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Permanent URI for this collectionhttps://hdl.handle.net/11443/932

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Author: search.filters.author.Berk, Barkin

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    Prognostic Significance of Tumor Tissue NeuGcGM3 Ganglioside Expression in Patients Receiving Racotumomab Immunotherapy
    (HINDAWI LTD, 2020-01-01) Uskent, Necdet; Ayla, Sule; Mandel, Nil Molinas; Ozkan, Metin; Teomete, Mehmet; Baloglu, Huseyin; Aydincer, Cenk; Yergok, Hale; Dogan, Ender; Berk, Barkin; Yazar, Aziz
    Expression ofN-glycolyl GM3 (NeuGcGM3) ganglioside was detected in the tumor specimens of patients who were on Racotumomab anti-idiotype vaccine maintenance treatment, and prognostic significance as a biomarker was investigated. No statistically significant association was observed in the multivariate analysis between overall survival and tissue NeuGcGM3 IHC levels. Although numerically there was a difference favoring less intense IHC for better prognosis, this did not reach statistical power. However, there was a strong correlation between Racotumomab doses and overall survival (OS). Mean OS of the patient with more than 10 Racotumomab application was significantly longer than the patient who had less than 10 injections (70.7 months vs. 31.1 months, p<0.001). We propose that, regardless of staining intensity, the presence of NeuGcGM3 in patient tissues might be an indicator of benefit in Racotumomab treatment.
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    Molecular modeling and antimycobacterial studies of Mannich bases: 5-hydroxy-2-methyl-4H-pyran-4-ones
    (SCIENTIFIC TECHNICAL RESEARCH COUNCIL TURKEY-TUBITAK, 2011-01-01) Berk, Barkin; Us, Demet; Oktem, Sinem; Kocagoz, Z. Tanil; Caglayan, Berrak; Kurnaz, Isil Aksan; Erol, Dilek Demir
    The World Health Organization lists tuberculosis among the top 3 leading causes of death from a single infectious agent, and reported cases of multidrug-resistant tuberculosis (MDR-TB) are on the rise. In an attempt to improve MDR-TB drug-directed therapy, we synthesized 11 4-substituted piperazine derivatives of 3-hydroxy-6-methyl-4H-pyran-4-one pharmacophore by reacting 5-hydroxy-2-methyl-4H-pyran-4-one with suitable piperazine derivatives under Mannich reaction conditions. Inhibitory effects of the 11 compounds on Escherichia coli DNA gyrase were evaluated via DNA gyrase supercoiling assay. The minimum inhibitory concentrations (MIC) of the 11 compounds and 41 compounds from our previous studies against Mycobacterium tuberculosis H37RV were assessed, in vitro, by a broth dilution method. To determine the interaction pattern between active site amino acids and all 52 compounds, homology modeling for the construction of M. tuberculosis DNA gyrase B subunit was performed, followed by a docking study. The data presented here could prove useful in future studies on interaction field analysis and high throughput virtual screening of the derivatives of the 3-hydroxy-6-methyl-4H-pyran-4-one pharmacophore toward the development of more clinically applicable compounds.
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    4H-Pyran-4-one derivatives:
    (SCIENTIFIC TECHNICAL RESEARCH COUNCIL TURKEY-TUBITAK, 2009-01-01) Us, Demet; Gurdal, Ece; Berk, Barkin; Oktem, Sinem; Kocagoz, Tanil; Caglayan, Berrak; Kurnaz, Isil Aksan; Erol, Dilek Demir
    A series of 3-hydroxy-6-methyl-2-((4-substitutedpiperazin-1-yl)methyl)-4H-pyran-4-on e structured compounds were synthesized by reacting 5-hydroxy-2-methyl-4H-pyran-4-one with suitable piperazine derivatives using Mannich reaction conditions. Antibacterial activities of the compounds for E. coli, S. paratyphi, S. flexneri, E. gergoviae, and M. smegmatis were assessed in vitro by using broth dilution for determination of the minimum inhibitory concentration (MIC). In addition, their inhibitory effects over DNA gyrase enzyme were evaluated using a DNA gyrase supercoiling assay. Among the synthesized compounds
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    Mannich base derivatives of 3-hydroxy-6-methyl-4H-pyran-4-one with antimicrobial activity
    (SCIENTIFIC TECHNICAL RESEARCH COUNCIL TURKEY-TUBITAK, 2010-01-01) Us, Demet; Berk, Barkin; Gurdal, Ece; Aytekin, Nihan; Kocagoz, Tanil; Caglayan, Berrak; Kurnaz, Isil Aksan; Erol, Dilek Demir
    A series of 3-hydroxy-6-methyl-2-{[}(substitutedpiperidine-1-yl)methyl]-4H-pyran-4-o ne structured compounds were synthesized by reacting 5-hydroxy-2-methyl-4H-pyran-4-one with suitable piperidine derivatives using Mannich reaction conditions. Antibacterial activities of the compounds for E. coli ATCC 25922, S. paratyphi ATCC BAA-1250, S. flexneri ATCC 12022, E. gergoviae ATCC 33426, and M. smegmatis ATCC 14468 were assessed in vitro by the broth dilution method for determination of minimum inhibitory concentration (MIC). In addition, their inhibitory effects over DNA gyrase enzyme were evaluated using a DNA gyrase supercoiling assay. All the synthesized compounds showed a MIC value of either 8 or 16 mu g/mL for M. smegmatis, whereas minimum to moderate activity was achieved for the others. Those tested in the supercoiling assay had at best a very mild inhibition of the enzyme. This series deserves further attention for testing over Mycobacterium species and topoisomerase II inhibition to develop new lead drugs to treat non-tuberculous mycobacterial infections.