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Öğe 1H-Benzimidazole-5-carboxamidine derivatives: design, synthesis, molecular docking, DFT and antimicrobial studies(Royal Soc Chemistry, 2020) Erol, Meryem; Celik, Ismail; Temiz-Arpaci, Ozlem; Goker, Hakan; Kaynak-Onurdag, Fatma; Okten, SuzanIn this study, 15 new N-(cyclohexyl)-2-substituted-1H-benzimidazole-5-carboxamidine derivatives that could be new antimicrobial agents were synthesized and their antimicrobial activities were determined using the microdilution method. Some of the derivatives showed significant efficacy against MRSA and VREF with an MIC value of 8 mu g mL(-1) compared to reference drugs. Molecular docking studies of the compounds against PBP4 and active and allosteric regions of PBP2a were performed and estimated ADME profiles were calculated. The nitrogens of the amidine group of M7, one of the most effective antimicrobial compounds compared to reference drugs, formed two separate hydrogen bonds with ASP275 (1.77 angstrom) and ASP295 (1.83 angstrom) in the allosteric region of PBP2a. Geometric optimization parameters, MEP analysis, and HUMO and LUMO quantum parameters of M7 were calculated using DFT/B3LYP theory and the 6-311G(d,p) basis set and the results are displayed.Öğe Antimicrobial and antiproliferative activity studies of some new quinoline-3-carbaldehyde hydrazone derivatives(Academic Press Inc Elsevier Science, 2020) Puskullu, Mustafa Orhan; Celik, Ismail; Erol, Meryem; Fatullayev, Hanifa; Uzunhisarcikli, Ebru; Kuyucuklu, GulcanIn this study, a total of 22 piece quinoline-3-carbaldehyde hydrazone derivative compounds were designed and synthesized, 2 of which were not original, their antimicrobial activities were determined with microdilution method and their in vitro cytotoxic effect was investigated in MCF-7 and A549 cells by MTT assay. When the activity results are examined, although the antimicrobial effects of quinoline derivatives, in general, are weaker than standard drugs; 3q5 and 3q6 against MRSA showed promising activity with MIC:16 mu g/ml compared to reference drugs. Compounds generally showed weaker cytotoxic activity on the A549 and MCF-7 cell line. 3q12, 3q17 and 3q22 at 100 mu M reduced cell viability to 59.28%, 76.24% and 72.92% on A549 cells, respectively. Compound 3q6, one of the most effective compounds against MRSA, formed a 2.10 angstrom long hydrogen bond between the quinoline nitrogen and ARG132 in the DNA topoisomerase IV active site (PDB: 3FV5). Theoretical ADME profiles of all compounds comply with Lipinski and other limiting rules. In addition, MEP analysis of 3q6, geometric optimization and molecular reactivity analysis were calculated with the 6-311G (d,p) base set DFT/ B3LYP theory, and Delta E = ELUMO-EHOMO, which is a measure of the stable structure of the molecule, was cal-culated as 0.13377 for 3q6 and had the most stable electronic structure among all compounds.Öğe Design, synthesis, molecular docking, density functional theory and antimicrobial studies of some novel benzoxazole derivatives as structural bioisosteres of nucleotides(Taylor & Francis Inc, 2021) Erol, Meryem; Celik, Ismail; Temiz-Arpaci, Ozlem; Kaynak-Onurdag, Fatma; Okten, SuzanA series of some novel 2-(p-tert-butylphenyl)-5-(3-substituted-propionamido)benzoxazole derivatives have been designed, synthesized, evaluated for antimicrobial activity and have performed molecular docking studies against penicillin-binding protein 4 (PBP4) and active and allosteric site of PBP2a; were calculated some theoretical quantum parameters and absorption, distribution, metabolism and excretion (ADME) descriptors. B9 acted at minimum inhibitory concentration (MIC) = 8 mu g/mL against S. aureus, E. faecalis and their drug-resistant isolates and also formed with GLU145 (1.74 angstrom) and ILE144 (1.89 angstrom) two hydrogen bonds at allosteric site of PBP2a with Glide emodel score: -42.168. Delta E of compound B9 had moderate value of all compounds with 0.14742. Communicated by Ramaswamy H. SarmaÖğe In VitroandIn SilicoStudies of Quinoline-2-Carbaldehyde Hydrazone Derivatives as Potent Antimicrobial Agents(Taylor & Francis Ltd, 2022) Celik, Ismail; Erol, Meryem; Puskullu, Mustafa Orhan; Uzunhisarcikli, Ebru; Ince, Ufuk; Kuyucuklu, Gulcan; Suzen, SibelWe previously synthesized a series of quinoline-2-carbaldehyde hydrazone derivatives and evaluated their antioxidant activities. In this study, the antimicrobial activities of these quinoline-2-carbaldehyde hydrazone derivatives were evaluated antimicrobial activity by the microdilution method, and there cytotoxic effect was investigated in MCF-7 and A549 cells by MTT assay. When the activity results were examined, although the antimicrobial activity of quinoline derivatives were equal or better than standard drugs in general, compound4(2 mu g/mL) and8(1 mu g/mL) againstE. faecalisand5(8 mu g/mL) againstP. aeruginosaare the most effective derivatives of the series. Besides, disk diffusion test was applied to these three compounds, and significant zone formation was observed at8(7 mm) compared to vancomycin (9 mm). Compounds showed no antiproliferative in A549 and MCF-7 cell lines, and compound4, 5,and8, which showed the most effective antimicrobial activity, were examined in healthy cells (Beas-2b) and no effect on cell viability was found. To understand the mechanism of this action of these compounds againstE. faecalis, molecular docking studies were performed on 15 different proteins, and it was concluded that the compounds interacted with FabH and not enough with other protein structures. The theoretical ADME profiles of compounds comply with Lipinski and other limiting rules. Also, some theoretical quantum parameters (HOMO-LUMO) of compounds, and both MEP analysis and geometric optimization analysis of8were calculated with 6-311 G (d,p) base set and DFT/B3LYP theory, and the results were shown.Öğe Molecular modeling, density functional theory, ADME prediction and antimicrobial activity studies of 2-(substituted)oxazolo[4,5-b]pyridine derivatives(Royal Soc Chemistry, 2021) Celik, Ismail; Erol, Meryem; Kuyucuklu, GulcanIn this study, the antimicrobial activities of previously synthesized 2-(substituted)oxazolo[4,5-b]pyridine derivatives toward six bacteria strains and twelve related drug-resistant isolates, and one fungus strain and two related drug-resistant isolates were investigated via the microdilution method. P6 (2-(4-trifluoromethylphenyl)oxazolo[4,5-b]pyridine) and P7 (2-(4-trifluoromethoxyphenyl)oxazolo[4,5-b]pyridine) showed better activity against E. faecalis isolate and E. coli isolate than ampicillin with a MIC of 16 mu g mL(-1). In addition, P5 (2-(4-methoxyphenyl)oxazolo[4,5-b]pyridine) and P6 showed gentamicin-equivalent activity against P. aeruginosa, with a MIC of 16 mu g mL(-1), while P7 showed better activity than gentamicin, with a MIC of 8 mu g mL(-1). The compounds generally showed good to strong antimicrobial activities. Molecular docking and molecular dynamics simulations of the compounds were performed using the DNA gyrase enzyme, and the interactions were evaluated. The compounds showed an overlap at the DNA gyrase ATP binding site with similar protein-ligand interactions. Average RMSD values of the apo form, and P5-4KTN, P6-4KTN and P7-4KTN holo forms were measured to be 0.149 nm, 0.152 nm, 0.165 nm, and 0.146 nm, respectively. The P7 ligand stabilized the protein via further increasing its stability. HOMO-LUMO orbital energies and other electronic parameters derived from these energies, MEP and NBO analysis, and geometric optimization were obtained using DFT/B3LYP theory and the 6-311G(d,p) basis set. The LUMO-HOMO Delta E values for the most active compounds, P5, P6 and P7, are 4.3508, 4.4471, and 4.4852 eV, respectively. The predicted ADME profiles of the compounds were calculated, and they were compliant with Lipinski and other restrictive rules.Öğe Synthesis, Molecular Docking, and DFT Studies of Some New 2,5-Disubstituted Benzoxazoles as Potential Antimicrobial and Cytotoxic Agents(Taylor & Francis Ltd, 2022) Erol, Meryem; Celik, Ismail; Uzunhisarcikli, Ebru; Kuyucuklu, GulcanIn this study, a total of 17 piece 2,5-disubstituted benzoxazole derivatives were synthesized, 2 of which were not original, their antimicrobial activities were determined using microdilution method and theirin vitrocytotoxic activities were investigated on MCF-7 and A549 cells by MTT test. When the activity results are examined, although the antibacterial effects of benzoxazole derivatives are weaker than standard drugs;3N13and3N19againstCandida albicansisolate showed the closest activity to fluconazole with MIC: 16 mu g/ml. The cytotoxicity test was measured at a concentration of 100 mu M and a 24-h incubation period. The results showed that the compounds had weak activities against two cell lines. Molecular docking studies of synthesized compounds were performed on sterol 14 alpha-demethylase protein (CYP51) and protein-ligand interactions of3N13, the most effective derivative againstC. albicansisolate, were showed (PDB: 5TZ1). Estimated ADME profiles of compounds were calculated and also3N13's were calculated HUMO-LUMO energies, molecular electrostatic potential analysis, and geometric optimization parameters with 6-311 G+ (d,p) base set using DFT/B3LYP theory, and the results were displayed.Öğe Synthesis, Molecular Docking, Molecular Dynamics, DFT and Antimicrobial Activity Studies of 5-substituted-2-(p-methylphenyl)benzoxazole Derivatives(Elsevier, 2021) Erol, Meryem; Celik, Ismail; Kuyucuklu, GulcanIn this study, new 2-(p-methylphenyl)-5-(2-substitutedacetamido)benzoxazole derivatives were synthesized, and antimicrobial activities on six bacteria and their twelve drug-resistant isolates and one fungus and its two drug-resistant isolates were investigated by microdilution method. B1 against Staphylococcus aureus isolate, and B1 and B2 against Escherichia coli isolate showed more potent antimicrobial activity with MIC value of 16 mu g/mL than some of the reference drugs. The compounds' interactions on the DNA gyrase enzyme were evaluated by molecular docking and molecular dynamics simulations. Docked compounds have demonstrated superimposition in the DNA gyrase ATP binding site with similar protein-ligand interactions. With 50 ns duration molecular dynamics simulations, the average RMSD value of the DNA gyrase subunit B protein and B1, B2, B3, and B4 complexes were measured at about 0.15 nm. The ligands-bound DNA gyrase subunit B protein is a little less RMSF value and more stable than the apoprotein form between 45-49 residues in the active site amino acids region. Geometric optimization parameters, HOMO-LUMO orbital energies, and other electronic parameters derived from these energies, MEP, and NBO analysis were performed the DFT/B3LYP theory and 6-311G (d,p) basis set. The Delta E: LUMO-HOMO of the two most active compounds B1 and B2 are 4.2928 and 4.3219, respectively. The compounds' predicted ADME profiles were in line with Lipinski and other limiting rules. (C) 2021 Elsevier B.V. All rights reserved.Öğe Synthesis, quantum mechanical calculations, antimicrobial activities and molecular docking studies of five novel 2,5-disubstituted benzoxazole derivatives(Elsevier, 2021) Temiz-Arpaci, Ozlem; Zeyrek, Celal Tugrul; Arisoy, Mustafa; Erol, Meryem; Celik, Ismail; Kaynak-Onurdag, FatmaIn this study, five new 2-(p-(Substituted)phenyl)-5-(3-(4-ethylpiperazine-1-yl) propionamido)benzoxazole derivatives (B7-B11) were designed, synthesized, and their antimicrobial activities were determined by the microdilution method. The novel benzoxazole compounds were characterized using FTIR, H-1 NMR, and C-13 NMR spectroscopy, mass spectroscopy, and elemental analysis. B7 and B11 showed promising activity against P. aeruginosa isolate at 16 mu g/mL compared to the reference drugs. Quantum mechanical calculations were performed on five compounds in the ground state using density functional theory (DFT) with the B3LYP/6-311G(d,p) level. Molecular docking studies of the compounds were also performed a complex structure of the DNA gyrase enzyme with ciprofloxacin (PDB: 2XCT), and it was observed that the binding poses were similar to ciprofloxacin. Theoretical ADME profiles of the compounds conform to Lipinski and other limiting rules. (C) 2021 Elsevier B.V. All rights reserved.
