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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 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 Synthesis and characterization of a new magnetic nanoparticles: Fe3O4-NPs-G1-Mu(Fırat Üniversitesi, 2018-06) Ekinci, Selma; İlter, Zülfiye; Çınar, Ercan
