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    Antioxidant enzyme activities, molecular docking studies, MM-GBSA, and molecular dynamic of chlorpyrifos in freshwater fish Capoeta umbla
    (Taylor & Francis Inc, 2024) Taysi, Mehmet Resit; Kirici, Muammer; Kirici, Mahinur; Tuzun, Burak; Poustforoosh, Alireza
    Chlorpyrifos (CPF), which was started to be used in 1965, is a broad spectrum organophosphate insecticide that is used more and more day by day. Commonly used to control pests in farmland and homes, CPF is more toxic to fish than organochlorine compounds. CPF poses a serious threat to the health of humans and aquatic organisms. This paper studies the relationship between CPF exposure and antioxidant enzyme activities in gill, kidney and liver tissues of Capoeta umbla. Different time intervals (12, 24, 48, 72, and 96 h) and CPF doses (55 and 110 mu g L-1) were used in the study. Spectrophotometrical measures were taken in all tissues for antioxidant enzyme activities and malondialdehyde (MDA) levels, as indices of the lipid peroxidation (LPO). A positive relationship between CPF and MDA levels was found in the study at a statistically significant level (p < 0.05). The study also found a negative relationship between CPF levels and catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), and glutathione reductase (GR) activity. Independent variables in the study can act as biomarkers of CPF exposure. The study recommends employing proper ecotoxicological risk evaluations in cases of CPF usage as a pesticide. The activities of the studied molecules against various proteins that are crystal structure of human peroxiredoxin 5 (PDB ID: 1HD2) has docking score value is -2.67, crystal structure of Bovine Xanthine Oxidase (PDB ID: 3NRZ) has docking score value is -3.76, and crystal structure of antibacterial FabH (PDB ID: 4Z8D) has docking score value is -3.16, were compared. Molecular dynamic (MD) calculations were made in 100 ns. MM/GBSA methods are calculated binding free energy. Afterwards, ADME/T analysis was performed to examine the some properties of the molecules.Communicated by Ramaswamy H. Sarma
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    Biological effects and molecular docking studies of Catechin 5-O-gallate: antioxidant, anticholinergics, antiepileptic and antidiabetic potentials
    (Journal of Biomolecular Structure and Dynamics, 04.10.2020) Taslimi, Parham; Kocyigit, Umit M.; Tüzün,Burak; Kirici, Mahinur
    Gallocatechin gallate is a form of catechin and an ester of gallocatechin and gallic acid. This is an epimer of the gallate epigallocatechin. In this study, the effect of this molecule, containing a biologically active group, was investigated in terms of important metabolic enzymes (carbonic anhydrase isoenzymes I and II (hCA I and II), achethylcholinesterase (AChE) and a-glycosidase (a-Gly) enzymes). The molecular docking method used to compare the biological activities of the Catechin 5-O-gallate molecule against enzymes was used. Afterwards, the ADME/T analysis was performed to investigate the drug availability of the Catechin 5-O-gallate molecule and the parameters obtained from ADME/T analysis were examined. Continuation of this study, for evaluating antioxidant and radical scavenging capacity Catechin 5-O-gallate, cupric ion (Cu2þ) reduction capacity by CUPRAC method, Fe3þ-Fe2þ reducing capacity, DPPH free radical clarifying (DPPH· ), ABTS radical clarifying (ABTS þ) were performed separately and during the study, trolox, a-tocopherol BHT and BHA were used as the reference antioxidant compound. Comparisons were applied with the four standard substances. Abbreviations: ADME: absorption, distribution, metabolism and excretion; ACR: acarbose; AZA: acetazolamide; AChE: achethylcholinesterase; ABTS: 2, 2’-azino-Bis-3-ethylbenzothiazoline-6-sulfonic acid (biochemical reagent); a-Gly: a-glycosidase; BHA: butylated hydroxyanisole; BHT: butylated hydroxytoluene; BChE: butyrylcholinesterase; CA: carbonic anhydrase; CUPRAC: cupric reducing antioxidant capacity; DPPH: 2,2-diphenyl-1-picrylhydrazyl; EGCG: gallate epigallocatechin; GA: gallic acid; GCG: gallocatechin gallate
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    In vitro anticancer, antioxidant and enzyme inhibitory potentials of endemic Cephalaria elazigensis var. purpurea with in silico studies
    (Taylor & Francis Inc, 2023) Erdogan, Mehmet Kadir; Gundogdu, Ramazan; Yapar, Yakup; Gecibesler, Ibrahim Halil; Kirici, Mahinur; Behcet, Lutfi; Tuzun, Burak
    In this study, the therapeutic potential and phytochemical composition of ethanolic extract of Cephalaria elazigensis var. purpurea (CE), an endemic species, were investigated. For this purpose, the antiproliferative effect of CE on the MCF-7 human breast cancer cell line was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, and its effectiveness on colony formation and cell migration was analyzed with clonogenic assay and wound healing assay, respectively. In addition, the cell death detection ELISA (CDDE) assay was conducted to determine the pro-apoptotic capacity of CE. The IC50 value of the CE was determined as 324.2 +/- 14.7 mu g/mL. Furthermore, upon 1000 mu g/mL CE treatment, there was 4.96-fold increase in the population of cells undergoing apoptosis compared to the untreated control cells. The antioxidant activity tests were performed by DPPH free radical, ABTS cation radical, ferric-ion reducing power (FRAP) and ferrous-ion chelating power (FCAP) assays. Antioxidant activity values for the DPPH, ABTS and FRAP assays were found to be 125.6 +/- 6.3, 34.09 +/- 0.1 and 123.4 +/- 4.2 mu mol TE/mg DE, respectively. We further determined the effect of CE ethanolic extract against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes. CE plays an effective inhibitory role in AChE and BuChE (AChE: IC50: 10.54 mu g/mL, BuChE: IC50: 6.84 mu g/mL) respectively. Further, molecular docking stuy was conducted to understand the nature of the all compound against AChE an BChE. It is revealed that alpha-Linolenic acid shows lowest binding energy (-7.90 kcal/mol) towards AChE, on the other side, Linoleic acid shows good binding affinity (-7.40 kcal/mol) for BChE.Communicated by Ramaswamy H. Sarma
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    Phenolic Compounds: Investigating Their Anti-Carbonic Anhydrase, Anti-Cholinesterase, Anticancer, Anticholinergic, and Antiepileptic Properties Through Molecular Docking, MM-GBSA, and Dynamics Analyses
    (Korean Institute Chemical Engineers, 2025) Akkus, Musa; Kirici, Mahinur; Poustforoosh, Alireza; Erdogan, Mehmet Kadir; Gundogdu, Ramazan; Tuzun, Burak; Taslimi, Parham
    Phenolic compounds are a new class of Carbonic Anhydrase inhibitors (CAIs). Despite numerous advancements in treatment approaches, cancer continues to be a growing health problem worldwide. In our study, we tested the effects of 4-hydroxy-3-methoxyacetophenone (1), doxycycline hydrochloride (2), 5,7-dichloro-8-hydroxyquinoline (3), methyl 3,4,5-trihydroxybenzoate (4), 2-hydroxy-4-methylacetophenone (5), 6-hydroxy-4-methylcoumarin (6), and 2,5-dihydroxyacetophenone (7) on Achetylcholynesterase (AChE), Butrycholynesterase (BChE), and Human Carbonic anhydrase I (hCA I) enzymes. The U2OS human osteosarcoma cell line was used to determine the anticancer potential of these phenolic compounds. The effects of the compounds on proliferation and colony formation were analyzed using the Neutral Red Uptake (NRU) assay and the clonogenic assay. The Ki values of arachidonoyl dopamine, 2,4,6-trihydroxybenzaldehyde, and 3,4-dihydroxy-5-methoxybenzoic acid were 203.80, 1170.00, and 910.00 mM, respectively, for hCA I, and 75.25, 354.00, and 1510.00 mM, respectively, for Human Carbonic anhydrase II (hCA II). Additionally, IC50 values from in vivo studies were found to range from 173.25 to 1360.00 mM for CA I and CA II, respectively, using CO2-hydratase activity methods. The NRU assay results revealed that the compounds had a dose-dependent cytotoxic effect on U2OS cells. The IC50 values of the compounds in U2OS osteosarcoma cells were determined to be > 100, 93.7, 81.4, 26.9, > 100, 53.1, and > 100 mu M, respectively. Notably, methyl 3,4,5-trihydroxybenzoate (4), the compound with the lowest IC50 value, significantly suppressed colony formation at 5 and 10 mu M concentrations. These results demonstrated that the phenolic compounds used in in vivo studies could inhibit approximately 30% of the CO2-hydratase activity of the total CA enzyme of rat erythrocytes. Furthermore, the anticancer potential of the tested compounds suggests that these molecules could pave the way for the development of new approaches in cancer treatment. The activities of the seven molecules studied were compared against AChE (PDB ID: 4M0E), BChE (PDB ID: 5NN0), hCA I (PDB ID: 2CAB), and E3 ubiquitin-protein ligase (PDB ID: 4HG7) proteins. The binding free energy of the molecule with the highest docking score is computed using MM/GBSA techniques. Finally, molecular dynamics simulations were performed between 6-hydroxy-4-methylcoumarin and the 4M0E protein over a 0-200 ns interval.
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    The Evaluation of Anticancer, Antioxidant, Antidiabetic and Anticholinergic Potentials of Endemic Rhabdosciadium microcalycinum Supported by Molecular Docking Study
    (Wiley-V C H Verlag Gmbh, 2022) Erdogan, Mehmet Kadir; Gundogdu, Ramazan; Yapar, Yakup; Gecibesler, Ibrahim Halil; Kirici, Mahinur; Behcet, Lutfi; Tuzun, Burak
    Lung cancer is the most common cancer worldwide and the leading cause of cancer-related death. Plant-derived natural products and compounds are an inspiring source of chemotherapeutic agents. Alzheimer's disease (AD) is linked to the decline of acetylcholine (ACh) effects in the brain, so acetylcholinesterase (AChE) inhibitors are important in the treatment of AD. In this study, the chemical components and bioactivity of ethanolic extract of Rhabdosciadium microcalycinum (RM) was investigated by various methods. The lipophilic components of RM was determined by gas chromagraphy-mass spectrometry (GC-MS). Antioxidant activicty tests were evaluated with FCAP (Ferrous chelating antioxidant power assay), FRAP (Ferric reducing antioxidant power assay), ABTS (2,2 '-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt assay) and DPPH (2,2-diphenyl-1-picrylhydrazyl assay). The anticancer effect of RM was evaluated by WST-1 (4-[3-(4-iodophenyl)-2-(4-nitrophenyl)-2H-5-tetrazolio]-1,3-benzene disulfonate), colony formation, wound healing and CDDE (cell death detection Elisa) analysis on A549 lung cancer cells. Enzyme inhibition effects of RM was determined against AChE and alpha-glycosidase (AG) enzymes. According to the results of molecular docking found in the study; With a docking score of -4.56 for HP5 protein, -6.23 for BXO protein, -5.25 for AFI protein, -3.90 for gly protein and -7.74 for AChE protein, Telecinobufagin molecule was found to have higher activity than other molecules. After docking calculations, Absorption, Distribution, Metabolism, Excretion and Toxicity (ADME/T) analysis was performed to examine the effects and reactions of molecules on human metabolism. RM inhibited the viability of A549 cells dose-dependent manner (IC50=117.15 +/- 8.58 mu g/mL), and it was also observed that RM suppressed colony formation, prevented cell migration and directed the cells to apoptosis. RM has important lipophilic components, and significant antioxidant and enzyme inhibition potential. IC50 values of RM for AChE and AG enzymes were found as 35.86 mg/mL, and 10.14 mg/mL, respectively. In conclusion, the findings of this study reveal that ethanol extract from the aerial part of Rhabdosciadium microcalycinum may be a potential therapeutic agent for the treatment of human lung cancer and Alzheimer's disease, due to its phytochemical components.
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    The impact of some metals, molecular docking and molecular dynamic calculations on glucose 6-phosphate dehydrogenase activity in Capoeta trutta (Heckel, 1843) tissue
    (Elsevier, 2024) Kirici, Muammer; Tuzun, Burak; Kirici, Mahinur; Atamanalp, Muhammed; Poustforoosh, Alireza; Beydemir, Sukru; Taysi, Mehmet Resit
    The first enzyme of the pentose phosphate metabolic pathway is glucose 6 -phosphate dehydrogenase (d -glucose6 -phosphate: NADP + oxidoreductase EC1.1.1.49; G6PD). G6PD has essential functions such as membrane lipid synthesis, ribose 5 -phosphate, and NADPH production. In this study, the G6PD enzyme was purified from kidney, liver, and gill tissues of Capoeta trutta, one of the dominant fish species in the Euphrates -Tigris River System, and the in vitro effects of some metals (Ag+, Cd2+, Cu2+, Fe2+, Ni2+, Pb2+ and Zn2+) on the enzyme activity were investigated. For this purpose, firstly, the G6PD enzyme was purified from tissues using a 2 ', 5 '-ADP Sepharose 4B affinity column. The purity of the enzyme was checked by the SDS-PAGE method and a single band was seen in the gel. After the purity of the enzyme was determined, the effects of metals on the enzyme activity were determined using the spectrophotometric method. As a result of the study, it was determined that the Ag+ ion was the most potent inhibitor for C. trutta gill, kidney, and liver G6PD enzymes. Lastly, calculations were made to examine the activity of the glucose 6 -phosphate dehydrogenase molecule against the G6PD enzymes. Afterwards, the interaction of the glucose 6 -phosphate dehydrogenase molecule with the protein (PDB ID: 5JYU and 2BH9) with the highest activity was calculated in the range of 0-100 ns. Finally, ADME/T calculation was made to predict the effects and reactions of glucose 6 -phosphate dehydrogenase molecule in human metabolism. This study explores the physiological functions and environmental sensitivities of G6PD in a dominant fish species, while also investigating its potential interactions and metabolic roles in humans. Understanding these aspects can contribute to environmental monitoring, fish health management, and even pharmaceutical development.