Yazar "Yildiz, Resit" seçeneğine göre listele

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    Comparison of new secondgeneration H1 receptor blockers with some molecules; a study involving DFT, molecular docking, ADMET, biological target and activity
    (BMC, 2025) Unsal, Velid; Oner, Erkan; Yildiz, Resit; Mert, Basak Dogru
    Although the antiallergic properties of compounds such as CAPE, Melatonin, Curcumin, and Vitamin C have been poorly discussed by experimental studies, the antiallergic properties of these famous molecules have never been discussed with calculations. The histamine-1 receptor (H1R) belongs to the family of rhodopsin-like G-protein-coupled receptors expressed in cells that mediate allergies and other pathophysiological diseases. In this study, pharmacological activities of FDA-approved second generation H1 antihistamines (Levocetirizine, desloratadine and fexofenadine) and molecules such as CAPE, Melatonin, Curcumin, Vitamin C, ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiles, density functional theory (DFT), molecular docking, biological targets and activities were compared by calculating. Since drug development is an extremely risky, costly and time-consuming process, the data obtained in this study will facilitate and guide future studies. It will also enable researchers to focus on the most promising compounds, providing an effective design strategy. Their pharmacological activity was carried out using computer-based computational techniques including DFT, molecular docking, ADMET analysis, biological targeting, and activity methods. The best binding sites of Desloratadine, Levocetirizine, Fexofenadine, CAPE, Quercetin, Melatonin, curcumin, Vitamin C ligands to Desmoglein 1, Human Histamine H1 receptor, IgE and IL13 protons were determined by molecular docking method and binding energy and interaction states were analyzed. Fexofenadine and Quercetin ligand showed the most effective binding affinity. Melatonin had the best Caco-2 permeability PPB values of Quercetin, CAPE and Curcumin were at optimal levels. On the OATP1B1 and OATP1B3 of curcumin and CAPE, Quercetin was found to have strong inhibition effects on BCRP. Melatonin and CAPE were found to have the highest inhibition values on CYP1A2, while CAPE had the highest inhibition values on CYP2C19 and CYP2C9. Vitamin C and Quercetin were found to be safer in terms of cardiac toxicity and mutagenic risks, while Desloratadine and Levocetirizine carried high risks of neurotoxicity and hematotoxicity, while CAPE was noted for its high enzyme inhibitory activities and low toxicity profiles, while the hERG blockade, DILI, and cytotoxicity values of other compounds pointed to various safety concerns. This study demonstrated the potential of machine learning methods in understanding and discovering H1 receptor blockers. The results obtained provide important clues in the development of important strategies in the clinical use of H1 receptor blockers. In the light of these data, CAPE and Quercetin are remarkable molecules.
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    Comparison of PDE-5 inhibitors used in erectile dysfunction with some candidate molecules: A study involving molecular docking, ADMET, DFT, biological target, and activity
    (BMC, 2025) Sagir, Suleyman; Unsal, Velid; Oner, Erkan; Yildiz, Resit; Mert, Basak Dogru
    Erectile dysfunction (ED) is a urological condition defined as the inability of a man to achieve or maintain an erection. This condition negatively affects his sexual performance and the performance of his partner. Phosphodiesterase type 5 (PDE5) inhibitors are commonly used to treat ED. Arginase II plays an important role in regulating L-arginine to NO synthase in the smooth muscle of the human corpus cavernosum of the penis. NO is a molecule essential for regulating a variety of functions, including arterial blood pressure, penile erection, and energy balance. Substances such as vardenafil, alprostadil, papaverine, and resveratrol increase NO production, thereby supporting sexual function and vascular health. Additionally, NO donors such as L-arginine, L-citrulline, and alpha-lipoic acid provide effective alternatives when used in combination with PDE5 inhibitors. Medications used in the treatment of ED include vardenafil, alprostadil, and papaverine. In addition, although molecules such as L-arginine, citrulline, resveratrol, alpha-lipoic acid, and rutin are thought to play a role in ED, their pharmacological and molecular effects have not been sufficiently elucidated. The aim of this study was to investigate the effects of these molecules in the treatment of ED by computer-based calculations, to obtain new information about them and to inspire new treatment strategies for ED. The physicochemical, molecular and pharmacokinetic properties of the compounds were determined by SwissADME software, and ADMET (absorption, distribution, metabolism, excretion and toxicity) data were determined by ADMETlab 3.0 software. Biological target and activity data were obtained by MolPredictX and PASS Online software. While the Gaussian 09 program was used for DFT calculations, PyMOL, AutodockTools 4.2.6, AutoDock Vina, and Biovia Discovery programs were used for molecular docking studies. It was found that L-arginine, citrulline, resveratrol and alpha-lipoic acid were well absorbed from the intestine, while rutin showed limited absorption. When their metabolic risks were evaluated, L-arginine and citrulline were found to have lower toxicity. Molecular docking results of rutin and resveratrol were remarkable. The electronic properties of the compounds were explained by DFT calculations. L-arginine and citrulline were found to have low toxicity and positive therapeutic effects. L-arginine and citrulline stand out as promising candidates for future research. Although resveratrol data are promising, unfortunately their potential toxicity and metabolic interactions require further investigation. It is important to learn more about these compounds or conduct research to improve their therapeutic efficacy. Although computer-based calculations play an important role in toxicity predictions, drug interactions, pharmacokinetics and toxicity properties should be carefully evaluated.
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    Evaluation of extra virgin olive oil compounds using computational methods: in vitro, ADMET, DFT, molecular docking and human gene network analysis study
    (BMC, 2025) Unsal, Velid; Yildiz, Resit; Korkmaz, Aziz; Mert, Basak Dogru; Caliskan, Cemile Gunbegi; Oner, Erkan
    This study investigates the phenolic compounds (PC), volatile compounds (VC), and fatty acids (FA) of extra virgin olive oil (EVOO) derived from the Turkish olive variety Sar & imath; Ulak, along with ADMET, DFT, molecular docking, and gene network analyses of significant molecules identified within the EVOO. Chromatographic methods (GC-FID, HPLC) were employed to characterize FA, PC, and VC profiles, while quality parameters, antioxidant activities (TAC, ABTS, DPPH) were assessed via spectrophotometry. The analysis revealed a complex composition of 40 volatile compounds, with estragole, 7-hydroxyheptene-1, and 3-methoxycinnamaldehyde as the primary components. Hydroxytyrosol, tyrosol, oleuropein, apigenin, ferulic acid, and vanillic acid emerged as main phenolic constituents, with hydroxytyrosol and apigenin exhibiting high bioavailability. Molecular docking highlighted oleuropein and pinoresinol as compounds with strong binding affinities, though only hydroxytyrosol, apigenin, and pinoresinol fully met Lipinski and other drug-likeness criteria. DFT analysis showed that oleuropein and pinoresinol have notable dipole moments, reflecting polar and asymmetrical structures. KEGG enrichment analysis further linked key molecules like oleuropein and apigenin with pathways related to lipid metabolism and atherosclerosis, underscoring their potential bioactivity and relevance in health-related applications.
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    Experimental and theoretical study on hydrogen production by using Ag nanoparticle-decorated graphite/Ni cathode
    (Wiley, 2021) Yildiz, Resit; Dogru Mert, Basak; Karazehir, Tolga; Gurdal, Yeliz; Toprak Doslu, Serap
    In this study, graphite (G) electrode was coated with nickel and decorated with silver nanoparticles (G/Ni/Ag) with the help of galvanostatic method, and electrodes were used as a cathode in alkaline water electrolysis system. The characterization was achieved using X-ray diffraction and field emission scanning electron microscopy. Hydrogen evolution performance of electrodes was investigated via cyclic voltammetry, chronoamperometry, cathodic polarization curves, and electrochemical impedance measurements. Electrochemical results showed that hydrogen production efficiency significantly increased and charge transfer resistance decreased via G/Ni/Ag. The electrochemical water splitting performance of G/Ni/Ag, was established in a joint experimental and computational effort. Water and proton adsorption on Ag-decorated Ni surface were investigated using density functional theory. Electronic structure calculations identified the role of Ag adatom and Ni surface on water and proton adsorptions. From the computational studies, O in water was more reliable to adsorb at the bridge position of the Ag and Ni atoms, leading improved orbital overlap between H and Ni atoms and maximized chemical and physical interactions between the H2O molecules. Therefore, the Ag-decorated Ni(111) surface provides preferable adsorption site for the O atom in water and direct interactions between water Hs and available surface Ni atoms promote water dissociation.
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    Experimental and theoretical study on hydrogen production by using Ag nanoparticle-decorated graphite/Ni cathode
    (Wiley, 2021) Yildiz, Resit; Dogru Mert, Basak; Karazehir, Tolga; Gurdal, Yeliz; Toprak Doslu, Serap
    In this study, graphite (G) electrode was coated with nickel and decorated with silver nanoparticles (G/Ni/Ag) with the help of galvanostatic method, and electrodes were used as a cathode in alkaline water electrolysis system. The characterization was achieved using X-ray diffraction and field emission scanning electron microscopy. Hydrogen evolution performance of electrodes was investigated via cyclic voltammetry, chronoamperometry, cathodic polarization curves, and electrochemical impedance measurements. Electrochemical results showed that hydrogen production efficiency significantly increased and charge transfer resistance decreased via G/Ni/Ag. The electrochemical water splitting performance of G/Ni/Ag, was established in a joint experimental and computational effort. Water and proton adsorption on Ag-decorated Ni surface were investigated using density functional theory. Electronic structure calculations identified the role of Ag adatom and Ni surface on water and proton adsorptions. From the computational studies, O in water was more reliable to adsorb at the bridge position of the Ag and Ni atoms, leading improved orbital overlap between H and Ni atoms and maximized chemical and physical interactions between the H2O molecules. Therefore, the Ag-decorated Ni(111) surface provides preferable adsorption site for the O atom in water and direct interactions between water Hs and available surface Ni atoms promote water dissociation.
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    Theoretical and experimental investigations on corrosion control of mild steel in hydrochloric acid solution by 4-aminothiophenol
    (Emerald Group Publishing Ltd, 2019) Yildiz, Resit; Mert, Basak Dogru
    Purpose This paper aims to study inhibitory effect of 4-aminothiophenol on the corrosion of mild steel (MS) in 0.5 M HCl. Design/methodology/approach In this study, electrochemical experiments, quantum chemical calculations, potentiodynamic measurements, linear polarization resistance and scanning electron microscopy were used. Findings The experimental results suggest that this compound is efficient corrosion inhibitor and the inhibition efficiencies increase with increasing their (from 0.5 to 10.0 mM.) concentrations. This reveals that inhibitive actions of inhibitors were mainly due to adsorption on mild steel surface. The adsorption of these inhibitors was found to obey Langmuir adsorption model. The computed quantum chemical features show good correlation with empirical inhibition efficiencies. Originality/value The 4-aminothiophenol is suitable inhibitor for application in closed-circuit systems against corrosion. The study is original and has great impact in industrial area. The obtained theoretical results have been adapted with the experimental data.
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    Theoretical and experimental investigations on corrosion control of mild steel in hydrochloric acid solution by 4-aminothiophenol
    (Emerald Group Publishing Ltd, 2019) Yildiz, Resit; Mert, Basak Dogru
    Purpose This paper aims to study inhibitory effect of 4-aminothiophenol on the corrosion of mild steel (MS) in 0.5 M HCl. Design/methodology/approach In this study, electrochemical experiments, quantum chemical calculations, potentiodynamic measurements, linear polarization resistance and scanning electron microscopy were used. Findings The experimental results suggest that this compound is efficient corrosion inhibitor and the inhibition efficiencies increase with increasing their (from 0.5 to 10.0 mM.) concentrations. This reveals that inhibitive actions of inhibitors were mainly due to adsorption on mild steel surface. The adsorption of these inhibitors was found to obey Langmuir adsorption model. The computed quantum chemical features show good correlation with empirical inhibition efficiencies. Originality/value The 4-aminothiophenol is suitable inhibitor for application in closed-circuit systems against corrosion. The study is original and has great impact in industrial area. The obtained theoretical results have been adapted with the experimental data.