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Öğe A Study on Natural Control against Nematodes and Whiteflies with Marigold, Known as an Antagonist Plant(Springer, 2023) Gökalp, FaikThe importance of finding natural solutions for the protection of our health in the fight against pests in agriculture is increasing day by day. In this study, the interaction of the active ingredients in marigolds as the great importance as a garden flower, with nematode and whitefly receptors as ligands in the fight against them, have been investigated by chemical calculation method. The inhibition effect of ligands (alpha-Terthienyl, Quercetagetin in marigold) on nematode and whitefly receptors in this plant was determined by comparing the binding energy values with reference drug active ingredients (imidacloprid, Perhexiline).This calculation method, the accuracy determined by different studies, is very important in terms of determining the most active substance in a short time, preventing time and substance loss, and will guide the experimental studies and applications to be made in this field.Öğe A Theoretical Investigation of TNT in Different Phases by Using DFT(DergiPark, 2019) Gökalp, Faik2,4,6-Trinitrotoluene (TNT) is an important aromatic organic based explosives. The computational analysis of the effect of phases (ethanol, methanol, and water) is essential to determine the sensitivity of it. In this study; I investigate the stability, the reactivity of TNT in different phases by using density functional theory (DFT). The results suggest optimization approaches for TNT based on DFT methods B3LYP functional and 6-31G containing polarizing functions (d,p) basis set for these explosives by selecting the sensitive phase of the explosive analyte. © 2019. All Rights Reserved.Öğe A theoretical overview of heavy metal treatment with agricultural wastes(2020) Gökalp, FaikTomato plant between Pb2+, Cd 2+ with tomato waste having amino and the other functional groups waste contain cellulose materials(lignin), polysaccharides having functional groups having the ability of binding heavy metals as sorbents is commonly cultivated plant for its fruits. Aim of this study to determine the best alternative way to search the binding capacity of agricultural waste as theoretical to remove heavy metals with tomato plant from waste waters as economically by comparing experimental results respectively. The capacities of adsorption for heavy metals (Pb(II), Cu(II) and Cd(II)) of the tomato plant residue were 0.092, 0.533 and 0.238 mmol/g sorbent. As theoretical, HF (Hartree-fock), lanl2dz methods were used for molecular calculation. The theoretical calculations were carried out by means of the lanl2dz functional base. The chemical activities were calculated by using this method. The removal of Pb2+ and Cd2+ found lower than Cu2+ because of the strong complex formation as experimental and theoretical calculations supported this issue. Theoretical calculations are important to prevent loss of time and cost.Keywords: Pb(II), Cu(II) ,Cd(II), biomass,HF, docking, heavy metalsÖğe An investigation into the usage of black cumin derivatives against cancer and COVID-19 as the nature medicine(Taylor & Francis Inc, 2024) Gökalp, FaikBlack cumin has been used as a spice and food preservative for years. Thymol, thymoquinone, thymohydroquinone and dihydrothymoquinone are the most important natural agents in black cumin. In order to determine the most active compound in black cumin the theoretical calculations have been carried out in different phases by using the density functional theory (DFT). The inhibition effect of black cumin derivatives on Histone deacetylase 2 (HDAC2) has been determined and supported the experimental studies without losing time and matter. The chemical activity, stability and solubility of the active substances in black cumin have been theoretically calculated. The chemical active compounds had been investigated in the black seeds when extracted with water. Their stability and polarity in blood and water are important parameters. HDAC2- dihydrothymoquinone interaction has been investigated. It has been determined that the active substances found in black cumin are very effective in protecting ACE2 against COVID-19 and by comparing the docking results of important receptors and selected ligands on COVID-19.Öğe An Investigation into the Usage of Monosaccharides with GLUT1 and GLUT3 as Prognostic Indicators for Cancer(Routledge Journals, Taylor & Francis Ltd, 2022) Gökalp, FaikThe monosaccharides, glucose, fructose and galactose, are the most common and simplest forms of carbohydrates. The aim of this study was to determine the uptake of glucose as a potential therapeutic target agent for cancer treatment. The stability and transportation calculations of the monosaccharides were carried out in the blood phase by using the density functional theory and docking. The reactivity of monosaccharides, disaccharides and their transportation with GLUT1 and GLUT3 as prognostic indicators for cancer were investigated. The theoretical results of this study were supported by those reported in the literature and used in the prediction of the mechanisms of monosaccharides and the interpretation of their reactivities.Öğe Composition characterization and biological activity study of Thymbra spicata l. var. spicata essential oil(2021) Eruygur, Nuraniye; Kocyıgıt, Umit M.; Atas, Mehmet; Cevık, Ozge; Gökalp, Faik; Taslimi, Parham; Gulcın, İlhamiThe current research aimed to determine and report in vitro antioxidant, antimicrobial, antibiofilm, cytotoxic, anti-cholinesterase, and anti-diabetic properties and the stability of the major component of basic oil of Thymbra spicata var. spicata through different phases as theoretically. Essential oil exhibits potential biological activities because of the multiple components it contains.In the current research, the evaluation of Thymbra spicata essential oil antioxidant properties was conducted utilizing 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2- azinobis[3-ethylbenzthiazoline]-6-sulfonic acid (ABTS) radical scavenging activity.Antimicrobial activity was assessed from minimum inhibition concentration (MIC) using the technique of microdilution and cytotoxicity activity was evaluated by MTT assay through MCF-7 and PC3 human cancer cell lines.Consequently, Cytotoxic activity was evaluated by means of MTT assay utilized. The essential oil was detected to have 340 ?g/mL inhibiting influence on the growth of PC3 prostate cancer cells with IC50 value. Also, the T. spicata plant was observed to significantly repress the enzymes, namely acetylcholinesterase (AChE), butyrylcholinesterase (BChE), ?-glycosidase. IC50 values of enzymes were obtained 0.23 ?g/mL for AChE, 1.64 ?g/mL for BChE, 7.78 ?g/mL for ?-glycosidase. It was concluded that this plant may be used for Alzheimer's and diabetes disease.Öğe Evaluation of Anticholinergic, Antidiabetic and Antioxidant Activity of Astragalus dumanii, an Endemic Plant(Kahramanmaras Sutcu Imam Univ Rektorlugu, 2022) Koçyiğit, Ümit Muhammet; Eruygur, Nuraniye; Ataş, Mehmet; Tekin, Mehmet; Taslimi, Parham; Gökalp, Faik; Gülçin, İlhamiThe research was conducted to separately evaluate and detect the possible in vitro antioxidant, antimicrobial activity of ethanol extracts prepared from aerial parts and roots of Astragalus dumanii and anti-cholinesterase and alpha-glucosidase inhibitory activity from only aerial parts of its The antioxidant capacity was tested by scavenging of DPPH and ABTS free radicals. Compared with the standard antioxidant compound gallic acid; Root and aerial part extract showed lower DPPH radical scavenging activity, however aerial part extract demonstrated higher ABTS radical scavenging activity. The phenolic contents were detected as 5.31 +/- 0.03 and 13.23 +/- 0.05 mg gallic acid equivalent g-1 extract, flavonoid contents were found as 8.26 +/- 0.004 and 7.93 +/- 0.005 mg Qercetin equivalent g-1 extract. In addition, the effects of the extracts obtained from aerial parts of the plant on acetylcholinesterase, butyrylcholinesterase and a-glycosidase enzymes were investigated in vitro and IC50 values were obtained as 1.47, 0.83 and 0.48 mu g mL-1, respectively. When these values were compared with standard substances, it was seen that Astragalus dumanii could be a good enzyme inhibitory agent. Antimicrobial activity of the plant extracts were determined using the microdilution method and the extracts was not observed to have any antimicrobial activities..Öğe The inhibition effect of natural food supplement active ingredients on TP63 carcinoma cell(HUMANA PRESS INC, 2020) Gökalp, FaikIn pancreatic cancer, the activities of inhibitory agents were investigated using docking, since the inhibition of TP63, which plays an important role in the spread of cancer with metastasis, in preventing the proliferation and proliferation of this type of cancer. It has been shown that the active ingredients in some plants used as traditional medicines have an inhibitory effect on this cancer type in preventing growth, reproduction and spread. These computational results guide experimental studies, preventing time and item loss; It is an important study in terms of choosing and using the right active substances.Öğe The Investigation Of Menthol's Bioactivity As Theoritical By Using DFT (Density Functional Theory)(2015) Gökalp, FaikMints are used tradational medicine for hundred years by humankind. The important constitiuent of mint, menthol, is especially in blood is eager to give reaction as an antioksidan. To understand menthol's bioactivity in body, some thermodynamical values (gibbs free energy, dipol moment HOMO, LUMO and the difference between HOMO, LUMO) of menthol are measured by using DFT. Menthol dissolves in blood easily, reacts as antioksidant and it is more stable than in gas form. So,It is so stable as protecting from radicalic attractsÖğe Purification of glutathione S-transferase enzyme from quail liver tissue and inhibition effects of (3aR,4S,7R,7aS)-2-(4-((E)-3-(aryl)acryloyl)phenyl)-3a,4,7,7a-tetrahydro-1H-4,7-methanoisoindole-1,3(2H)-dione derivatives on the enzyme activity(Wiley, 2018) Temel, Yusuf; Koçyigit, Ümit M.; Taysi, M. Şerif; Gökalp, Faik; Gürdere, Meliha Burcu; Budak, Yakup; Çiftci, MehmetThe use of quail meat and eggs has made this animal important in recent years, with its low cost and high yields. Glutathione S-transferases (GST, E.C.2.5.1.18) are an important enzyme family, which play a critical role in detoxification system. In our study, GST was purified from quail liver tissue with 47.88-fold purification and 12.33% recovery by glutathione agarose affinity chromatography. The purity of enzyme was checked by SDS-PAGE method and showed a single band. In addition, inhibition effects of (3aR,4S,7R,7aS)-2-(4-((E)-3-(aryl)acryloyl)phenyl)-3a,4,7,7a-tetrahydro-1H-4,7methanoisoindole-1,3(2H)-dion derivatives (1a-g) were investigated on the enzyme activity. The inhibition parameters (IC50 and K-i values) were calculated for these compounds. IC50 values of these derivatives (1a-e) were found as 23.00, 15.75, 115.50, 10.00, and 28.75M, respectively. K-i values of these derivatives (1a-e) were calculated in the range of 3.04 +/- 0.50 to 131.50 +/- 32.50M. However, for f and g compounds, the inhibition effects on the enzyme were not found.Öğe A Study on Piperine, Active Compound of Black Pepper(2016) Gökalp, FaikPiperine, the most important compound of black pepper, is used for treating several diseases such as breast, colon, rectal, and stomach cancer. In this study, the thermodynamical properties of this molecule in blood were obtained by using DFT and HF at the level of B3LYP/6-31+g(d,p). The results of calculations are supported with the experimental literatüre knowledges. DFT and HF basis set calculations support to the each other as comparing theoretical calculations of the interactions taking place within the molecular species.Öğe The curative effect of some natural active compounds for liver cancer(Humana Press Inc, 2022) Gökalp, FaikCancer is a disease that has become widespread recently and has been studied extensively. It is of great importance to find an active and effective treatment quickly due to the emergence of the disease and its spread to many tissues in the organism by metastasis. In this study, it is aimed to detect active and active substances that are highly effective on cancer cells in a short time by using docking scores, the accuracy of which has been proven by many studies. Today, many medicinal plants are being studied for therapeutic purposes. In this study, the activities of the prominent active substances in these medicinal plants were compared with the docking scores and the molecules with the highest inhibition effect on liver cancer receptors were determined. The data obtained in this study are of great importance in terms of guiding experimental studies by detecting active substances effective on liver cancer by preventing time and material loss. Considering the results obtained from this study, it can be concluded that Cucurbitacin I and Cucurbitacin E, Thymol, Piperine, and Carvacrol are very effective for the inhibition of liver cancer cell receptors.Öğe The Effective Ethanol Rate Against the Toxicity of Ethylene Glycol(DergiPark, 2021) Gökalp, FaikEthylene glycol (EG) is a toxic substance and EG metabolites cause metabolic acidosis. The major emphasis in this study is to get rid of the toxicity of EG before conversion to its metabolites. The interaction between ethylene glycol and ethanol has been studied using DFT (Density functional theory method). In ethylene glycol metabolites in the blood; Glycolic acid is more stable and gloxal less stable. The interaction of ethylene glycol with ethanol has been considered for ethylene glycol metabolism. Thermodynamic values obtained from ethylene glycol metabolites and ethanol were also analyzed. According to the analyst results of ethanol and ethylene glycol ratios; The maximum effective point is very stable in the blood and its solubility is determined at this rate. It is very important to determine the most appropriate rate in the prevention of toxicity. This study is an important study in terms of the use of ethanol in the prevention of toxicity of EG, the first of its rates and in terms of preventing the loss of time and substance. © 2021. All Rights Reserved.Öğe The effective natural compounds for inhibiting Cervical cancer(Humana Press Inc, 2021) Gökalp, FaikThe secondary compounds found in plants are of great importance in the treatment of many diseases in medicine and pharmacy. Some of these compounds have been reported to exhibit anticarcinogenic effects by inhibiting the growth and metastatic potential of cancer cells. Consumption of the required amount of vegetables and fruits appears to have a protective effect of these secondary compounds on cancer, since most of these drugs are synthesized from natural or natural origin compounds. Secondary compounds in medicinal plants have been found to have an antiproliferative effect by increasing the expression of p53 in cervical cancer cells and decreasing the expression of cyclin D1, one of the cell proliferation markers. The most important step in the fight against cancer is the development of drugs that are selectively targeted against tumor cells and targeting cancer cells to reduce damage to normal cells and prevent the growth and spread of cancer cells. Molecular insertion test is an effective tool for evaluating the bioactivity of possible molecules. In this study, the effect of natural compounds in some medicinal plants in inhibiting cervical cancer, the points where they are effective using docking has been investigated.Öğe The highly protective natural medical agents against COVID-19(Aepress Sro, 2021) Gökalp, Faik; Sayın, K.OBJECTIVE: The studies to prevent the Corona virus, which is a huge epidemic nowadays and causes the death of many people, are of great importance. Drugs to be developed to prevent the proliferation and spread of it. The active substances of the drugs have been used to prevent the attack of the COVID-19. The natural phytochemicals obtained from the traditional medicine play a big role in the inhibition of functional structures in many harmful microscopic structures. METHODS: The active role of the substances for protecting from the attack of COVID-19 have been calculated and determined by using docking. RESULTS: It has been clarified that drug active substances inhibit COVID-19. The selected active ingredients seem to have considerable inhibition effects for COVID-19. Molecular mechanical Poisson-Boltzman (MM-PSBA) calculations were used to analyse the selected molecules. CONCLUSION: This study is the first in terms of reducing the harmful effect of COVID-19 by providing effective results in a short time by guiding the experimental studies to reveal the inhibitory effect of COVID-19 Ref. Text in PDF www.elis.skÖğe Therapeutic effect of some natural active compounds for breast cancer(Humana Press Inc, 2022) Gökalp, FaikThe extracts obtained from plants have been used in the treatment of many diseases since the earliest times. Today, it is of great importance to investigate the effects of the active molecules in these plant extracts at the molecular level together with the analysis. The effect of certain active compounds found in some plants, widely used as medicinal plants, on breast cancer has been investigated using docking. As a result of the docking scores obtained, it can be understood that the active molecules used in this study can be quite effective in controlling breast cancer. Promyelocytic leukemia is an important checkpoint from the literature for breast cancer and the docking energy values of Thymoquinone, Piperine and Carvacrol, as the active molecules in the control of this pathway. This study is very important when evaluated in terms of directing experimental studies by determining the most suitable active substances by comparing the activities of molecules in a short time.Öğe Zeytin Etken Maddesi Olan Oleuropein’in Kimyasal Aktivitesinin Teorik Olarak Araştırılması(2017) Gökalp, FaikBu çalışmanın amacı: zeytinin yapraklarında, olgunlaşmamış meyvelerinde bulunan ona acı tadı veren oleuropein ile önemli bir etken madde olan timolün termodinamiksel özellikleri, kimyasal aktiflik parametrelerinin (?G, HOMO, LUMO, ?(HOMO-LUMO), dipol moment) hesaplanmasıdır. Ayrıca bu değerlerin karşılaştırmasıyla birlikte radikalik yapılara karşı reaktif olup olmadıklarının tespit edilerek bununla ilgili yapılacak deneysel çalışmalara yön verilmesidir. Hesaplama yöntemi olarak RHF yöntemi kullanılmıştır. Bu yöntemler ve temel küme kullanılarak bileşiklerin tam optimize geometrik yapıları belirlenerek kimyasal aktivitesi değerlendirilmiştir. Hesaplamalarda Gaussian09W paket programından yararlanılmıştır. Bu yöntemi seçmemizin nedeni; molekülümüzün özelliklerini kısa sürede teorik olarak görmek, diğer yandan madde ve zaman kaybını önlemesi açısından oldukça önemli ve tercih edilebilir bir yöntem olmasıdır. Diğer önemli bir etken antioksidan madde olan timol ile karşılaştırıldığında; Oleuropeinde ki fenolik yapılardan dolayı kararsız özellikle radikalik yapılara karşı reaksiyon vermeye yatkın olduğu görülmektedir. Sonuç olarak; Oleuropein'in RHF ile yapılan hesaplamalarından elde edilen veriler ışığında; fenolik yapılardan dolayı kararsız, reaksiyon vermeye yatkın olduğunu ve metabolizmada zararlı mikroorganizmaların hücre yapısını bozarak antimikrobiyal etkili olacağı söylenebilir
