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Öğe 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, GirayThis 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.Öğe 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, SelamiNowadays, 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.Öğe Lewatit partikülüne üreaz enziminin immobilizasyonu(Batman Üniversitesi, 2017) Çınar, Ercan; Ercan, Selami; Güleşçi, NuriTicari olarak alınan Lewatit VP OC 1600 partiküllerine üreaz enzimi immobilizasyon tekniği uygulanılarak partiküle immobilize edildi. Enzim immobilizasyonlarında araştırma parametrelerinden biri olan enzimin tekrar kullanılabilirliği immobilze olan partikülün kullanılması ve sonuçların alınması enzimin ticari alınan lewatit partiküller üzerine immobilize olduğunu gösterdi. Lewatit VP OC 1600, metakrilik esterlere dayanılarak küresel boncuk biçiminde macropor içeren ve divinilbenzen (DVB) ile çapraz bağlanmış polimerdir. Lewatit VP OC 1600’ün maksimum üreaz immobilize etme kapasitesi 480 mg.g -1 ‘dir. Serbest ve immobilize olan enzimler, 7.5 ve 6.5 gibi farklı optimum pH'lar sergiledi. İmmobilize olan enzimin optimum sıcaklığı 60 oC'e kayarken, serbest enzim 50 oC olarak belirlendi. İmmobilize olan enzim ile serbest enzim yüksek sıcaklıklara maruz bırakıldığında tutuklanan enzim serbest enzime göre sıcaklığa daha fazla direnç gösterdiği tespit edildi. Tutuklanan ve serbest enzimin kinetik parametreleri belirlendi. Buna göre, serbest enzimin substrata ilgisinin tutuklanan enzimin substrata olan ilgisinden düşük olduğu gözlemlendi. Tutuklanan enzimin, termostabilitesi, tekrar kullanılabilirliği ve depolama parametrelerinin serbest enzime kıyasla daha yüksek bir etkinlik gösterdiği tespit edildi.Öğe 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, ReşitIn 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.Öğe Yeni tasarlanan ve daha önceden çalışılmış bazı anti-HIV integraz ligandlarının autodock vina ile HIV-1 integraz enzimi katalitik öz bölgesine yerleştirilmesi ve analizleri(Batman Üniversitesi, 2016) Ercan, SelamiKazanılmış İmmün Yetmezlik Sendromu (AIDS) modern dünyanın en önemli hastalıklarından biridir. Bu hastalığa insan immün yetmezlik virüsü (HIV) neden olmaktadır. HIV-1 integraz enzimi diğer çalışılan enzimler proteaz ve ters transkriptaza göre daha geç ilgi görmüştür. Geliştirilen ilaçlara sürekli direnç oluşması yeni ilaç adaylarının bulunmasını zorunlu kılmaktadır. Bu çalışmada HIV-1 integraz enziminin katalitik öz bölgesinin bir modeli hazırlanarak moleküler dinamik simülasyonuyla davranışları incelendi. Bu model hedef alınarak, yeni geliştirilen 6 ligandın yanı sıra, bilinen ancak HIV-1 integraz inhibitör adayı olarak ilk defa kullanılan 4 ligand ve daha önce teorik ve/veya uygulamalı olarak çalışılan 32 ligand yerleştirildi. Yerleştirilen ligandların proteinle etkileşimleri incelendi. Yeni geliştirilen ligandlardan LGA, LGD ve LGE’nin ortalamanın üzerinde bir yerleştirme skoruna sahip olduğu görüldü
