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Öğe A broad assessment of Eremurus spectabilis M. Bieb: chemical and elemental composition, total phenolic and antimicrobial activity analysis, and quantum chemical calculations of radical scavenging potential(Taylor & Francis Ltd, 2024) Tegin, Ibrahim; Hallac, Bulent; Sabanci, Nazmiye; Sadik, Betul; Fidan, Mehmet; Yabalak, ErdalEremurus spectabilis M. Bieb was extensively investigated experimentally and theoretically, including the antioxidant properties of compounds such as flavonoids, hydroxycinnamic acid derivatives, hydroxybenzoic acid derivatives, and organic acids. Antioxidant activity was investigated using the Density Functional Theory (DFT) method based on three known mechanisms: hydrogen atom transfer (HAT), single electron transfer followed by proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET). Subcritical water extraction (SWE), soxhlet extraction (SE), and solvent extraction (SOE) techniques were applied in the extraction process. Malic acid was the major compound with an extract concentration of 38,532.84 +/- 1849.58 mu g analyte/kg, total phenolics, and free radical scavenging activity were 10.67 mg gallic acid/mL extract and 73.89% per mg/mL extract, respectively. P, Fe, Na, Mg, K, and Ca were the main elements. The antibacterial activity of E. spectabilis against seven bacteria was evaluated, and it was found to be higher than the commercial antibiotics P10 and AMC30.Öğe DNA Cleavage Properties, Antimicrobial and Cytotoxic Activity and 4D-QSAR Analysis of Some Pyrazole Derivatives(Bentham Science Publ Ltd, 2019) Kopru, Semiha; Kup, Fatma Ozturk; Sabanci, Nazmiye; Cadir, Mehmet; Bulut, Duygu Cemre; Duman, Fatih; Ilhan, Ilhan OzerBackground: An extensive study of 19 pyrazole derivatives were carried out based on the evaluation of DNA cleavage properties, antimicrobial and cytotoxic activities and 4D-QSAR analysis including pharmacophore modelling and bioactivity prediction by the Electron Conformational-Genetic Algorithm (EC-GA) method. Methods: The pyrazole derivatives were tested for their antimicrobial activity against certain human pathogenic organisms using the agar diffusion procedure. Binding of compounds with DNA was studied by gel electrophoresis using plasmid pBR322 DNA. The compounds were investigated for their properties as cytotoxic agents by brine shrimp lethality bioassay. To identify the pharmacophoric elements and find out the most important molecular properties which govern cytotoxic activity, multiple conformations of the compounds were used. Results: The urea derivatives of pyrazole had higher antibacterial activities against Gram-negative bacteria than against Gram-positive bacteria. Many of the compounds were found to cleave plasmid pBR322 DNA from the supercoiled form to the nicked circular. The cytotoxicity values of the compounds ranged from 13.87 to 84.1 mu g/mL. The generated QSAR model was evaluated through the use of the Leave-One-Out Cross Validation (LOO-CV) method. A statistically significant and considerably predictive QSAR model was obtained with 4- descriptors resulting in R2 training = 0.8223, R2 test = 0.9346, q2=0.6201, q2 ext1 0.8672, q2 ext2= 0.8662 and q2 ext3=0.9511. Discussion: The generated model demonstrates that geometrical parameters are more correlated with cytotoxic activity. The resulting EC-GA model would provide benefits to design novel bioactive pyrazole derivatives which are more potent and have less side effects. Conclusion: It is believed that the generated QSAR model gives insight into developing new more potent pyrazole derivative drugs.Öğe Pharmacophore Modelling and 4D QSAR Analysis of Some Indole Glyoxamide Derivatives as HIV-1 Binding Inhibitors(Chem Soc Pakistan, 2022) Sabanci, NazmiyeThe main aim of this study is to uncover the main pharmacophoric features of a series of indole glyoxamide derivatives which are known as HIV-1 attachment inhibitors and to estimate the biological activity to develop a 4D-QSAR model by using the EC-GA method. Conformational analysis and quantum mechanical calculations were accomplished by using the Hartree Fock method with the 3-21G basis set. Based on the data produced from the quantum chemical calculations, the electron conformational matrices of congruity (ECMC)s, as the 3D- arrangement of electronic and geometric properties, were generated by the EMRE program. An individual ECMC was formed for each conformer of each indole glyoxamide derivative in the data set. Conformational flexibility was considered for each compound. Totally 1510 ECMCs were produced by EMRE software to be used in the comparison process. By analogizing the ECMCs in a predetermined tolerance value, the subset of common features matching all active compounds but not matching the low activity compounds was determined. The final ECSA was obtained as a set of nine atoms including predominantly hydrogen bond donors, hydrogen bond acceptors and lipophilic units. Key elements are mainly placed in indole nitrogen, carbonyl groups and piperazine ring. In the bioactivity prediction and variable selection, the genetic algorithm and non-linear least square techniques were employed. The obtained models were internally and externally validated by the leave-oneout cross-validation method. The resulting 4D QSAR EC-GA models were compared with the other methods and the best model with the high prediction ability was defined according to R-training(2)=, R-test(2)=0.8 cross-validatedated q(2)=0.860, q(ext1)(2)= 0.850 and q(ext1)(2) = 0.850 values. Attained EC-GA model provides insight into the vital interaction between indole glyoxamide derivatives and the target protein. EC-GA models can be utilized as an effective and confidential tool in the design of more potent indole glyoxamide derivatives.Öğe Pharmacophore Modelling and 4D-QSAR Study of Ruthenium(II) Arene Complexes as Anticancer Agents (Inhibitors) by Electron Conformational-Genetic Algorithm Method(Bentham Science Publ Ltd, 2018) Yavuz, Sevtap Caglar; Sabanci, Nazmiye; Saripinar, EminObjective: The EC-GA method was employed in this study as a 4D-QSAR method, for the identification of the pharmacophore (Pha) of ruthenium(II) arene complex derivatives and quantitative prediction of activity. Methods: The arrangement of the computed geometric and electronic parameters for atoms and bonds of each compound occurring in a matrix is known as the electron-conformational matrix of congruity (ECMC). It contains the data from HF/3-21G level calculations. Compounds were represented by a group of conformers for each compound rather than a single conformation, known as fourth dimension to generate the model. ECMCs were compared within a certain range of tolerance values by using the EMRE program and the responsible pharmacophore group for ruthenium(II) arene complex derivatives was found. For selecting the sub-parameter which had the most effect on activity in the series and the calculation of theoretical activity values, the non-linear least square method and genetic algorithm which are included in the EMRE program were used. In addition, compounds were classified as the training and test set and the accuracy of the models was tested by cross-validation statistically. Results: The model for training and test sets attained by the optimum 10 parameters gave highly satisfactory results with R-training(2) = 0.817, q(2) = 0.718 and SEtraining = 0.066, q(2) (ext1) = 0.867, q(2) (ext2) = 0.849, q(2) (ext3) = 0.895, ccc(tr) = 0.895, ccc(test) = 0.930 and cc(call) = 0.905. Conclusion: Since there is no 4D-QSAR research on metal based organic complexes in the literature, this study is original and gives a powerful tool to the design of novel and selective ruthenium(II) arene complexes.Öğe Unlocking the potential of Allium dictyoprasum CA Meyer ex Kunth: quantum chemical insights into radical scavenging, chemical composition, phenolic content, and antimicrobial activity(Taylor & Francis Ltd, 2024) Tegin, Ibrahim; Yabalak, Erdal; Hallac, Bulent; Sabanci, Nazmiye; Fidan, Mehmet; Sadik, BetulAllium dictyoprasum C.A. Meyer ex Kunth (A. dictyoprasum) underwent comprehensive analysis, encompassing quantum chemical computations to assess its radical scavenging potential, chemical and elemental composition, total phenolic content, and antimicrobial activity. Experimental and theoretical investigations focused on elucidating the radical scavenging properties of polyhydroxy phenolic compounds present in the plant. Quantum chemical calculations were employed to evaluate the antioxidants employed to evaluate selected polyhydroxy phenolic molecules including flavonoids, hydrocinnamic acid derivatives, and hydroxybenzoic acid derivatives from natural sources. Thermochemical parameters of these compounds were calculated by the B3LYP/6-311 G++(d,p) level in both gas and solvent phases to elucidate the radical scavenging mechanism including hydrogen atom transfer (HAT), single electron transfer followed by proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET). Analysis of A. dictyoprasum extracts obtained via various extraction methods revealed the presence of several major compounds, including dimethyl trisulfide, 3,5-Dihydroxy-6-methyl-2,3-dihydro-4 H-pyran-4-one, 2-Methoxy-4-vinylphenol, Dimethyl phthalate, Methyl palmitate, Methyl oleate, Methyl stearate, (9Z)-9-Octadecenamide. Notably, Malic acid and Quinic acid were identified as major compounds, with concentrations of 43.31 and 17.47 mg kg(-1) extract, respectively, based on LC-MS/MS analysis. The total phenolic content of the extract was measured as 17.83 mg gallic acid/mL, while its free radical scavenging activity was 80.89% per mg/mL. Elemental analysis revealed significant levels of Mg, K, Na, Fe, and P, with minor concentrations of elements such as Ti, Tl, B, and Be. Furthermore, A. dictyoprasum exhibited notable antibacterial activity against various bacteria strains, surpassing the efficacy of some commercial antibiotics. HIGHLIGHTS Quantum chemical calculations of radical scavenging analysis were performed. Thermochemical parameters were calculated by the B3LYP/6-311 G++(d,p) level. Radical scavenging mechanism was evaluated based on HAT, SET-PT and SPLET. Chemical composition of Allium dictyoprasum C.A. Meyer ex Kunth was determined. A. dictyoprasum has a greater antibacterial effects than some commercial antibiotics.
