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    Global gene expression profiling in congenital diaphragmatic hernia (CDH) patients
    (Springer Heidelberg, 2022) Gurunluoglu, Kubilay; Dundar, Muhammed; Unver, Turgay; Akpinar, Necmettin; Gokce, Ismail Kursad; Gurunluoglu, Semra; Demircan, Mehmet
    Congenital diaphragmatic hernia (CDH) is an anomaly characterized by a defect in the diaphragm, leading to the passage of intra-abdominal organs into the thoracic cavity. Herein, the presented work analyzes the global gene expression profiles in nine CDH and one healthy newborn. All of the patients had left posterolateral (Bochdalek) diaphragmatic hernia, operated via an abdominal approach, and stomach and bowels in the thorax cavity. Some patients also had additional anomalies. A total of 560 differentially regulated genes were measured. Among them, 11 genes showed significant changes in expression associated with lung tissue, vascular structure development, and vitamin A metabolism, which are typical ontologies related to CDH etiology. Among them, SLC25A24 and RAB3IL1 are involved in angiogenesis, HIF1A and FOXC2-AS1 are related with the alveolus, MAGI2-AS3 is associated with the diaphragm, LHX4 and DHH are linked with the lung, and BRINP1, FZD9, WNT4, and BLOC1S1-RDH5 are involved in retinol. Besides, the expression levels of some previously claimed genes with CDH etiology also showed diverse expression patterns in different patients. All these indicated that CDH is a complex, multigenic anomaly, requiring holistic approaches for its elucidation.
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    Global gene expression profiling in congenital diaphragmatic hernia (CDH) patients (vol 22, pg 359, 2022)
    (Springer Heidelberg, 2022) Gurunluoglu, Kubilay; Dundar, Muhammed; Unver, Turgay; Akpinar, Necmettin; Gokce, Ismail Kursad; Gurunluoglu, Semra; Demircan, Mehmet
    [Abstract Not Available]
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    Investigation of the Neuroprotective Effect of N-(p-amylcinnamoyl) Anthranilic Acid on Hippocampal Endoplasmic Reticulum Stress in WAG/Rij Rats with Absence Epilepsy
    (Wiley, 2022) Kaya, Gul Busra; Duzova, Halil; Kaya, Mehmet; Dundar, Muhammed; Koc, Ahmet
    [Abstract Not Available]
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    N-alkylbenzimidazole silver(I) complexes: Synthesis, biological evaluation and molecular docking study
    (Pergamon-Elsevier Science Ltd, 2024) Ari, Erkan; Sahin, Neslihan; Ustun, Elvan; Dundar, Muhammed; Karci, Huseyin; Ozdemir, Lknur; Koc, Ahmet
    A series of N-alkylbenzimidazole silver(I) complexes were synthesized and fully characterized by FT-IR, Mass, 1H, 13C{1H} NMR spectroscopy, and elemental analysis. Synthesized N-alkylbenzimidazole silver(I) complexes were investigated for their antimicrobial activities against bacteria Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and the fungal strains Candida albicans and Candida glabrata. All the complexes (2a-f) showed higher antimicrobial activity against bacteria than fungi strains. In particular, complexes 2b and 2e showed comparable activity to Ampicillin against Escherichia coli. Also, all complexes showed better activity than Ampicillin against Pseudomonas aeruginosa. The complex 2e showed remarkable activity against Candida albicans (12.5 mu g/mL) and Candida glabrata (25 mu g/mL). The molecules that were first optimized by DFT-based calculation methods were also analyzed by molecular docking methods against DNA gyrase of E. Coli, CYP51 from Candida glabrata, and Penicillin Binding Protein-3.
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    Silver (I)-N-heterocyclic carbene complexes: Synthesis and characterization, biological evaluation of Anti-Cholinesterase, anti-alpha-amylase, anti-lipase, and antibacterial activities, and molecular docking study
    (Elsevier Science Sa, 2021) Sandeli, Abd El-Krim; Khiri-Meribout, Naima; Benzerka, Saida; Gurbuz, Nevin; Dundar, Muhammed; Karci, Huseyin; Bensouici, Chawki
    A series of novel silver(I)-N-heterocyclic carbene complexes have been prepared and fully characterized by spectroscopic methods and X-ray crystallographic analyses. The biological capacity of the synthesized compounds was evaluated in vitro for their anti-microbial, anti-cholinesterase, anti-lipase, anti-diabetic activities in search of potent inhibitors compound. All compounds were tested against two types of fungi and three bacterias. The results proved that most compounds indicated moderate to excellent activity against all types of bacteria and fungi except compound 2f that didn't show any antibacterial activity. The synthesized compound's capacity to inhibit the enzymes AChE, BChE, Lipase, and alpha-amylase were evaluated. The results showed that silver(I)-NHC complexes 3a-f are effective against all types of enzymes. The highest activity was reported toward AChE, BChE, and alpha-amylase enzymes, and at a lower rate against Lipase enzyme compared to the references drug. In contrast, benzimidazolium salts 2a-f, which showed significant inhibitory activity against AChE and BChE enzymes, while all salts were not active against both Lipase and alpha-amylase enzymes. Molecular docking simulations using AutoDock, have been performed of the new compounds as a representative set of our molecules into AChE and BChE enzymes for lead optimization of the binding interaction template of the most active inhibitors docked into the active site of their relevant AChE and BChE enzymes inhibitors.
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    Synthesis, antimicrobial activity and molecular docking study of benzyl functionalized benzimidazole silver(I) complexes
    (Springer, 2023) Ari, Erkan; Sahin, Neslihan; Ustuen, Elvan; Dundar, Muhammed; Karci, Hueseyin; Ozdemir, Ilknur; Koc, Ahmet
    In this study, a series of N-functionalized benzimidazole silver(I) complexes were prepared and characterized by FT-IR, H-1, C-13{H-1} NMR spectroscopy, and elemental analysis. Synthesized N-benzylbenzimidazole silver(I) complexes were evaluated for their antimicrobial activities against bacteria Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and the fungal strains Candida albicans and Candida glabrata. The results indicated that N-alkylbenzimidazole silver(I) complexes exhibited good antimicrobial activity compared to N-alkylbenzimidazole derivatives. Especially, complex 2e presented perfect antimicrobial activity than the other complexes. The characterized molecules were optimized by DFT-based calculation methods and the optimized molecules were analyzed in detail by molecular docking methods against bacterial DNA-gyrase and CYP51. The amino acid residues detected for both target molecules are consistent with expectations, and the calculated binding affinities and inhibition constants are promising for further studies.
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    Sythesis, characterisation, anticancer and antimicrobial activity of Ag-N-heterocyclic carbene complexes containing benzimidazole derivatives
    (Elsevier Science Sa, 2024) Karci, Huseyin; Dundar, Muhammed; Nawaz, Zahid; Ozdemir, Lknur; Gurbuz, Nevin; Koc, Ahmet; Ozdemir, Ismail
    To prepare a novel series of silver(I) complexes, the interaction of benzimidazolium salts having their two nitrogen atoms substituted by bulky groups with Ag2O in DCM has been carried out. Their structures were characterized by elemental analyses, 1H NMR, 13C NMR, elemental analysis, and IR spectroscopy techniques. Further, the antimicrobial and antifungal activities properties of both the salts and their silver(I)-NHC complexes were tested against positive and negative bacteria using the Clinical and Laboratory Standards Institute (CLSI) and the European Committee for Antimicrobial Susceptibility Testing (EUCAST) respectively. The results show that silver complexes are effective against E. coli, P. aeruginosa and S. aureus bacterial species with moderate to high activity, and their minimum inhibitory concentrations ranging from 25 to 400 mu g/Ml. It was also observed that 3b compound, which has the best antifungal properties among the synthesized compounds, showed high antimicrobial activity when all bacterial species were taken into account. In addition, the salts and complexes were then evaluated for their ability to inhibit the proliferation of four different cancer cell lines (A549, MCF-7, HCT116, SH-SY5Y and BEAS-2B cells lines). AlamarBlue assay demonstrated that the salts and complexes exhibited potent cytotoxicity towards all cancer lines. 2c compound showed the highest cytotoxic activity against BEAS-2B, A549 and MCF-7 cell lines. Except for 2c, compounds 3d, 3e and 3f showed cytotoxic activity at the lowest concentrations against MCF7 cell line.The study highlights the importance of N-heterocyclic carbene ligands in the development of silver-based drugs with anticancer properties.