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    Design of l -lysine-based organogelators and their applications in drug release processes
    (American Chemical Society, 2019) Kaplan, Şeref; Çolak, Mehmet; Hoşgören, Halil; Pirinççioğlu, Necmettin
    This work reports on the synthesis of three new l-lysine-based organogelators bis(N2-alkanoyl-N6-l-lysyl ethylester)oxalylamides, where alkanoyls are lauroyl, myristoyl, and palmitoyl. The gels of these gelators were prepared with high yields in eco-friendly solvents commonly used in cosmetics such as ethyl and isopropyl esters of lauric and myristic acids, liquid paraffin, 1-decanol, and 1,2-propanediol. Fourier transform infrared measurements revealed the involvement of intermolecular hydrogen bonds in the gelation. Scanning electron microscopy images of xerogels indicated different morphologic patterns with regard to the alkanoyl chain length and the solvent employed in their preparation. The gel formation was supported by rheological measurements. Three gels prepared in liquid paraffin were loaded with naproxen (Npx) with a quite high loading capacity (up to 166.6% as percentage of gelator) without gel disruption. The release of Npx from the gel matrix into the buffered solution at physiologic pH was evaluated using UV-vis spectroscopy. The results revealed that the release rate of Npx from the organogels significantly retarded with increasing organogelator concentration, whereas it enhanced with increasing Npx concentration. The rate was also found to be pH-dependent; the lower the pH, the lower the rate. Furthermore, molecular dynamic calculations performed on the octamer of myristoyl-bearing gelator (N2M/N6Lys) in 1,2-propanediol provided useful information regarding the structural properties of the gels, which may be of interest to interpret the structure of the gel matrix. Altogether, this work provided valuable outcomes, which may be relevant to the pharmaceutical industry. It may be suggested that l-lysine-based gels have potentials in the delivery of nonsteroidal anti-inflammatory drug molecules. Besides, the release of the drug can be fine-tuned by the correct choice of gelator-solvent combination.
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    DNA cleavage activity of diazonium salts: Chemical nucleases
    (2003) Pirinççioğlu, Necmettin; Aytekin, Mehmet Çetin; Yılmaz, Ebru İnce; Kızıl, Murat
    4-Fenoldiazonium tetrafluoroborate and 4-benzoicaciddiazonium tetrafluoroborate was prepared and was shown to be an effective DNA cleavage agent in the presence of the 1-electron donor copper(II) chloride. Its mechanism involves the generation of the aryl radical cleaving DNA by hydrogen atom abstraction from deoxyribose sugar.
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    Investigation of angucycline compounds as potential drug candidates against SARS Cov-2 main protease using docking and molecular dynamic approaches
    (Springer, 2021) Al-Bustany, Hazem Abbas; Ercan, Selami; İnce, Ebru; Pirinççioğlu, Necmettin
    The emerged Coronavirus disease (COVID-19) causes severe or even fatal respiratory tract infection, and to date there is no FDA-approved therapeutics or efective treatment available to efectively combat this viral infection. This urgent situation is an attractive research area in the feld of drug design and development. One of the most important targets of SARScoronavirus-2 (SARS Cov-2) is the main protease (3CLpro). Actinomycetes are important resources for drug discovery. The angucylines that are mainly produced by Streptomyces genus of actinomycetes exhibit a broad range of biological activities such as anticancer, antibacterial and antiviral. This study aims to investigate the binding afnity and molecular interactions of 157 available angucycline compounds with 3CLpro using docking and molecular dynamics simulations. MM-PBSA calculations showed that moromycin A has a better binding energy (−30.42 kcal mol−1) compared with other ligands (in a range of−18.66 to−22.89 kcal mol−1) including saquayamycin K4 (−21.27 kcal mol−1) except the co-crystallized ligand N3. However, in vitro and in vivo studies are essential to assess the efectiveness of angucycline compounds against coronavirus.
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    A study on a primitive artificial esterase model: Reactivity of a calix[4]resorcinarene bearing carboxyl groups
    (2008) Cevasco, Giorgio; Galatini, Andrea; Pirinççioğlu, Necmettin; Thea, Sergio; Williams, Andrew; 0000-0001-9805-9745
    The host molecule octacarboxymethyl calix[4]resorcinarene 1 catalyses the hydrolysis of substituted phenyl N-methylpyridinium-4-carboxylate esters 3a-f by complexation followed by intracomplex reaction via an anhydride intermediate. The reactivity in the presence of 1 is higher than that of the background at low pH; at high pH an inversion of reactivity occurs, the background becomes predominant since the host inhibits hydrolysis of the esters. The reactivity of esters 3a-f complexed with the host suffers little change in effective charge on the phenolic oxygen (-0.15 units) in contrast with the changes observed in alkaline hydrolysis (-0.28 units) and in the hydrolysis of the model monoaryl glutarate esters (-1.02 units). The less negative effective charge in the transition state for host 1 catalysis compared with that in the glutarate case is ascribed to stronger solvation by water molecules in the complex compared with that due to water molecules in the bulk solvent.