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Bölüm: Batman Üniversitesi Sağlık Yüksekokulu Hemşirelik Bölümü × Dil: en ×

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    Docking and molecular dynamics calculations of some previously studied and newly designed ligands to catalytic core domain of HIV-1 integrase and an investigation to effects of conformational changes of protein on docking results
    (Türkiye Kimya Derneği, 2017-01-09) Ercan, Selami
    Nowadays, AIDS still remains as a worldwide pandemic and continues to cause many deaths which arise from HIV-1 virus. For nearly 35 years, drugs that target various steps of virus life cycle have been developed. HIV-1 integrase constitutes one of these steps which is essential for virus life cycle. Computer-aided drug design is being used in many drug development and drug improvement studies as also used in development of the first HIV-1 integrase inhibitor Raltegravir. In this study, 3 ligands which are already used as HIV-1 integrase inhibitors and 4 newly designed ligands were docked to catalytic core domain of HIV-1 integrase. Each ligand docked to three different conformations of protein. Prepared complexes (21 items) were carried out by 50 ns MD simulations and results were analyzed. Finally, the binding free energies of ligands were calculated. It was determined that designed ligands L01 and L03 gave favorable results. The questions about the ligands which have low docking scores in a conformation of protein could give better scores in another conformation of protein and if the MD simulations carry the different oriented and different localized ligands in same position at the end of simulation were answered.
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    Design, preparation and application of a Pirkle-type chiral stationary phase for enantioseparation of some racemic organic acids and molecular dynamics studies
    (ACG Publications, 2017-11) Çakmak, Reşit; Ercan, Selami; Sünkür, Murat; Yılmaz, Hayrullah; Topal, Giray
    This study consists of two parts. In the first part of the study; a Pirkle-type chiral stationary phase was prepared by synthesizing an aromatic amine derivative of (R)-2-amino-1-butanol as a chiral selector and binding to L-tyrosine-modified cyanogen bromide (CNBr)-activated Sepharose 4B and then, packed into the separation column. The chromatographic performance of the separation column was evaluated with racemic mandelic acid and 2-phenylpropionic acid by using phosphate buffers at three different pHs as mobile phase. In the resolution processes, the prepared solutions were loaded onto the separation column at two different concentrations and at three different pHs for each racemic organic acid, separately. Enantiomeric excess (ee%) of the eluates was determined on CHIRALPAK AD-H chiral analytical column by HPLC. The maximum ee% for mandelic acid and 2-phenylpropionic acid was determined to be 60.84 and 27.4, respectively. Separation factors (k1 ’ , k2 ’ , α, and Rs) were calculated for each acid. The structures of the obtained compounds were characterized using the spectroscopic methods (NMR, and elemental analysis). In the second part of the study; enantioselective interactions between the prepared CSP and the analytes have been widely studied by docking, molecular dynamics simulation and quantum mechanical computation methods. The reason of column eluation of rac-2-phenylpropionic acid with lower enantiomeric yield was explained by these techniques.
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    Magnetite nanoparticles grafted with murexide-terminated polyamidoamine dendrimers for removal of lead (II) from aqueous solution: synthesis, characterization, adsorption and antimicrobial activity studies
    (Journals & Books, 2021-03) Ekinci, Selma; İlter, Zülfiye; Ercan, Selami; Çınar, Ercan; Çakmak, Reşit
    In this study, new, efficient, eco-friendly and magnetically separable nanoadsorbents, MNPs-G1-Mu and MNPs-G2-Mu, were successfully prepared by covalently grafting murexide-terminated polyamidoamine dendrimers on 3-aminopropyl functionalized silica-coated magnetite nanoparticles, and used for rapid removal of lead (II) from aqueous medium. After each adsorption process, the supernatant was successfully acquired from reaction mixture by the magnetic separation, and then analyzed by employing ICP-OES. Chemical and physical characterizations of new nanomaterials were confirmed by XRD, FT-IR, SEM, TEM, and VSM. Maximum adsorption capacities (qm) of both prepared new nanostructured adsorbents were compared with each other and also with some other adsorbents. The kinetic data were appraised by using pseudo-first-order and pseudo-second-order kinetic models. Adsorption isotherms were found to be suitable with both Langmuir and Freundlich isotherm linear equations. The maximum adsorption capacities for MNPs-G1-Mu and MNPs-G2-Mu were calculated as 208.33 mg g−1 and 232.56 mg g−1, respectively. Antimicrobial activities of nanoparticles were also examined against various microorganisms by using microdilution method. It was determined that MNPs-G1-Mu, MNPs-G2-Mu and lead (II) adsorbed MNPs-G2-Mu showed good antimicrobial activity against S. aureus ATTC 29213 and C. Parapsilosis ATTC 22019. MNPs-G1-Mu also showed antimicrobial activity against C. albicans ATTC 10231.
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    Synthesis and characterization of iron oxide nanoparticles modified with pamam dendrimer
    (Fırat Üniversitesi, 2018-06) Ekinci, Selma; İlter, Zülfiye; Çınar, Ercan
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    Correlation of nutritional element levels in drinking water with body compositions of women aged 55-70 years living in Batman province
    (Dicle Üniversitesi, 2017-02-02) Çetin, İhsan; Nalbantçılar, Tahir; Güler Saban, Meryem; İnci, Ramazan; Tosun, Kezban; Nazik, Aydan
    Objective: A growing interest in cellular targets of nutritional minerals and biochemical mechanisms has attracted the attentions of researchers towards their role in formation of obesity. However, there is no study investigating the effects of nutritional element levels of drinking water on body composition of the elderly. Therefore, we aimed to examine the effects of nutritional element levels in drinking water on body composition of women aged 55-70. Methods: The study population consisted of 80 participants in total, and was divided into three groups as overweight, obese and control women aged between 55-70. The bioelectric impedance device was used for measurements of body composition of the participants. Iron (Fe), copper (Cu), cobalt (Co), zinc (Zn), manganese (Mn) and selenium (Se) levels of drinking water were measured via plasma mass spectrometry coupled inductively. Results: It was found that Se mineral content in drinking water correlated with the body mass index of the individuals living in Batman, Turkey. Moreover, it was found that Fe, Cu, Co, Zn, Mn and Se levels of drinking water significantly correlated with the abdominal adiposity of women of 55-70. Conclusion: It may be suggested that the obesity risk may be higher in women who are between 55-70 and consume drinking water with high levels of Fe, Cu, Co, Zn, Mn and especially Se.
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