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Öğe 4D-QSAR Study of Some Pyrazole Pyridine Carboxylic Acid Derivatives By Electron Conformational-Genetic Algorithm Method(BENTHAM SCIENCE PUBL LTD, 2018) Tuzun, Burak; Yavuz, Sevtap Caglar; Sabanci, Nazmiye; Saripinar, EminIntroduction: In the present work, pharmacophore identification and biological activity prediction for 86 pyrazole pyridine carboxylic acid derivatives were made using the electron conformational genetic algorithm approach which was introduced as a 4D-QSAR analysis by us in recent years. In the light of the data obtained from quantum chemical calculations at HF/6-311 G** level, the Electron Conformational Matrices of Congruity (ECMC) were constructed by EMRE software. Comparing the matrices, electron conformational submatrix of activity (ECSA, Pha) was revealed that are common for these compounds within a minimum tolerance. A parameter pool was generated considering the obtained pharmacophore. Methods: To determine the theoretical biological activity of molecules and identify the best subset of variables affecting bioactivities, we used the nonlinear least square regression method and genetic algorithm. Results: The results obtained in this study are in good agreement with the experimental data presented in the literature. The model for training and test sets attained by the optimum 12 parameters gave highly satisfactory results with R-training(2) = 0.889, q(2)=0.839 and SEtraining=0.066, q(ext1)(2) = 0.770, q(ext2)(2) = 0.750, q(ext3)(2)=0.824, ccc(tr) = 0.941, ccc(test) = 0.869 and ccc(all) = 0.927.Öğe Molecular docking and 4D-QSAR model of methanone derivatives by electron conformational-genetic algorithm method(Springer, 2020) Tuzun, Burak; Saripinar, EminIn our QSAR study, pharmacophore identification and biological activity estimation of 80 methanone derivatives were performed with the Electron Conformation Genetic Algorithm approach. Using the geometric, thermodynamic and topological properties of molecules from the data obtained from quantum chemical calculations in the HF/3-21 G basis set, the Electron Conformational Matrices of Congruity were generated by the EMRE software. Taking into account the pharmacophores atoms, 804 parameters were prepared. The nonlinear least squares optimization technique and genetic algorithm were used to determine the variables affecting the biological activity values for the calculation of the biological activity values of the studied molecules. 4D-QSAR approach the EC-GA method, that ensures pharmacophore detection, variable selection and quantitative bioactivity prediction, is used to calculate biological activity values of methanone derivatives. The model for the training and test sets attained by the optimum 8 parameters gave highly satisfactory results with Rtraining2 = 0.834, q(2) = 0.768 and SEtraining = 0.075, qext12 = 0.875, qext22 = 0.839, qext32 = 0.764, ccc(tr) = 0.908, ccc(test) = 0.929 and ccc(all) = 0.920. The interaction between the studied molecules and the live cancer protein which ID is 2H80 at DockingServer was examined to find the activity of the molecules examined in molecular placement calculations.Öğe Synthesis, Biological Activity Evaluation and Molecular Docking of Imidazole Derivatives Possessing Hydrazone Moiety(Wiley-V C H Verlag Gmbh, 2023) Kekecmuhammed, Huseyin; Tapera, Michael; Aydogdu, Ekrem; Saripinar, Emin; Karatas, Elanur Aydin; Uc, Eda Mehtap; Akyuz, MesutIn an attempt to identify potential active anticancer agents with low cytotoxic properties and CA inhibitors, a new series of hybrid compounds incorporating imidazole ring and hydrazone moiety as part of their structure were synthesized by aza-Michael addition reaction followed by intramolecular cyclization. The structure of synthesized compounds was elucidated using various spectral techniques. Synthesized compounds were evaluated for their in vitro anticancer (prostate cell lines; PC3) and CA inhibitory (hCA I and hCA II) activity. Among them, some compound displayed remarkable anticancer activity and CA inhibitory activity with K-i values in range of 17.53 +/- 7.19-150.50 +/- 68.87 nM against cytosolic hCA I isoform associated with epilepsy, and 28.82 +/- 14.26-153.27 +/- 55.80 nM against dominant cytosolic hCA II isoforms associated with glaucoma. Furthermore, the theoretical parameters of the bioactive molecules were calculated to establish their drug-likeness qualities. The proteins used for the calculations are prostate cancer protein (PDB ID: 3RUK and 6XXP). ADME/T analysis was carried out to examine the drug properties of the studied molecules.Öğe Synthesis, Molecular Docking and Antiproliferative Activity Studies of a Thiazole-Based Compound Linked to Hydrazone Moiety(Wiley-V C H Verlag Gmbh, 2022) Kekecmuhammed, Huseyin; Tapera, Michael; Tuzun, Burak; Akkoc, Senem; Zorlu, Yunus; Saripinar, Emin(A new 4-oxothiazolidin-2-ylidene derivative bearing hydrazone moiety was synthesized via Michael addition between the reaction of 4-(4-nitrophenyl)-3-thiosemicarbazide and dimethyl acetylenedicarboxylate (DMAD). The structure of synthesized compound was elucidated using various spectral techniques such as FTIR, UV-spec, H-1 NMR and C-13 NMR. The structure of the related compound was confirmed by single-crystal X-ray analysis. Antiproliferative activity of the synthesized compound was evaluated in two human cancer cell lines, HepG2 (liver hepatocellular carcinoma cell line) and DLD-1 (human colon cancer cell line). In addition, molecular docking of synthesized compound was investigated to give an insight of its activity against Epidermal Growth Factor Receptor tyrosine kinase domain proteins (EGFR) (lung cancer) (PDB ID: 1 M17), deleted in Liver Cancer 2 proteins (DLC2) (liver cancer) (PDB ID: 2H80), and MLK4 kinase proteins (colon cancer) (PDB ID: 4UYA) were investigated. Furthermore, the ability of the molecule to be a drug was examined by ADME/T analysis.)
