Dissecting molecular mechanisms underlying the inhibition of β-glucuronidase by alkaloids from Hibiscus trionum: Integrating in vitro and in silico perspectives

Computers in Biology and Medicine, Год журнала: 2024, Номер 180, С. 108969 - 108969

Опубликована: Июль 31, 2024

Язык: Английский

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Exploring the anti-gout potential of sunflower receptacles alkaloids: A computational and pharmacological analysis

Computers in Biology and Medicine, Год журнала: 2024, Номер 172, С. 108252 - 108252

Опубликована: Март 11, 2024

Язык: Английский

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Hesperetin acts as a potent xanthine oxidase inhibitor: New evidence from its reactive oxygen suppression and enzyme binding

International Journal of Biological Macromolecules, Год журнала: 2025, Номер unknown, С. 141429 - 141429

Опубликована: Фев. 1, 2025

Язык: Английский

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In Silico Prediction of New Inhibitors for Kirsten Rat Sarcoma G12D Cancer Drug Target Using Machine Learning-Based Virtual Screening, Molecular Docking, and Molecular Dynamic Simulation Approaches

Pharmaceuticals, Год журнала: 2024, Номер 17(5), С. 551 - 551

Опубликована: Апрель 25, 2024

Single-point mutations in the Kirsten rat sarcoma (KRAS) viral proto-oncogene are most common cause of human cancer. In humans, oncogenic KRAS responsible for about 30% lung, pancreatic, and colon cancers. One predominant mutant G12D variants is pancreatic cancer an attractive drug target. At time writing, no

Язык: Английский

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Quantum mechanics insights into melatonin and analogs binding to melatonin MT1 and MT2 receptors

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Май 13, 2024

Abstract Melatonin receptors MT 1 and 2 are G protein-coupled that mediate the effects of melatonin, a hormone involved in circadian rhythms other physiological functions. Understanding molecular interactions between these their ligands is crucial for developing novel therapeutic agents. In this study, we used docking, dynamics simulations, quantum mechanics calculation to investigate binding modes affinities three ligands: melatonin (MLT), ramelteon (RMT), 2-phenylmelatonin (2-PMT) with both receptors. Based on results, identified key amino acids contributed receptor-ligand interactions, such as Gln181/194, Phe179/192, Asn162/175, which conserved Additionally, described new meaningful Gly108/Gly121, Val111/Val124, Val191/Val204. Our results provide insights into recognition’s structural energetic determinants suggest potential strategies designing more optimized molecules. This study enhances our understanding offers implications future drug development.

Язык: Английский

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Geometry-encoded molecular dynamics enables deep learning insights into P450 regiospecificity control

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Март 3, 2025

Язык: Английский

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Identification and Exploration of Immunity‐Related Genes and Natural Products for Alzheimer's Disease Based on Bioinformatics, Molecular Docking, and Molecular Dynamics

Immunity Inflammation and Disease, Год журнала: 2025, Номер 13(4)

Опубликована: Апрель 1, 2025

ABSTRACT Background Recent research highlights the immune system's role in AD pathogenesis and promising prospects of natural compounds treatment. This study explores immunity‐related biomarkers potential products using bioinformatics, machine learning, molecular docking, kinetic simulation. Methods Differentially expressed genes (DEGs) were analyzed GSE5281 GSE132903 datasets. Important module identified a weighted co‐expression algorithm (WGCNA), immune‐related (IRGs) obtained from ImmPortPortal database. Intersecting these yielded important IRGs. Then, least absolute shrinkage selection operator (LASSO) other methods screened common markers. Biological pathways explored through Gene Ontology (GO), Kyoto Encyclopedia Genes Genomes (KEGG), Set Enrichment Analysis (GSEA). The accuracy markers was assessed by subject signature (ROC) curves validated GSE122063 dataset. datasets then subjected to immunoinfiltration analysis. Multiple compound databases used analyze core Chinese medicines components. Molecular docking simulation verification for further verification. Results A total 1360 differential 5 (PGF, GFAP, GPI, SST, NFKBIA) identified, showing excellent diagnostic efficiency. GSEA revealed associated with Oxidative phosphorylation, Nicotine addiction, Hippo signaling pathway. Immune infiltration analysis showed dysregulation multiple cell types brains, significant interactions between types. 27 possible herbs 7 eventually identified. binding environment GPI‐luteolin GPI‐stigasterol relatively stable good affinity. Conclusions PGF, NFKBIA early diagnosis, cells brains. compounds, including luteolin stigmasterol, targeting biomarkers.

Язык: Английский

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Inhibitory Effect of Whey Protein‐Derived Peptide Leu‐Asp‐Gln‐Trp on Xanthine Oxidase

Food Science & Nutrition, Год журнала: 2025, Номер 13(4)

Опубликована: Апрель 1, 2025

ABSTRACT Hyperuricemia is associated with various diseases, and xanthine oxidase (XO) the rate‐limiting enzyme in uric acid (UA) production. A previous study reported that Leu‐Asp‐Gln‐Trp (LDQW) whey protein hydrolysate (WPH) suppressed lipid droplet accumulation differentiated 3T3‐L1 adipocyte‐like cells. However, our understanding of LDQW remains limited, further, its efficacy against hyperuricemia has not been elucidated. This evaluated XO inhibitory activity LDQW, one bioactive peptides WPH. In this study, UA produced by reaction between was determined using two methods: monitoring absorbance at 290 nm absorptiometry detection liquid chromatography tandem mass spectrometry (LC–MS/MS) analysis. Allopurinol used as positive control, whereas tryptophan Ala‐Leu‐Pro‐Met (ALPM) were for comparison. Both LC–MS/MS analyses demonstrated significantly inhibited a concentration‐dependent manner. The analysis results indicated tryptophan, ALPM inhibition ratios 20 mM 58.0% ± 2.8%, 4.4% 3.7%, 45.0% 1.0%, respectively. Moreover, it suggested Asp‐Gln‐Trp, potential digestive peptide predicted enzymatic digestion silico , also possessed comparable to These findings suggest promising ameliorative effects hyperuricemia, similar those other peptides.

Язык: Английский

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Exploration of novel non-purine xanthine oxidase inhibitors based on oxadiazolones by an integrated simulation study

New Journal of Chemistry, Год журнала: 2024, Номер 48(12), С. 5530 - 5542

Опубликована: Янв. 1, 2024

A systematic simulation study on a novel series of oxadiazolones as xanthine oxidase inhibitors.

Язык: Английский

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Integrating Computational and Experimental Methods to Identify Novel Sweet Peptides from Egg and Soy Proteins

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(10), С. 5430 - 5430

Опубликована: Май 16, 2024

Sweetness in food delivers a delightful sensory experience, underscoring the crucial role of sweeteners industry. However, widespread use has sparked health concerns. This underscores importance developing and screening natural, health-conscious sweeteners. Our study represents groundbreaking venture into discovery such derived from egg soy proteins. Employing virtual hydrolysis as novel technique, our research entailed comprehensive process that evaluated biological activity, solubility, toxicity compounds. We harnessed cutting-edge machine learning methodologies, specifically latest graph neural network models, for predicting sweetness molecules. Subsequent refinements were made through molecular docking screenings dynamics simulations. meticulous approach culminated identification three promising sweet peptides: DCY(Asp-Cys-Tyr), GGR(Gly-Gly-Arg), IGR(Ile-Gly-Arg). Their binding affinity with T1R2/T1R3 was lower than -15 kcal/mol. Using an electronic tongue, we verified taste profiles these peptides, IGR emerging most favorable terms value 19.29 bitterness 1.71. not only reveals potential natural peptides healthier alternatives to traditional applications but also demonstrates successful synergy computational predictions experimental validations realm flavor science.

Язык: Английский

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