 3,3m₂-PFOA, binding energy of −2.45 kcal·mol⁻¹) had weaker binding energies than their straight-chain counterparts due to spatial site-blocking effect. In addition, validation group experiments further confirmed the regulation law of binding strength by physicochemical properties. In order to verify the binding stability of the key complexes predicted by molecular docking, and to investigate the dynamic behavior under the conditions of solvation and protein flexibility, molecular dynamics simulations were conducted on PFBA, PFOA, 3,3m₂-PFOA, and PFHxA. The results confirmed the dynamic stability of the binding of the high-affinity ligands selected through docking to PPARδ. Moreover, the influence of molecular weight and branched structure on the binding strength was quantitatively verified from the perspectives of energy and RMSD trajectories. The present study revealed the molecular mechanism of PFAAs interfering with metabolic homeostasis through the PPARδ pathway, providing a theoretical basis for assessing its ecological and health risks. Full article

Background: Thymol, a natural phenol with antimicrobial and antioxidant activities, and its derivatives offer promising scaffolds for antimalarial drug development, potentially helping overcome resistance. Materials and Methods: In this study, thymol derivatives were synthesized and assessed as antiplasmodial agents against both resistant and sensitive strains of P. falciparum, as well as Plasmodium knowlesi. The ligand molecules were assessed with Plasmodium falciparum chloroquine resistance transporter (PfCRT)’s potential using in silico molecular docking and ADMET analysis. The parent compound, thymol, was chemically modified through esterification and conjugation with hydroxybenzoic acid and cinnamic acid derivatives to generate analogs with varied substitution patterns. Results: The findings showed that among seven successfully synthesized thymol derivatives, compounds 4 and 6 exhibited notable potency against Plasmodium falciparum 3D7 (EC₅₀ = 6.01 ± 1.7 µM and 6.8 ± 1.1 µM, respectively) with high SI values (16.5 and 14.6, respectively), indicating improved selectivity relative to thymol. The cytotoxicity evaluation against HCF mammalian cells revealed that most thymol derivatives were non-toxic, with CC₅₀ values greater than 99 µM, except for compound 3 (CC₅₀ = 71.4 ± 4.5 µM) and compound 1 (CC₅₀ = 58.4 ± 2.3 µM), which exhibited moderate cytotoxic effects. The molecular docking results showed that compounds 3 (−8.4 kcal/mol), 4 (−8.3 kcal/mol), and 6 (−8.3 kcal/mol) exhibited strong binding affinities toward the PfCRT protein. Conclusions: Therefore, thymol derivative compounds 4 and 6 exhibited stronger antiplasmodial activity in vitro against P. falciparum and P. knowlesi with safety profiles against mammalian cells, targeting PfCRT, highlighting their potential as lead antimalarial candidates. Full article

Zanthoxylum piperitum is a food and culinary plant commonly used in East Asia. In traditional medicine, its fruits, seeds, and bark have been utilized to treat digestive disorders, pain, and stomachache. Prior research has demonstrated its health benefits, particularly its significant antioxidant properties. However, limited research has investigated the specific metabolites responsible for these pharmacological effects. In this study, the antioxidant activities (EC₅₀: 9.1–1084.5 μg/mL) and metabolite profiles of different organs (fruits, pericarps, and seeds) of Z. piperitum collected from different regions were comparatively analyzed. Chemical structures of 91 metabolites from different organs were identified using UHPLC-Orbitrap-MS/MS based on untargeted metabolomics. The LC-DPPH method was employed to screen antioxidants from the extracts of the most active organ (the pericarps). The potential effects of the active compounds on oxidation-related diseases were evaluated by integrating compound–target interaction network analysis. Protein–protein interaction (PPI) networks revealed EGFR, STAT3, AKT1, TNF, BCL2, CASP3, ESR1, PPARA, CYP19A1, and CDK2 as central hub genes. The significance of compound and target interactions was further supported by molecular docking studies, which demonstrated favorable binding affinities, with most proteins exhibiting docked scores below −4.27 kcal/mol. The extracts of Z. piperitum fruits and pericarps also exhibited antioxidative activity against ROS production in LPS-stimulated RAW264.7 cells. Our findings demonstrate the application of an optimized extraction process and underscore the medicinal value of this food-plant by characterizing its bioactive constituents. The results indicate that Z. piperitum may serve not only as a health-promoting food but also has the potential for prevention or treatment of oxidative-stress-related diseases. Future research should focus on in vivo studies by exploring the therapeutic mechanisms of actions of the active extracts. Full article

An ethnobotanical survey in the northern mountainous region of Vietnam identified four Elsholtzia species, E. blanda, E. ciliata, E. communis, and E. penduliflora, growing naturally above 1500 m and traditionally used by local ethnic communities to treat skin-related ailments. This study investigates their essential oil possible chemotypes, antimicrobial properties, and potential mechanisms of action through molecular docking. Essential oils obtained by steam distillation were analyzed using GC–MS. E. blanda (yield 1.17%) was characterized by high levels of 1,8-cineole (29.0%) and camphor (17.0%). E. ciliata (1.02%) represented a possible limonene-dominant chemotype (71.0%). E. communis (1.91%) contained an exceptionally high proportion of rosefuran oxide (86.2%), whereas E. penduliflora (0.91%) exhibited a pronounced 1,8-cineole chemotype (92.1%). All essential oils showed antimicrobial activity against Staphylococcus aureus (MSSA and MRSA), Escherichia coli, and Candida albicans, with MIC values ranging from 0.4% to 3.2%. Except for E. ciliata against C. albicans, MBC/MIC and MFC/MIC ratios ≤ 4 indicated predominantly bactericidal or fungicidal effects. Molecular docking further identified nine of twenty-eight detected constituents as strong binders to microbial target proteins. These findings expand current knowledge on possible chemotypic diversity within the genus, particularly the discovery of a high-altitude limonene chemotype in E. ciliata and the identification of E. penduliflora as a rich natural source of 1,8-cineole. The convergence of chemical, biological, and in silico evidence supports the ethnomedicinal relevance of Elsholtzia species and highlights their potential as candidates for developing natural antimicrobial agents. Full article

The ongoing COVID-19 pandemic, caused by SARS-CoV-2, continues to pose major global health challenges despite extensive vaccination efforts. Variant escape, waning immunity, and reduced vaccine efficacy in immunocompromised populations underscore the urgent need for complementary antiviral therapeutics. Here, we report the design, synthesis, and biological evaluation of precision-engineered dermatan sulfate (DS)-mimetic glycopolymers as multi-targeted inhibitors of SARS-CoV-2. Guided by molecular docking and virtual screening, sulfation at the C2 and C4 positions of iduronic acid was identified as critical for binding to the viral spike protein and inhibiting host and viral enzymes, including heparanase (HPSE) and main protease (M^pro). Chemically synthesized DS disaccharides were covalently grafted onto polymer scaffolds via a post-modification strategy, yielding glycopolymers with well-defined assembly that form uniform nanoparticles under physiological conditions. Surface plasmon resonance and pseudovirus assays revealed strong binding to the viral spike protein (K_D ≈ 177 nM), potent viral neutralization, and minimal cytotoxicity. Cellular uptake studies further demonstrated efficient internalization of nanoparticles and intracellular inhibition of HPSE and M^pro. These results establish a modular, non-anticoagulant, and glycosaminoglycan-mimetic platform for the development of broad-spectrum antiviral agents to complement vaccination and enhance preparedness against emerging coronavirus variants. Full article

Marrubium vulgare L. is a medicinal plant widely used in traditional medicine, with emerging evidence of anticancer potential. This study investigated its bioactive compounds as inhibitors of Heat Shock Protein 90 alpha (Hsp90α), a molecular chaperone essential for oncogenic protein stability. Organic and aqueous extracts were profiled using high-performance liquid chromatography–mass spectrometry (HPLC–MS), revealing a diverse phytochemical composition. Identified compounds were screened against the full-length crystal structure of Hsp90α using a structure-based computational workflow that included extra-precision and domain-specific molecular docking, molecular dynamics (MD) simulations, and MM/GBSA binding free energy calculations. Pharmacokinetic and toxicity profiles were evaluated through ADMET predictions. This study elucidated the chemical composition of the plant and identified two hit compounds: Forsythoside B bound preferentially to the middle domain, potentially interfering with client protein interactions, and chlorogenic acid targeted the C-terminal domain, which regulates dimerization and allosteric activity. Both ligands displayed stable protein–ligand interactions during MD and favorable ADMET properties. These findings provide the first integrated chemical and computational prediction framework, suggesting that some M. vulgare metabolites may interact with Hsp90, highlighting its potential as a source of novel anticancer scaffolds and laying the groundwork for experimental validation and drug development. Full article

Objectives: One of the major trends in modern computational toxicology is the development of explainable predictive tools. However, the complex nature of the mechanistic representation of biological organisms and the lack of relevant data remain limiting factors. Methods: This work provides a publicly available dataset of 12,654 compounds with mouse intravenous ${\mathrm{LD}}_{50}$ values, as well as docking scores (Vina-GPU 2.0) against 44 toxicity-associated proteins. NIH and Brenk filters were applied to refine the chemical space. Results: Across the entire protein panel, the human ether-a-go-go–related gene channel (hERG/KCNH2), vasopressin receptor 1A (AVPR1A), the L-type voltage-gated calcium channel Cav1.2 (CACNA1C), the potassium voltage-gated channel subfamily KQT member 1 (KCNQ1) and endothelin receptor A (EDNRA) showed the strongest association with acute toxicity. Statistically significant differences were found in the distribution of ${\mathrm{LD}}_{50}$ values for compounds that bind antitargets compared with non-binders. Using known bioactive molecules such as anisodamine, butaperazine, soman, and several cannabinoids as examples confirmed the effectiveness of inverse docking for elucidating mechanism of action. Conclusions: The dataset offers a resource to advance transparent, mechanism-aware toxicity modeling. The data is openly available. Full article

Background/Objectives: This study focused on synthesizing novel alkenyl derivatives of azinylferrocenes and evaluating their potential as Alzheimer’s disease (AD) therapeutics. Methods: 1-Azinyl-1′-acetylferrocenes were obtained by regioselective acetylation of azinylferrocenes, followed by the Wittig reaction or reduction of 1-azinyl-1′-acetylferrocenes and subsequent dehydration of the resulting alcohols. The synthesized compounds underwent the following biological activity testing relevant to AD: inhibition of acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and off-target carboxylesterase (CES); antioxidant capacity (ABTS and FRAP assays); inhibition of Aβ₄₂ self-aggregation (thioflavin method); blocking AChE-induced β-amyloid aggregation (propidium displacement); and cytotoxicity in SH-SY5Y and MSC-Neu cells (MTT assay). Results: Quinoline and bipyridine derivatives demonstrated effective cholinesterase inhibition, especially quinoline 7b (AChE IC₅₀ 3.32 μM; BChE IC₅₀ 3.68 μM), while acridine derivatives were poor inhibitors. Quantum chemical (QC) calculations predicted that acridine derivatives were especially prone to form stable dimers. Molecular docking into protein targets generated by an AlphaFold3 reproduction code showed that these dimers were too bulky to access enzyme active sites, yet they could bind to protein surfaces to inhibit Aβ₄₂ self-aggregation and displace propidium from the AChE peripheral anionic site. All compounds showed high antioxidant activity in ABTS and FRAP assays, with quinoline derivatives being 2–4 times more potent than Trolox. QC calculations supported these findings. Quinoline and bipyridine derivatives also exhibited low cytotoxicity and scant CES inhibition. Conclusions: Overall, the synthesized ferrocenes, particularly the quinoline and bipyridine derivatives, appear promising for further research as multifunctional therapeutic agents targeting AD due to their anticholinesterase, antiaggregating, and antioxidant activities combined with low toxicity. Full article

Plutella xylostella, a major pest of cruciferous vegetables, depends predominantly on chemoreception to locate host plants. Legs are crucial in insect chemical perception, particularly during close-range and contact chemoreception. However, the molecular basis underlying the chemosensory repertoire in P. xylostella legs remains elusive. To address this, we sequenced chemosensory-related genes in diamondback moth legs. Sequencing identified 32 odorant binding protein (OBP), 18 chemosensory protein (CSP), 26 odorant receptor (OR), 20 gustatory receptor (GR), 15 ionotropic receptor (IR), and 3 sensory neuron membrane protein (SNMP) genes. Comparative analysis with antennal transcriptome data revealed three CSPs, seven ORs, and two GRs newly identified in the legs. Transcriptome analysis showed higher fragments per kilobase of transcript per million mapped reads values for CSPs than for other chemosensory-related gene families. Furthermore, qRT-PCR confirmed the highest expression of PxylCSP9 in the legs, suggesting its role in perceiving external compounds. Fluorescent binding assays revealed high binding affinity of PxylCSP9 for several host plant semiochemicals. Molecular docking predicted a hydrophobic binding pocket in PxylCSP9 with Met11, Leu13, and Leu43 frequently participating in ligand interactions. Our findings indicate that leg-enriched PxylCSP9 is pivotal for host plant recognition during close-range chemoreception, suggesting its potential as a molecular target for precision management through behavior-based strategies. Full article

Background/Objectives: GuaB, which is known as inosine 5′-phosphate dehydrogenase (IMPDH), is an enzymatic target involved in the de novo guanine biosynthetic pathway of the multidrug-resistant (MDR) Acinetobacter baumannii. GuaB has emerged as a potential therapeutic target to cope with increasing antibiotic resistance. Here, we used machine learning-based virtual screening as a verification technique to find potential inhibitors possessing different chemical scaffolds, using structure-based drug design as a discovery platform. Methods: Four machine learning models, built based on chemical fingerprint data, were trained, and the best models were used for virtual screening of the ChEMBL library, which covers 153 active molecules. Molecular dynamics (MD) simulations of 200 ns were carried out for all three compounds in order to explain conformational changes, evaluate stability, and provide validation of the docking results. Post-simulation analyses include principal component analysis (PCA), bond analysis, free-energy landscape (FEL), dynamic cross-correlation matrix (DCCM), radial distribution function (RDF), salt-bridge identification, and secondary-structure profiling, etc. Results: For molecular docking, the screened compounds were used against the GuaB protein to achieve proper docked conformation. Upon visual examination of the best-docked compounds, three leads (lead-1, lead-2, and lead-3) were found to have better interaction with the GuaB protein in comparison to the control. The mean RMSD scores between the three leads and the control were between 2.54 and 2.89 Å. In addition, the three leads as well as the control were characterized for pharmacokinetic features. All three leads met Lipinski’s Rule 5 and were thus drug-like. PCA and FEL analyses showed that lead-2 exhibited improved conformational stability, identified as deeper energy minima, whereas RDF and DCCM analyses revealed that lead-2 and lead-3 exhibited strong local structuring and concerted dynamics. In addition, lead-2 displayed a very rich hydrogen-bonding network with a total of 460 frames possessing such interactions, which is the highest among the complexes investigated here. Based on entropy calculations and the maximum entropy method of gamma–gram, lead-1 proved to be the most stable one with the lowest binding free-energy. Conclusions: This study provides an integrated machine learning-based virtual screening pipeline for the identification of new scaffolds to moderate infections associated with AMR; however, in vitro validation is still required to assess the efficacy of such compounds. Full article

Kinases, which make up 20% of the druggable genome, are thought to be essential signaling enzymes. Protein phosphorylation is induced by protein kinases. Proliferation, the cell cycle, apoptosis, motility, growth, differentiation, and other biological processes are all regulated by kinases. Their dysregulation disrupts several cellular functions, leading to a variety of illnesses, the most important of which is cancer. As a result, kinases are thought to be crucial targets in a number of malignancies and other diseases. Researchers from all over the world are hard at work developing inhibitors using various chemical structures. The scaffolds of imidazole and benzimidazole provide a versatile structure for a variety of physiologically active substances. Moreover, they serve as specialized scaffolding for the creation of target-specific pharmaceuticals to address various diseases. This article seeks to illustrate the application of imidazole and benzimidazole frameworks in the formulation of inhibitors that target various tyrosine kinases, including fibroblast growth factor receptors (FGFRs), c-Met kinase, epidermal growth factor receptors (EGFRs), vascular endothelial growth factor receptors (VEGFRs), and FMS-like tyrosine kinase 3 (FLT3), from 2020 to the present. The major structure–activity correlations (SARs) of imidazole and benzimidazole derivatives were examined, and, also, a docking study highlighted the varied interactions occurring inside the active site of tyrosine protein kinases. The objective of this effort is to consolidate the fundamental structural information necessary for the synthesis of imidazole- or benzimidazole-based tyrosine kinase inhibitors with enhanced efficacy. Full article

Perilla seed oil (PSO), rich in alpha-linolenic acid (ALA), has been traditionally used to relieve exterior syndrome and promote digestion, with modern studies confirming its anti-hyperlipidemic and anti-atherosclerotic properties. This study investigated the lipid-lowering effects of PSO and its underlying mechanisms in high-fat-diet-induced hyperlipidemic rats. Chemical standardization by UPLC-MS and GC-MS identified 591 compounds in PSO, with ALA accounting for 57.5% of its composition. The PSO administration significantly improved the general condition of hyperlipidemic rats, reduced body weight, lowered serum total cholesterol and LDL-C levels, and alleviated liver tissue injury and lipid accumulation. Serum metabolomics analysis revealed that PSO upregulated ALA and eicosapentaenoic acid while downregulating pro-inflammatory metabolites, including arachidonic acid, prostaglandin H2, and prostaglandin E2. Integrated network pharmacology and molecular docking studies identified the PI3K/Akt/NOS3 pathway as the primary signaling mechanism, which was further confirmed by Western blot analysis showing that PSO upregulated expression of p-PI3K, p-Akt, and NOS3 proteins. These results demonstrated that PSO-ameliorated hyperlipidemia, through PI3K/Akt/NOS3 pathway activation, coordinately modulated fatty acid metabolism and endogenous inflammatory responses. Our findings provided scientific evidence supporting PSO as a dietary intervention for managing hyperlipidemia and related metabolic disorders. Full article

The emergence of SARS-CoV-2 and its rapid global spread underscores the urgent need for novel therapeutic strategies. This study investigates the antiviral potential of Allium sativum (garlic) extracts against SARS-CoV-2, focusing on disruption of the spike protein’s receptor-binding domain (RBD) interaction with angiotensin-converting enzyme 2 (ACE2), a critical step in viral entry. Two garlic cultivars (Tigre and Fermín) were processed via oven-drying or freeze-drying, followed by maceration with CH₂Cl₂/MeOH (1:1) and fractionation with liquid–liquid partition. ELISA immunoassays revealed that freeze-dried Tigre (TL) extracts had the highest inhibitory activity (42.16% at 0.1 µg/mL), with its aqueous fraction achieving 57.26% inhibition at 0.01 µg/mL. Chemical profiling via GC-MS found sulfur and other types of compounds. Molecular docking identified three garlic TL-derived aqueous fraction compounds with strong binding affinities (ΔG = −7.5 to −6.9 kcal/mol) to the RBD-ACE2 interface. Furthermore, ADME in silico analysis highlighted one of them (L17) as the main candidate, having high gastrointestinal absorption, blood–brain barrier permeability, and compliance with drug-likeness criteria. These findings underscore garlic-derived compounds as promising inhibitors of SARS-CoV-2 entry, calling for further preclinical validation. The study integrates experimental and computational approaches to advance natural product-based antiviral discovery, emphasizing the need for standardized formulations to address therapeutic variability across viral variants. Full article

Protein–protein interactions (PPIs) take place in many cellular processes, including the activation of cellular cascades, such as the MAPK/ERK (Mitogen-Activated Protein Kinase/Extracellular-Regulated Kinase) pathway. Deregulation of these pathways leads to the development of diseases, such as cancer. DEL-22379 is an ERK2 dimerization inhibitor, which presents anti-tumoral effects, without affecting ERK2 phosphorylation. Our aim was to identify new therapeutic molecules targeting ERK2 dimerization, based on DEL-22379 structure. In this study, we implemented a combination of computational and experimental workflow, which includes in silico techniques, such as scaffold hopping and virtual screening to generate a dataset of candidate compounds, a native PAGE (PolyAcrylamide Gel Electrophoresis) electrophoresis to experimentally screen the potential inhibitors, and a detailed molecular docking and chemical profile prediction to understand the potential mechanism of action of the selected compounds. From an initial dataset of 536 compounds, we obtained two hit molecules that exhibited inhibitory effects on ERK2 dimerization: Drug73 and Drug120. A computational analysis of the mechanism of action, unveiled that Drug73 and Drug120 presented an improved docking score, and better drug-like properties when compared to DEL-22379. This study shows that computational studies, in combination with experimental evaluation, can be useful and efficient to find new therapeutic compounds. Full article