Biyoinformatik ve Genetik Bölümü Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12469/46

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"2-pirazolin Yapısındaki Yeni Bir Bileşiğin Sentezi, Moleküler Modellemesi ve Monoaminoksidaz İnhibitörü Etkisinin Araştırılması"
(Türkiye Halk Sağlığı Kurumu, 2018) Aksöz Evranos, Begüm; Uçar, Gülberk; Yelekçi, Kemal
Amaç: Nöromediatörlerin yıkımından sorumlu olan monoamin oksidaz (MAO) enziminin izoformlarının (MAO-A ve -B) birçok hastalık ile yakından ilişkili olduğu; MAO inhibitörlerinin depresyon, Parkinson ve Alzheimer hastalığı gibi hastalıkların tedavisinde kullanıldığı bilinmektedir. Grubumuzca daha etkin, tersinir ve az yan etkili yeni bir MAO inhibitörü (SH2U bileşiği) sentezlenmiş ve bu bileşiğin insan MAO enzimini (hMAO) inhibe etme yeteneği incelenmiştir. Ayrıca bu yeni bileşiğin hMAO ile etkileşimi, moleküler modelleme çalışmaları ile detaylı bir şekilde araştırılmıştır. Sentezlenen yeni bileşiğin hMAO’yu kuvvetli bir şekilde yarışmalı ve tersinir olarak inhibe ettiği bulunmuştur. Söz konusu bileşiğin Parkinson ve Alzheimer hastalıklarının tedavisinde ümit verici bir ilaç etken maddesi olabileceği düşünülmektedir. Yöntem: 3’,5’-Dikloro-2’-hidroksi asetofenon ile p-tolualdehit’in metanol içinde KOH varlığında reaksiyona girmesiyle 1-(3,5-dikloro-2-hidroksifenil)- 3-p-tolil prop-2-en-1-on (3’,5’-Dikloro-2’-hidroksi-4- metil şalkon) bileşiği sentez edilmiştir. Daha sonra elde edilen bu bileşiğin etanol içerisinde geri çeviren soğutucu altında izonikotinik asit hidrazit ile muamele edilmesiyle [3-(3,5-dikloro-2-hidroksifenil)-5-p-tolil-4,5- dihidropirazol-1-il] (piridin-4-il) metanon bileşiği sentez edilmiştir. Yapısı doğrulanan bu bileşiğin hMAO enzimi ile etkileşimi, ticari tayin kiti kullanılarak fluorometrik bir yöntemle incelenmiştir. Ayrıca, söz konusu yeni bileşik ile hMAO arasındaki etkileşimler, moleküler modelleme çalışmaları ile aydınlatılmıştır. Bulgular: Sentezlenen bileşiğin yapısı, IR, Mass, 1H-NMR ve elemental analiz yöntemleri kullanılarak doğrulanmıştır. Yapısı doğrulanan bu bileşiğin etkin, seçici, tersinir, toksik olmayan bir hMAO-B inhibitörü olduğu ve inhibisyonun yarışmalı olduğu görülmüştür. Moleküler yerleştirme programı kullanılarak bileşiğin hMAO-B enziminin aktif bölgesinde hangi amino asit yan zincirleri ile ne tür girişimleri yaptığı belirlenmiştir. Sonuç: Yeni sentezlenen SH2U bileşiği, hMAO-B enzimini kuvvetle, seçici, yarışmalı ve tersinir olarak inhibe etmiştir. Sentezlediğimiz bileşik, bilinen seçici ama tersinmez MAO-B inhibitörü olan selejilin’den daha etkin ve seçici, tersinir olarak hMAO-B enzimini inhibe etmiştir ve Parkinson ile Alzheimer hastalığı tedavisinde kullanılabilecek bir ilaç etken maddesi olarak ümit vadetmektedir.
The Association of Gvhd With Hla Dr Alleles, Ifn-Gamma, Tgf-Beta, and Mbl2 Gene Polymorphism
(Wiley, 2019) Oğuz, Rusdu; Çiftçi, Hayriye Şentürk; Gökçe, Muge; Öğret, Yeliz; Karadeniz, Sedat Tanju; Pehlivan, Sacide; Aydın, Filiz
[Abstract Not Available]
Atomic Collisions and Free Lepton Pair Production
(2005) Güçlü, Mehmet Cem; Yılmaz, Melek
In this work we have calculated the total cross sections of electron-positron pair production for the collisions of fully stripped gold ions for various energies. We have also compared our calculation with other methods.
Citation - WoS: 1
Citation - Scopus: 1
Collectivity in Heavy Nuclei in the Shell Model Monte Carlo Approach
(EDP Sciences, 2014) Özen, Cem; Alhassid, Yoram; Nakada, Hitoshi
The microscopic description of collectivity in heavy nuclei in the framework of the configuration-interaction shell model has been a major challenge. The size of the model space required for the description of heavy nuclei prohibits the use of conventional diagonalization methods. We have overcome this difficulty by using the shell model Monte Carlo (SMMC) method which can treat model spaces that are many orders of magnitude larger than those that can be treated by conventional methods. We identify a thermal observable that can distinguish between vibrational and rotational collectivity and use it to describe the crossover from vibrational to rotational collectivity in families of even-even rare-earth isotopes. We calculate the state densities in these nuclei and find them to be in close agreement with experimental data. We also calculate the collective enhancement factors of the corresponding level densities and find that their decay with excitation energy is correlated with the pairing and shape phase transitions.
Citation - WoS: 21
Citation - Scopus: 24
Conductivity Percolation of Carbon Nanotubes (cnt) in Polystyrene (ps) Latex Film
(Canadian Science Publishing Nrc Research Press, 2010) Uğur, Şaziye; Yargı, Önder; Pekcan, Önder
In this study the effect of multiwalled carbon nanotubes (MWNT) on film formation behaviour and electrical conductivity properties of polystrene (PS) latex film was investigated by using the photon transmission technique and electrical conductivity measurements. Films were prepared by mixing PS latex with different amounts of MWNTs varying in the range between 0 and 20 wt%. After drying MWNT content films were separately annealed above the glass transition temperature (T-g) of PS ranging from 100 to 270 degrees C for 10 min. To monitor film formation behavior of PS-MWNT composites transmitted light intensity I-tr was measured after each annealing step. The surface conductivity of annealed films at 170 degrees C was measured and found to increase dramatically above a certain fraction of MWNT (4 wt%) following the percolation theory. This fraction was defined as the percolation threshold of conductivity R-c. The conductivity scales with the mass fraction of MWNT as a power law with exponent 2.27 which is extremely close to the value of 2.0 predicted by percolation theory. In addition the increase in I-tr during annealing was explained by void closure and interdiffusion processes. Film formation stages were modeled and the corresponding activation energies were measured.
Citation - WoS: 3
Citation - Scopus: 3
Critical Exponents of Thermal Phase Transitions of Kappa-Carrageenan in Various Salt Solutions
(Wiley-VCH Verlag GmbH, 2009) Tarı, Özlem; Pekcan, Önder
The steady state fluorescence (SSF) technique was employed to study the phase transitions Of kappa-carrageenan in NaCl and KCl solutions. Pyranine was used as a fluorescence probe for monitoring these transitions. Scattered light I(sc) and fluorescence intensity 1 was monitored against temperature to determine transition temperatures and exponents. It was observed that transition temperatures are strongly correlated with the NaCl and KCl contents. The weight-average degree of polymerization DP(w) and gel fraction G exponents (gamma and beta) were measured and found to be in accord with the classical Flory-Stockmayer model.
Citation - Scopus: 1
Effect of Temperature and Graphene Oxide on the Swelling of Paam-Go Composite Gels
(Avestia Publishing, 2019) Osma, Büşra; Akın Evingür, Gülşen; Pekcan, Önder
Graphene oxide (GO) is a two dimensional carbon material with similar one-atom thickness, and is a light material having extremely high strength and thermal stability [1]. Thus, GO is an efficient filler for the enhancement of the electrical, mechanical and thermal properties of composite materials [2]. We focused on GO as a nanofiller in polyacrylamide hydrogels and PAAm-GO composites to investigate the effect of temperature and graphene oxide on the swelling. Polyacrylamide (PAAm) hydrogels have been proposed for use as promising biomaterials in biomedical and tissue engineering. The composite gels were prepared by free radical crosslinking copolymerization with GO content varying in the range between 8 and 50 μl of GO. The effects of temperature and graphene oxide on the swelling of the composites were studied. The swelling experiment was performed in the distilled water. Decreasing in pyranine (Py) as a fluorescence probe and emission light intensity (Iem) were monitored by steady state fluorescence spectroscopy. Since the increase in Isc corresponds to the increase in turbidity of the swelling composite gel, the corrected fluorescence intensity, I was introduced to analyze the swelling processes. The Stern-Volmer equation combined with Li-Tanaka models was used to explain the behaviour of I during swelling processes. The cooperative diffusion coefficients and time constants were calculated as a function of temperature and GO, respectively.
Citation - WoS: 3
Citation - Scopus: 4
Elasticity Study of Paam-Kappa C Composite Prepared in Various Kappa C Content and Measured at Several Temperatures
(Polish Acad Sciences Inst Physics, 2015) Evingür, Gülşen Akin; Pekcan, Önder
Polyacrylamide (PAAm)-kappa carrageenan (kappa C) composite gels were prepared via free radical crosslinking copolymerization with various (w/v) percentages of kappa C in the range between 0.5 and 3 (w/v)% of kappa C . Elasticity properties such as stress strain and compressive elastic modulus S of these composite gels were studied in various kappa C content and at several temperatures. The content and temperature dependence of the compressive elastic modulus S of the swollen PAAm-kappa C composite gels due to volume phase transition were produced by using tensile testing technique. It is understood that the compressive elastic modulus was found to decrease up to 1 (w/v)% of kappa C and then increase by increasing kappa C contents at constant temperatures. The composite preserves the ability to undergo the volume phase transition and its compressive elastic modulus is found to be strongly dependent on the kappa C content and temperature. It is observed that the compressive elastic modulus increased when temperature is increased up to 40 degrees C and then decreases below this temperature for all composite gels. However PAAm-kappa C composite gel presented lower values for the compressive elastic modulus showing a minima at 40 degrees C for 1 (w/v)% of kappa C content gel.
Citation - WoS: 14
Citation - Scopus: 14
Exploration of the Binding Pocket of Histone Deacetylases: the Design of Potent and Isoform-Selective Inhibitors
(Tübitak, 2017) Auba, Budullahi İbrahim; Yelekçi, Kemal
Histone deacetylases (HDACs) are enzymes that act on histone proteins to remove the acetyl group and thereby regulate the chromatin state. HDACs act not only on histone protein but also nonhistone proteins that are key players in cellular processes such as the cell cycle, signal transduction, apoptosis, and more. “Classical” HDACs have been shown to be promising targets for anticancer drug design and development. However, the selectivity of HDAC inhibitors for HDAC isoforms remains the motivation of current research in this field. Here, we explored Class I HDACs and HDAC6 by sequence alignment and structural superimposition, catalytic channel extraction, and identification of critical residues involved in HDAC catalysis. Based on the general pharmacophore features of known HDAC inhibitors, we developed a library of compounds by scaffold hopping on a fragment hit identified via structurebased virtual screening of the molecular fragment library retrieved from the Otava database. Molecular docking assay revealed five of these compounds to have increased potency and selectivity for HDACs 1 and 2. Furthermore, their predicted absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties were consistent with those of drug-like compounds. With further modelingbased and experimental investigations, we believe that these findings may offer additional potential HDAC inhibitors with improved selectivity
Citation - WoS: 2
Citation - Scopus: 2
Fractal Features and Structural Morphological Optical Characteristics of Sol-Gel Derived Silica Nanoparticled Thin Films
(Polish Acad Sciences Inst Physics, 2018) Uysal, Bengü Özuğur; Pekcan, Önder
Nanostructured silica films using a simple and effective sol-gel spin coating technique were synthesized and the influence of ammonia/sol ratios on the particle size and thickness of this film was investigated. In addition fractal dimensions of the prepared films were determined using the scattering response technique. The samples were characterized by atomic force microscopy and UV-vis spectroscopy. Comparing optical method and image analysis of atomic force microscopy micrographs the fractal dimension of silica nanoparticled thin films was determined. The fractal dimensions of the films verified by atomic force microscopy analysis were found to be around 2.03 which is very close to the values (2.0358 2.0325 and 2.0335) obtained using optical method. As a result of these findings precise determination of the nanoparticled silica thin films fractal dimension using both optical and surface analysis methods was realized.
Level Densities of Heavy Nuclei in the Shell Model Monte Carlo Approach
(EDP Sciences, 2016) Alhassid, Yoram; Bertsch, George F.; Gilbreth, Christopher N.; Nakada, Hitoshi; Özen, Cem
Nuclear level densities are necessary input to the Hauser-Feshbach theory of compound nuclear reactions. However the microscopic calculation of level densities in the presence of correlations is a challenging many-body problem. The configuration-interaction shell model provides a suitable framework for the inclusion of correlations and shell effects but the large dimensionality of the many-particle model space has limited its application in heavy nuclei. The shell model Monte Carlo method enables calculations in spaces that are many orders of magnitude larger than spaces that can be treated by conventional diagonalization methods and has proven to be a powerful tool in the microscopic calculation of level densities. We discuss recent applications of the method in heavy nuclei.
Citation - WoS: 4
Citation - Scopus: 4
Modelling of Swelling by the Fluorescence Technique in Kappa Carrageenan Gels
(Amer Inst Physics, 2011) Tari, Özlem; Pekcan, Önder
Kappa (-kappa) carrageenan gels prepared with various carrageenan concentrations in pure water were completely dried and then swelled in water vapor. Steady state fluorescence measurements were performed using a spectrometer equipped with temperature controller. Pyranine was embedded in kappa-carrageenan gels as a fluorescence probe during gel preparation. The fluorescence intensity I increased exponentially as swelling time is increased for all gel samples. The increase in I was modelled using Li-Tanaka equation from which swelling time constants tau(c) and cooperative diffusion coefficients D-c were determined. It was observed that D-c increased as the swelling temperature was increased. On the other hand at each temperature it was seen that D-c decreased as kappa carrageenan concentration was increased. Activation energies for swelling were obtained and found to be 57.4 58.3 and 62.73kJ mol(-1) for the gels with increasing amount of kappa-carrageenan content.
Citation - WoS: 4
Citation - Scopus: 6
Oxygen Diffusion Into Polymer-Clay Composite Films as a Function of Clay Content and Temperature
(Wiley-VCH Verlag GmbH, 2009) Uğur, Şaziye; Yargı, Önder; Elaissari, Abdelhamid; Pekcan, Önder
A simple fluorescence technique is proposed for the measurement of the diffusion coefficient of oxygen into polystyrene-clay composite films as a function of clay content and temperature. The composite films were prepared from a mixture of surfactant-free pyrene-labeled polystyrene latexes and modified Na-montmorillonite clay of various compositions at room temperature. Diffusion measurements were performed with films at room temperature for seven different clay contents (0 5 10 20 30 50 and 60 wt.%). The diffusion coefficients of oxygen increased from 7.4 x 10(-10) to 26.9 x 10(-10) cm(2)s(-1) with increasing clay content. On the other hand diffusion measurements were performed over a temperature range Of 25-70 degrees C for 0 5 and 20 wt.% clay content films. The calculated diffusion activation energies decreased from 2.44 to 0.44 kcal/mol with increasing clay content. No clay content and temperature effects were observed on quenching rate constant and mutual diffusion coefficient values. The results showed that the diffusion coefficients are strongly dependent on both the temperature and clay content in the film.
Citation - WoS: 4
Citation - Scopus: 4
Paam-Kappa Carrageenan Composites: Drying and Swelling With Various Kappa Carrageenan Contents
(Polish Acad Sciences Inst Physics, 2012) Akın-Evingür, Gülşen; Pekcan, Önder
The purpose of this study is to discuss the role of kappa-carrageenan (kappa-car) in the drying and swelling of polyacrylamide (PAAm)-kappa-car composite. The fluorescence intensity of pyranine increased and decreased as drying and swelling time were increased respectively for all samples. The desorption coefficient D-d decreased as kappa-car contents were increased for a given temperature during drying. However cooperative diffusion coefficient D-s increased as kappa-car contents were increased during swelling at a given temperature.
Phase Transitions in Pure and Hybrid Hydrogels: a Fluorescence Study
(Wiley, 2009) Aktas, Demet Kaya; Evingür, Gülşen Akin; Pekcan, Önder
Recent observations on phase transitions around the critical point showed that the critical exponents differed drastically from percolation results and classical results for pure hydrogel systems depending on monomer concentration. in addition to pure hydrogels the sol-gel phase transition during radical crosslinking copolymerization of acrylamide (AAm) and N-isopropylacrylamide (NIPA) hybrid was studied by using the steady state fluorescence (SSF) technique. NN'-methylenebis(acrylamide) (BIS) and ammonium persulfate (APS) were used as crosslinker and initiator respectively. Pyranine (trisodium 8-hydroxypyrene-136-trisulfonate acid HPTS) was added as a fluoroprobe for monitoring the polymerization. It was observed that pyranine binds to AAm and NIPA chains on the initiation of the polymerization thus the fluorescence spectra of the bonded pyranines shift to shorter wavelengths. Fluorescence spectra of the bonded pyranines allowed to monitor the sol-gel phase transition without disturbing the system mechanically and to test the universality of the sol-gel transition as a function of polymer concentration ratios. The observations around the gel point of PAAm-PNIPA hybrid show that the gel fraction exponent beta obeyed the percolation result.
Polymer-Ceramic Nanocomposites
(Spie-Int Soc Optical Engineering, 2009) Pekcan, Önder; Uğur, Şaziye
Steady state fluorescence (SSF) and photon transmission (PT) techniques were used for studying film formation from TiO2 and Al2O3 covered polystyrene (PS) latex particles. These films were annealed at elevated temperatures in 10 min time intervals above glass transition (T-g) temperature of polystyrene. Fluorescence emission I-P and transmitted photon I-tr intensities were measured after each annealing step to monitor the stages of film formation. Films present dramatic increase in both I-tr and I-P above the certain onset temperature called minimum film forming temperature T-0. Dissolution of annealed PS film with high TiO2 content presented a nice ordered nano-sized ceramic structure which may predict the construction of nano-layer photonic crystals. It was observed that latex particles are encapsulated above a critical Al2O3 content of 33 wt% which corresponds to the critical occupation probability of p(c)=0.33 at which the film obey the site-percolation model with a critical exponent of 0.45.
Signatures of Phase Transitions in Nuclei at Finite Excitation Energies
(Amer Inst Physics, 2012) Alhassid, Yoram; Özen, Cem; Nakada, Hitoshi
The mean-field approximation predicts pairing and shape phase transitions in nuclei as a function of temperature or excitation energy. However in the finite nucleus the singularities of these phase transitions are smoothed out by quantal and thermal fluctuations. An interesting question is whether signatures of these transitions survive despite the large fluctuations. The shell model Monte Carlo (SMMC) approach enables us to calculate the statistical properties of nuclei beyond the mean-field approximation in model spaces that are many orders of magnitude larger than spaces that can be treated by conventional diagonalization methods. We have extended the SMMC method to heavy nuclei and used it to study the transition from vibrational (spherical) to rotational (deformed) nuclei in families of rare-earth isotopes. We have calculated collective enhancement factors of level densities as a function of excitation energy and found that the decay of the vibrational and rotational enhancements is well correlated with the pairing and shape phase transitions respectively.
Citation - WoS: 6
Citation - Scopus: 6
Synthesis Molecular Modelling and Antibacterial Activity Against Helicobacter Pylori of Novel Diflunisal Derivatives as Urease Enzyme Inhibitors
(Bentham Science Publ Ltd, 2019) Coşkun, Göknil Pelin; Djikic, Teodora; Kalaycı, Sadık; Yelekçi, Kemal; Şahin, Fikrettin; Küçükgüzel, Şükriye Güniz
Background: The main factor for the prolongation of the ulcer treatment in the gastrointestinal system would be Helicobacter pylori infection which can possibly lead to gastrointestinal cancer. Triple therapy is the treatment of choice by today's standards. However observed resistance among the bacterial strains can make the situation even worse. Therefore there is a need to discover new targeted antibacterial therapy in order to make success in the eradication of H. pylori infections. Methods: The targeted therapy rule is to identify the related macromolecules that are responsible for the survival of the bacteria. Thus 2-[(2'4'-difluoro-4-hydroxybiphenyl-3-yl)carbonyl]-N-( substituted)hydrazinocarbothioamide (3-13) and 5-(2'4'-difluoro-4-hydroxybiphenyl-3-yl)-4-( substituted)-24-dihydro-3H-124-triazole-3-thiones (14-17) were synthesized and evaluated for antibacterial activity in vitro against H. pylori. Results: All of the tested compounds showed remarkable antibacterial activity compared to the standard drugs (Ornidazole Metronidazole Nitrimidazin and Clarithromycin). Compounds 4 and 13 showed activity as 2 mu g/ml MIC value. Conclusion: In addition we have investigated binding modes and energy of the compounds 4 and 13 on urease enzyme active by using the molecular docking tools.
Citation - WoS: 8
Citation - Scopus: 10
Synthesis, in Silico Studies and Cytotoxicity Evaluation of Novel 1,3,4-Oxadiazole Derivatives Designed as Potential Mpges-1 Inhibitors
(MARMARA UNIV, 2020) Erensoy, Gizem; Ding, Kai; Zhan, Chang-Guo; Elmezayen, Ammar D.; Yelekçi, Kemal; Duracık, Merve; Özakpınar, Özlem Bingol; Küçükgüzel, İlkay
A series of new 1,3,4-oxadizole derivatives containing thioether group, has been synthesized to investigate their mPGES-1 inhibitory activities. The synthesized compounds were also evaluated for their anticancer and COX-1/2 inhibitory activities. All compounds were checked for their purity using TLC and HPLC analyses. The melting points, elemental analysis, FT-IR, H-1-/C-13-NMR and LR-MS data were utilized for structural characterization. The most potent derivative was 2-[5-{[2-methyl-5-(propan-2-yl)phenoxy]methyl}-1,3,4-oxadiazol-2-yl)sulphanyl]-1-(phenyl)ethan-1-one 3a, which showed inhibitory activity against mPGES-1 with an IC50 of 4.95 mu M. Docking studies with mPGES-1 and COX-1/2 enzymes revealed their affinity and potential binding mechanism for the tested compounds.
Citation - WoS: 4
Citation - Scopus: 4
Universality of Elasticity on Paam-Nipa Copolymer Gels
(EDP Sciences, 2015) Evingür, Gülşen Akin; Pekcan, Önder
Polyacrylamide (PAAm)-N-isopropylacrylamide (NIPA) copolymers were prepared via free radical crosslinking copolymerization with different molar of NIPA varying in the range between 0 and 2 M. The mechanical properties of swollen PAAm-NIPA copolymers were characterized by the compressive testing technique. It is understood that the compressive elastic modulus was found to increase by increasing NIPA contents keeping temperature constant at 30 degrees C. The critical exponent of elasticity y above the critical NIPA concentration is found to be as 0.74 which is consistent with the suggestions of percolation for superelastic percolation network (SEPN) and the critical theory for PAAm-NIPA copolymers.

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