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Öğe Antiquorum Sensing Effect, Theoretical, and X-Ray Studies of a Schiff Base Molecule Containing Pyrimidine Nucleus(Wiley-V C H Verlag Gmbh, 2024) Karatas, Halis; Onem, Ebru; Akkoc, Senem; Zeyrek, Celal Tugrul; Sahin, Zarife Sibel; Kokbudak, ZulbiyeCompound 4, a Schiff base-containing pyrimidine moiety, was synthesized from the reaction of N-amino pyrimidine derivative with 4-fluorobenzaldehyde. The molecular and crystallographic structure of 4 was determined by the SC-XRD method. According to these results, compound 4 crystallized in the triclinic P-1 space group, and the stability of its crystal structure was ensured through intermolecular C-H & sdot;& sdot;& sdot;pi and pi & sdot;& sdot;& sdot;pi interactions. In addition to the antibacterial effects of the molecule on some Gram-positive and Gram-negative bacteria, the inhibition of biofilm formation in P. aeruginosa PAO1 and the production of violacein pigment in Chromobacterium violaceum (C. violaceum) 12472 were studied. The results demonstrated that compound 4 had strong effectiveness in preventing the formation of biofilms produced by PAO1 with an inhibition rate of 69 %. Extensive theoretical calculation studies of molecule have been conducted and the molecular structure of 4 has been optimized in the ground state using density functional theory (DFT). The investigated compound's frontier molecular orbitals, chemical parameters, and molecular electrostatic potential surfaces were examined. Molecular docking studies were performed to explain the binding interaction 4 with the high inhibitory effect against C. violaceum phenylalanine hydroxylase D139A (PDB ID: 4Q3Y), D139E (PDB ID: 4Q3W), D139K (PDB ID: 4Q3Z), and D139N (PDB ID: 4Q3X) mutations.Öğe Design, Synthesis, Cytotoxic Activity, and In Silico Studies of New Schiff Bases Including Pyrimidine Core(Wiley-V C H Verlag Gmbh, 2023) Karatas, Halis; Aydin, Meltem; Turkmenoglu, Burcin; Akkoc, Senem; Sahin, Onur; Kokbudak, ZuelbiyeIn here, two new Schiff base molecules (3 and 4) were synthesized from the condensation reaction of 1-amino-5-benzoyl-4-phenylpyrimidine-2(1H)-one (1) and 1-amino-5-(4-methylbenzoyl)-4-p-tolylpyrimidin-2(1H)-one (2) with 4-bromobenzaldehyde. These molecules were completely characterized by IR, NMR, and HR-MS. Moreover, molecule 4 was determined by single crystal x-ray diffraction (SC-XRD) patterns. The crystallographic analysis revealed that molecule 4 crystallizes in the monoclinic system, space group P2(1)/c. The molecules were screened in colon, lung and liver cell lines. The results showed that molecule 4 had cytotoxic activity in all screened cancer cell lines. Molecular docking studies of molecules 3 and 4, which were synthesized experimentally and whose cytotoxic activities were examined, were carried out with in silico approaches. Binding parameter values and active binding sites were determined by interacting the compounds with EGFR (PDB ID : 1M17) and VEGFR-2 (PDB ID : 4ASD) crystal structures, respectively, in molecular docking. In addition, the theoretical pharmacokinetic properties of compounds 3 and 4 were evaluated using ADME analysis.Öğe Efficient synthesis and molecular docking studies of new pyrimidine-chromeno hybrid derivatives as potential antiproliferative agents(Taylor & Francis Inc, 2021) Yavuz, Sevtap Caglar; Akkoc, Senem; Tuzun, Burak; Sahin, Onur; Saripinar, EminVarious novel heterocyclic compounds containing pyrimidine nuclei 5H-chromeno[4,3-d]pyrimidine (4a-c, e-h, l-r, t) and pyrimidine-5-yl-(2-hydroxyphenyl)methanone (5a, c, d, f-k, m-o, r, s, u) were synthesized from the reaction of guanylhydrazones (2a-u) and 3-formylchromone (3). These compounds were tested against human liver hepatocellular carcinoma cell line (HepG2) and human breast adenocarcinoma cell line (MDA-MB-231) using the MTT assay method. Furthermore, molecular docking calculations were performed to compare the biological activities of various novel heterocyclic compounds against cancer proteins. In these calculations, the protein used are crystal structure of the BRCT repeat region from the breast cancer associated protein, 1JNX, crystal structure of VEGFR kinase (liver cancer) protein, 3WZE, and crystal structure of an allosteric Eya2 phosphates inhibitor (lung cancer) protein, 5ZMA, respectively. After molecular docking calculations, absorption, distribution, metabolism, and excretion/toxicity analysis was performed to examine the properties of various novel heterocyclic compounds for their future use as drugs.Öğe Novel Thioether-Bridged 2,6-Disubstituted and 2,5,6-Trisubstituted Imidazothiadiazole Analogues: Synthesis, Antiproliferative Activity, ADME, and Molecular Docking Studies(Wiley-V C H Verlag Gmbh, 2023) Ozcan, Ibrahim; Akkoc, Senem; Alici, Hakan; Capanlar, Seval; Sahin, Onur; Tahtaci, HakanIn this study, starting from 2-amino-1,3,4-thiadiazole derivatives (3-5), a new series of 2,6-disubstituted (compounds 7-15) and 2,5,6-trisubstituted (compounds 16-33) imidazo[2,1-b][1,3,4]-thiadiazole derivatives were synthesized using cyclization and Mannich reaction mechanisms, respectively. All synthesized compounds were characterized by H-1-NMR, C-13-NMR, FT-IR, elemental analysis, and mass spectroscopy techniques. Also, X-ray diffraction analysis were used for compounds 4, 7, 11, 17, and 19. The cytotoxic effects of the new compounds on the viability of colon cancer cells (DLD-1), lung cancer cells (A549), and liver cancer cells (HepG2) were investigated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method in vitro. Compound 15 was found to be the most potent anticancer drug candidate in this series with an IC50 value of 3.63 mu M against HepG2 for 48 h. Moreover, the absorption, distribution, metabolism, and excretion (ADME) parameters of the synthesized compounds were calculated and thus, their potential to be safe drugs was evaluated. Finally, to support the biological activity experiments, molecular docking studies of these compounds were carried out on three different target cancer protein structures (PDB IDs: 5ETY, 1M17, and 3GCW), and the amino acids that play key roles in the binding of the compounds to these proteins were determined.
