Publications without Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
Browse
35 results
Search Results
Publication Metadata only Discovery of the aminated quinoxalines as potential active molecules(Bentham Science Publishers, 2024) Bener, Sedef; Bayrak, Nilüfer; Mataracı-Kara, Emel; Yıldız, Mahmut; Sever, Belgin; Tuyun, Amaç Fatih; Department of Molecular Biology and Genetics; Çiftçi, Halil İbrahim; Department of Molecular Biology and Genetics; College of SciencesBackground: In recent years, as the biological activity of the quinoxaline skeleton has been revealed in numerous studies, interest in synthesizing new prototype molecules for the treatment of many chronic diseases, especially cancer, has increased. Methods: The desired alkoxy substituted aminoquinoxalines (AQNX1-9) were synthesized by the reaction of QNX and alkoxy substituted aryl amines such as 2-methoxyaniline, 4-methoxyaniline, 2ethoxyaniline, 3-ethoxyaniline, 4-ethoxyaniline, 4-butoxyaniline, 2,4-dimethoxyaniline, 3,4dimethoxyaniline, and 3,5-dimethoxyaniline according to the previously published procedure. QNX was aminated in DMSO at 130°C. We synthesized various alkoxy substituted aminoquinoxaline compounds (AQNX1-9) and evaluated their anticancer and antimicrobial activities in order to expand the search to related structures. In particular, two aminoquinoxaline (AQNX5 and AQNX6) compounds, coded as NSC D-835971/1 and NSC D-835972/1 by the National Cancer Institute in the USA, were screened for anticancer screening at a dose of 10-5 M on a full panel of 60 human cell lines obtained from nine human cancer cell types (leukemia, melanoma, non-small cell lung, colon, central nervous system, ovarian, kidney, prostate, and breast cancer). Results: Further in silico studies were also conducted for the compound AQNX5 (NSC D835971/1), which was found to be the most active antiproliferative agent, especially against leukemia cell lines. Molecular docking studies showed that AQNX5 interacted with Glu286 and Lys271 through hydrogen bonding and π-stacking interaction in the ATP binding region of Abl kinase, which is indicated as a potential target of leukemia. Besides, AQNX5 occupied the minor groove of the double helix of DNA via π-stacking interaction with DG-6. Conclusion: According to in silico pharmacokinetic determination, AQNX5 was endowed with drug-like properties as a potential anticancer drug candidate for future experiments. In the light of these findings, more research will focus on aminated quinoxalines' ability to precisely target leukemia cancer cell lines.Publication Metadata only Unfolded protein response is involved in trans-platinum (ii) complex-induced apoptosis in prostate cancer cells via ros accumulation(2019) Karakaş, Didem; Oral, Arzu Y.; Yılmaz, Veysel T.; Ulukaya, Engin; Animal Laboratory; Cevatemre, Buse; Researcher; Animal Laboratory; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; N/A; N/ABackground: Prostate cancer is one of the most common cancer types and it is the sixth leading cause of cancer-related death in men worldwide. Even though novel treatment modalities have been developed, it still a lifethreatening disease. Therefore novel compounds are needed to improve the overall survival. Methods: In our study, it was aimed to evaluate the anti-cancer activity of newly synthesized Platinum (II) [Pt(II)] complex on DU145, LNCaP and PC-3 prostate cancer cell lines. The cytotoxic activity of Pt(II) complex was tested by SRB and ATP cell viability assays. To detect the mode of cell death; fluorescent staining, flow cytometry and western blot analyses were performed. Results: The Pt(II) complex treatment resulted in a decrease in cell viability and increasing levels of apoptotic markers (pyknotic nuclei, annexin-V, caspase 3/7 activity) and a decrease in mitochondrial membrane potential in a dose dependent manner. Among cell types, tested PC-3 cells were found to be more sensitive to Pt(II) complex, demonstrating elevation of DNA damage in this cell line. In addition, Pt(II) complex induced Endoplasmic Reticulum (ER) stress by triggering ROS generation. More importantly, pre-treatment with NAC alleviated Pt(II) complex-mediated ER stress and cell death in PC-3. Conclusion: These findings suggest an upstream role of ROS production in Pt(II) complex-induced ER stressmediated apoptotic cell death. Considering the ROS-mediated apoptosis inducing the effect of Pt(II) complex, it warrants further evaluation as a novel metal-containing anticancer drug candidate.Publication Metadata only Determination of thyroglobulin levels by radioimmunoassay method in anti thyroglobulin positive differentiated thyroid patients: one center clinical experience(Pergamon-Elsevier Science Ltd, 2020) Uçar, Burcu; Şen, Melis; Acar, Tayfun; N/A; Demirkol, Mehmet Onur; Faculty Member; School of Medicine; 196946It is very crucial to determine Tg accurately and precisely in thyroid cancer cases. Although there are many studies on the detection of Tg in thyroid cases in the literature, there are no sufficient clinical studies examining many cases with different features by using RIA methodology. Here, a radiometric and chromatographic method has been studied for the first time to eliminate the interference from anti-Tg positive patients. In this paper, radioimmunoassay (RIA) and immunoradiometric (IRMA) techniques were used for the analysis of 302 sera collected from patients for Tg and TgAb quantification. By the RIA technique, a reliable result was obtained by calculating the real Tg value quantitatively in 41 patients showing TgAb positivity out of 208 patients. Our findings show that the RIA assay is the most suitable approach for detection of changeable (low or undetectable) Tg value and metastases detected by post-therapeutic imaging in early-stage DTC cases showing preoperative and postoperative TgAb positivity. The new immunoradiometric method allows the real (%) Tg value to be reached in a part of TgAb-positive DTC. Even if TgAb positive in the metastatic and nonmetastatic DTC patient group. This allows the accurate clinical follow-up of patients.Publication Metadata only Structures and properties of NbOF3 and TaOF3 - with a remark to the O/F ordering in the SnF4 type structure(Wiley-V C H Verlag Gmbh, 2002) Köhler, J; Simon, A; van Wullen, L; Cordier, S; Roisnel, T; Poulain, M; Department of Chemistry; Somer, Mehmet Suat; Faculty Member; Department of Chemistry; College of Sciences; 178882Powder samples of NbOF3 und TaOF3 were prepared by heating mixtures of NbO2F and NbF5 or TaO2F and TaF5, respectively, in the corresponding stoichiometric ratio in platinum crucibles under argon atmosphere (180-220degreesC). Both oxide fluorides are coulourless with a slight greyish tinge. They are sensitive to moisture and decompose in air at room temperature within hours. Both, NbOF3 and TaOF3 crystallize as a variant of the SnF4 type structure, space group 14/mmm. The structures have been refined from X-ray powder diffraction data using the Rietveld method (a = 3.9675(1) Angstrom, c = 8.4033(1) Angstrom, R-B = 3.60%, R-p = 4.58% for NbOF3 and a = 3.9448(1) Angstrom, c = 8.4860(1) Angstrom, R-a = 2.07%, R-p = 2.44% for TaOF3). Characteristic building units are sheets of corner sharing MX6 octahedra which are stacked via van der Waals interactions to a three dimensional framework. The occupancy of the two crystallographic sites for the anions by O and F is discussed on the basis of structure refinements, bond order summations, IR and NMR data and calculations of the Madelung parts of the lattice energy.Publication Metadata only Nanoparticle silicalite-1 crystallization from clear solutions: nucleation(Elsevier Science Bv, 2009) Tokay, Begüm; Erdem-Şenatalar, Ayşe; Schueth, Ferdi; Thompson, Robert W.; Department of Chemistry; Somer, Mehmet Suat; Faculty Member; Department of Chemistry; College of Sciences; 178882Despite much effort spent by various research groups, there remain many aspects of nanoparticle silicalite-1 crystallization from clear solutions which require further investigation. In order to shed light, especially on the nucleation of silicalite-1, particle growth at 100 degrees C from several starting compositions known to yield colloidal silicalite-1, which have been studied previously by other researchers using various techniques, was followed in this study by laser light scattering using scattering angles of 90 degrees and 173 degrees, and zeta potential and pH measurements. Crystallinity was monitored by X-ray diffraction, Fourier transform infrared analysis and transmission electron microscopy. Thermogravimetric analyses and density measurements were also used to characterize the products obtained at various times during the syntheses. The results demonstrate that the distinct time of sudden jump in the effective diameter of the nanoparticles in solution, as observed more clearly by using the back-scattering device, and which marks the beginning of the constant linear growth rate of the particles, corresponds to the nucleation of the silicalite-1 crystal structure. This time was also shown to coincide with the exo-endo thermal switch time of the reaction mechanism, which has been observed previously by another research group. Nucleation was accompanied by an aggregation of a population of smaller particles, as indicated by the broadening of the particle size distribution, and the variation of the pH and zeta potential values during synthesis.Publication Metadata only Structure of mono- and bimetallic heterogeneous catalysts based on noble metals obtained by means of fluid technology and metal-vapor synthesis(Maik Nauka/Interperiodica/Springer, 2012) Said-Galiev, E. E.; Vasil'kov, A. Yu.; Nikolaev, A. Yu.; Lisitsyn, A. I.; Naumkin, A. V.; Volkov, I. O.; Abramchuk, S. S.; Lependina, O. L.; Khokhlov, A. R.; Shtykova, E. V.; Dembo, K. A.; Department of Chemical and Biological Engineering; Erkey, Can; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 29633Monometallic nanocomposites are obtained with the use of supercritical carbon dioxide (fluid technique) and metal-vapor synthesis (MVS), while bimetallic nanocomposites of Pt and Au noble metals and gamma-Al2O3 oxide matrix are synthesized by a combination of these two methods. The structures, concentrations, and chemical states of metal atoms in composites are studied by means of small-angle X-ray scattering (SAXS), transparent electron microscopy (TEM), X-ray fluorescent analysis (XFA), and X-ray photoelectron spectroscopy (XPS). The neutral state of metal atoms in clusters is shown by XPS and their size distribution is found according to SAXS; as is shown, it is determined by the pore sizes of the oxide matrices and lies in the range of 1 to 50 nm. The obtained composites manifest themselves as effective catalysts in the oxidation of CO to CO2.Publication Metadata only Crystal structure of bis[µ2-(3-benzimidazol-2-yl)-2-ethanethiolato-N,S,S)- chloro-palladium(II)], [(C6H4N2HCCH2CH2S)PdCl]2 C2H5OH(Walter de Gruyter GmbH, 2005) Agh-Atabay, N.M.; Borrmann, H.; Department of Chemistry; Department of Chemistry; Somer, Mehmet Suat; Haciu, Durata; Faculty Member; Teaching Faculty; Department of Chemistry; College of Sciences; College of Sciences; 178882; N/AC20H24Cl2N4OPd2S2, triclinic, P1 (no. 2), a = 8,796(1) Å, b = 9.844(1) Å, c = 14.718(2) A, α = 94.330(6)°, β = 98.546(6)°,γ = 99.258(7)°, V= 1237.3 Å3, Z= 2, Rgt(F) = 0.068, wRref(F2)= 0.142, T= 295 K.Publication Metadata only Inferring transferable intermolecular potential models(2008) Üçyigitler, Sinan; Çamurdan, Mehmet C.; Elliott, J. Richard; Department of Industrial Engineering; Türkay, Metin; Faculty Member; Department of Industrial Engineering; College of Engineering; 24956Discontinuous molecular dynamics is combined with thermodynamic perturbation theory to provide an efficient basis for characterising molecular interactions based on vapour pressure and liquid density data. Several prospective potential models are discretised to permit treatment by Barker–Henderson perturbation theory. The potentials are characterised by 11 wells ranging over radial distances from the site diameter to three times that diameter. Considered potential models include the Lennard-Jones (LJ), square-well, Yukawa (Yuk) and multi-line potentials, and their combinations. The optimal model is found to be a combination of square-well and Yuk potentials, with the switch position and Yuk decay set to universal values. This model provides average vapour pressure deviations of less than 10% for a database of 86 aliphatic, aromatic and naphthenic compounds. The LJ potential provides the least competitive accuracy. Considering statistical information criteria facilitates the identification of the optimal model.Publication Metadata only Crystal structure of mono(silver, gallium) trimagnesium, Ag 0.55Ga0.45Mg3(Walter de Gruyter GmbH, 2005) Kudla, C.; Prots, Yu.; Kleiner, G.; Department of Chemistry; Oruçoğlu, Egemen; Undergraduate Student; Department of Chemistry; College of Sciences; N/AAg0.55Ga0.45Mg3, trigonal, R3̄ (no. 148), a = 8.248(1) Å, c = 25.658(4) Å, V = 1511.8 Å3, Z = 18, Rgt(F) = 0.031, wRref(F 2) = 0.060, T = 293 K.Publication Metadata only Novel barium beryllates Ba[Be2N2] and Ba-3[Be5O8]: syntheses, crystal structures and bonding properties(Wiley-V C H Verlag Gmbh, 2005) Leoni, Stefano; Niewa, Rainer; Akselrud, Lev; Prots, Yurii; Schnelle, Walter; Kniep, Rüdiger; Department of Chemistry; Department of Chemistry; Department of Chemistry; Göksu, Tahsin; Çetinkol, Mehmet; Somer, Mehmet Suat; Undergraduate Student; Undergraduate Student; Faculty Member; Department of Chemistry; College of Sciences; College of Sciences; College of Sciences; N/A; N/A; 178882Ba[Be2N2] was prepared as a yellow-green microcrystalline powder by reaction of Ba2N with Be3N2 under nitrogen atmosphere. The crystal structure Rietfeld refinements (space group I4/mcm, a = 566.46(5) pm, c = 839.42(9) pm, R-int = 4.73 %, R-prof = 9.16 %) reveal the compound to crystallize as an isotype of the nitridoberyllates A[Be2N2] (A = Ca, Sr) consisting of planar 4.8(2) nets (2)(infinity)[(Be2N2)(2-)] of mutually trigonal planar coordinated Be and N species. Averaged magnetic susceptibility values for the anion [(Be2N2)(2-)] determined from measurements on A[Be2N2] with A = Mg, Ca, Ba allow to derive a diamagnetic increment for N3- chi(dia) = (-13 +/- 1stat.) (.) 10(-6)emu mol(-1). Colorless Ba-3[Be5O8] was first obtained as an oxidation product of Ba[Be2N2] in air. The crystal structure was solved and refined from single crystal X-ray diffaction data (space group Pnma, a = 942.9(1) pm, b = 1163.47(7) pm, c = 742.1(1) pm, R1 = 2.99 %, wR2 = 7.15 %) and contains infinite rods of Be in trigonal planar, tetrahedral and 3 + 1 coordination by O. The crystal structure is discussed in context with other known oxoberyllates. Electronic structure calculations and electron localization function diagrams for both compounds support the classification as nitrido- and oxoberyllate, respectively.