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2016 - 20173
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Ayarlar

Yazar: Ercan, Selami × Konu: Docking ×

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  • Küçük Resim
    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, 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.
  • Küçük Resim
    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, 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.
  • Küçük Resim
    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, Selami
    Kazanılmış 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