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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 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 Modification of benzoxazole derivative by bromine-spectroscopic, antibacterial and reactivity study using experimental and theoretical procedures(Elsevier, 2017) Aswathy, V. V.; Alper-Hayta, Sabiha; Yalcin, Gozde; Mary, Y. Sheena; Panicker, C. Yohannan; Jojo, P. J.; Kaynak-Onurdag, FatmaN-[2-(2-bromophenyl)-1,3-benzoxazol-5-yl]-2-phenylacetamide (NBBPA) was synthesized in this study as an original compound in order to evaluate its antibacterial activity against representative Gram-negative and Gram-positive bacteria, with their drug-resistant clinical isolate. Microbiological results showed that this compound had moderate antibacterial activity. Study also encompassed detailed FT-IR, FT-Raman and NMR experimental and theoretical spectroscopic characterization and assignation of the ring breathing modes of the mono-, ortho- and tri-substituted phenyl rings is in agreement with the literature data. DFT calculations were also used to identify specific reactivity properties of NBBPA molecule based on the molecular orbital, charge distribution and electron density analysis, which indicated the reactive importance of carbonyl and NH2 groups, together with bromine atom. DFT calculations were also used for investigation of sensitivity of the NBBPA molecules towards the autoxidation mechanism, while molecular dynamics (MD) simulations were used to investigate the influence of water. The molecular docking results suggest that the compound might exhibit inhibitory activity against GyrB complex. (C) 2017 Elsevier B.V. All rights reserved.Öğe Synthesis and Antimicrobial Evaluation of 2-(p-Substituted Phenyl)-5-[(4-substituted piperazin-1-yl)acetamido]-benzoxazoles(Walter De Gruyter Gmbh, 2014) Arisoy, Mustafa; Temiz-Arpaci, Ozlem; Kaynak-Onurdag, Fatma; Ozgen, SeldaA series of 2-(p-substituted phenyl)-5-(2-{4-[(p-chloro-fluorophenyl)/phenyl] piperazin-1-yl}-lacetamido)-benzoxazoles were synthesized and tested for their antimicrobial activities. The structures of the new derivatives were elucidated by spectral techniques. The minimum inhibitory concentrations (MIC) of the new benzoxazoles, along with those of previously synthesized analogues, were determined against standard bacterial and fungal strains and drug-resistant isolates, and compared with those of several reference drugs. The new benzoxazole derivatives were found to possess a broad spectrum of antimicrobial activity with MIC values of 32 - 1024 mu g/ml. Although the standard drugs were more active against the tested pathogens, the activities of the new benzoxazoles and the reference drugs were largely similar against the drug-resistant isolates.Öğe Synthesis and antimicrobial evaluation of novel 5-substituted-2-(p-tert-butylphenyl)benzoxazoles(Natl Inst Science Communication & Information Resources-Niscair, 2018) Tasci, Meryem; Temiz-Arpaci, Ozlem; Kaynak-Onurdag, Fatma; Okten, SuzanIn the present study, a series of nine novel 5-substituted-2-(p-tert-butylphenyl)benzoxazole derivatives have been synthesized and their structures confirmed by spectral techniques and also tested for their antimicrobial activities. The minimum inhibitory concentrations (MIC) of the new benzoxazoles have been determined against standard bacterial and fungal strains and drug-resistant isolates and compared to those of several reference drugs. The new benzoxazole derivatives are found to possess a broad spectrum of antibacterial activity with MIC values of 8-256 mu g/mL. Especially, compound 9 is more active than standard drugs ciprofloxacin and cefotaxime against E. coli isolate with a MIC value of 8 mu g/mL. Also new compounds are less active than fluconazole with a MIC value of 256 mu g/mL against C. albicans and its isolate except for compound 9 that shows better activity other compounds with a MIC value of >4 mu g/mL for their antifungal activity.Öğe SYNTHESIS AND ANTIMICROBIAL EVALUATION OF SOME NOVEL SULFONYLAMIDO-BENZOXAZOLES(Akademiai Kiado Zrt, 2016) Temiz-Arpaci, Ozlem; Doganc, Fatma; Sac, Duygu; Sari, Elmas; Kaynak-Onurdag, Fatma; Okten, SuzanA series of 2-(p-substituted phenyl)-5-[(4-substituted phenyl) sulfonylamido]-benzoxazoles were synthesized and tested for their antimicrobial activities. The structures of the new derivatives were elucidated by spectral techniques. The minimum inhibitory concentrations (MIC) of the new benzoxazoles were determined against standard bacterial and fungal strains and drug-resistant isolates and compared to those of several reference drugs.Öğe Synthesis of some piperazinobenzoxazole derivatives and their antimicrobial properties(Council Scientific & Industrial Res, 2016) Arisoy, Mustafa; Temiz-Arpaci, Ozlem; Kaynak-Onurdag, Fatma; Ozgen, SeldaA series of 2-(p-substitutedphenynenzy1)-5-[3-[4-[(p-chlorophenyl)/phenyl]piperazin-1-yl]propionamido]-benzoxazoles (3-22) have been synthesized towards discovering new antimicrobial compounds in order to fight against pathogens, which have become resistant to antibiotics and are the cause of increased mortality and morbidity throughout the world. Structures of new derivatives have been elucidated by spectral techniques. New and previously synthesized benzoxazoles have been evaluated for their antibacterial and antifungal activity against standard strains, and their drug-resistant isolates in comparison with reference drugs. This study is aimed to investigate the efficacy of the antimicrobial effect of different amido bridges on the same homologue structures of benzoxazole compounds. Compounds 3-22 exhibit broad antibacterial activity with MIC (Minimum Inhibitory Concentration) values of 128-256 mu g/mL against Staphylococcus aureus and its isolate except for derivative 7 that has a MIC value of 32 mu g/mL against S. aureus isolate and compounds 3 and 22 which have MIC value of 512 mu g/mL against S. aureus. Also, the tested compounds 3-22 possess low antifungal activity with MIC values of 128 mu g/mL against Candida albicans in comparison with antifungal reference drugs, fluconazole and amphotericin B.Öğe Synthesis, Antimicrobial Activities of New Sulfonamidobenzoxazoles and Molecular Docking Studies on Escherichia coli TEM-1 ?-Lactamase(Croatian Chemical Soc, 2017) Ertan-Bolelli, Tugba; Bolelli, Kayhan; Okten, Suzan; Kaynak-Onurdag, Fatma; Aki-Yalcin, Esin; Yalcin, Ismailbeta-Lactam antibiotics are frequently used for treatment of multi-drug resistant microbial infections and the most common mechanism of resistance against these antibiotics is bacterial beta-lactamase production. Herein, we reported the design, synthesis and in vitro antimicrobial activities of some new 2-substituted-5-(2,4-dinitrophenylsulfonamido) benzoxazole derivatives. Compounds TN1, TN2, and TN3 were found to be significantly active against E. coli isolate which contains extended spectrum beta-lactamase enzyme at the MIC value of 8 mu g mL(-1) and that is 4-fold higher than the reference drug ampicillin. We performed molecular docking studies into active site of Escherichia coli TEM-1 beta-lactamase enzyme in order to predict the protein-ligand interactions. According to the docking results, compounds TN1, TN2, and TN3 showed strong interactions between the important active site residues which are responsible for the catalytic mechanism of TEM-1 beta-lactamase enzyme and a good correlation is found with the experimental data.Öğe Synthesis, Antimicrobial Activity, and Molecular Modeling Studies of Some Benzoxazole Derivatives(Bentham Science Publ Ltd, 2022) Muhammed, Muhammed Tilahun; Kuyucuklu, Gulcan; Kaynak-Onurdag, Fatma; Aki-Yalcin, EsinBackground: The need to develop novel antimicrobial agents is apparent as infectious diseases are increasing and resistance is rapidly developing against the drugs used in the treatment. Objective: This study aimed at the synthesis, antimicrobial susceptibility testing, and computational elucidation of the mechanism of action of benzoxazole derivatives. It also aimed to compare the results obtained in this study with the previous studies by our group. This would pave the way for designing novel molecules with better antimicrobial activity. The other goal was pharmacophore analysis and in silico ADMET analysis of them. Methods: In this study, synthesis, antimicrobial susceptibility testing, molecular docking, pharmacophore analysis, and ADMET prediction were carried out. Results: The antimicrobial activity studies demonstrated that the synthesized compounds were active against standard strains and clinical isolates at high concentrations. Then, the antimicrobial testing results were compared to similar benzoxazoles tested by our group previously. Benzoxazole derivatives without a methylene bridge between oxazole and phenyl ring were found to be more active than those with the methylene bridge. This was also confirmed by molecular modeling undertaken in this study. The computational results indicated that the antibacterial activity could be achieved by DNA gyrase inhibition. Pharmacophore analysis showed that hydrogen bond acceptor (HBA), hydrogen bond donor (HBD), and hydrophobicity features would contribute to the inhibition. In addition, in silico ADMET property investigation of the compounds exhibited that they had the desired pharmacokinetics. Conclusion: Although antibacterial activity by inhibiting DNA gyrase is selective, the synthesized compounds were active at much higher concentrations than the standards. Therefore, in prospective antimicrobial studies, it is better to focus on benzoxazole derivatives without the methylene bridge. Since the compounds had suitable in silico ADMET properties, screening them against the other pharmacologic activities should be carried out. It is recommended to support the molecular modeling results with in vitro or in vivo studies.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.
