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    Characterization of thermostable ?-amylase isozymes from Lactobacillus fermentum
    (Elsevier Science Bv, 2016) Kocabay, Samet; Cetinkaya, Serap; Akkaya, Birnur; Yenidunya, Ali Fazil
    A strain of Lactobacillus fermentum producing two isozymes of a 20 kDa beta-amylase was isolated from the faecal sample of a newborn. The starin was identified by sequencing its 16S rRNA gene. The two beta-amylase isozymes were resolved and visualized by two dimensional protein gel electrophoresis (2-D gel electrophoresis). Some of the physical and biochemical properties of the enzymes were characterized. The beta-amylase displayed two optimum pH s, 5.0 and 10.0 and two optimum temperatures, 45 degrees C and 37 degrees C, respectively. The isozymes hydrolyzed different substrates: glycogen at pH 5.0, and corn starch at pH 10.0. The activity did not require Ca2+, though the activity at pH 10.0 was enhanced in the presence of 5.0 mM and 10.0 mM CaCl2, 110% and 130%, respectively. (C) 2016 Elsevier B.V. All rights reserved.
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    Chemical and biological characterization of sulfated chitosan oligomer as heparin mimics
    (Sage Publications Ltd, 2021) Kocabay, Samet; Bahar, Mehmet Refik; Tekin, Suat; Akkaya, Recep; Akkaya, Birnur
    In the present study, chitosan oligomer was modified to sulfated chitosan oligomer (ShCsO) to mimic heparin. Its chemical structure was determined by infrared spectroscopy (FT-IR), X-ray diffractometry (XRD), differential scanning calorimetry (DSC), and thermogravimetric analysis. The results showed that the FT-IR spectrum band at 799 cm(-1) corresponds to C-O-S and that at 1212 cm(-1) corresponds to S=O bond stretching, which prove that the sulfate groups are incorporated into chitosan oligomer successfully. The antimicrobial activity of ShCsO against to Bacillus subtilis in 1% concentration was 89.1 +/- 1.7%. The IC50 (mu g/ml) of ShCsO was 67.75, 56.07, 85.47, and 84.68 for A2780, MCF-7, DU-145, and HepG2, respectively. The results show that this newly synthesized material is a potential candidate to heparin-like chitosan derivatives. According to the literature, it was the first time that chitosan oligomer was modified to mimic heparin.
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    In Silico Studies of Synthetic Sulfatide as a Potential Drug Candidate Against Covid-19
    (2022) Kocabay, Samet; Alagöz, Mehmet; Bakır, Hıncal Gokhan; Akkaya, Birnur
    Sulfatides play various roles in many biological processes such as cancer metastasis, viral infections and regulation in nerve cells. The sulfatide molecules are related with hypertension diseases in which ACE2 (Angiotensin converting enzyme) is important for regulating blood pressure. ACE2 is also a key receptor for Covid-19 and highly expressed many different tissue types. Understanding the interaction between the sulfatides and ACE2 might be a key factor to develop potential novel treatments against Covid-19. Here we studied the interaction of main protease enzyme (6LU7) of Covid-19 with native sulfatide(A), chitosan based synthetic sulfatide(B) and inhibitor N3, through in silico studies such as molecular docking, molecular dynamics, ADMET prediction and target selection analysis. The compounds A, B and N3 bind the virus protease enzyme with docking score of -5.420, -6.009, -6.161 kcal/mol respectively indicates synthetic sulfatide binds better than native sulfatide and comparable to N3. Besides, molecular dynamics studies were carried out to reveal the stability of the complexes of interest. ADMET and target prediction studies carried out to reveal pharmacological properties and toxicity of the complexes and synthetic sulfatide found to be a drug-like molecule. We anticipate that computational investigation of virus interaction mechanisms will be an important starting point for experimental research in drug development efforts against Covid-19.
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    Investigation of inhibitory effect of sulfated chitosan oligomer on human heparanase enzyme: in silico and in vitro studies
    (Taylor & Francis Inc, 2024) Kocabay, Samet; Alagoez, M. Abdullah; Akkaya, Birnur
    Deaths from cancer are widespread worldwide and the numbers continue to increase day by day. During the disease progression of cancer in cells, many of its metabolic activities change. Increased heparanase enzyme release is just one example. Following heparanase enzyme activity, many molecules interact with the remodeling of glycosaminoglycan structures, which triggers the release of different enzymes, cytokines, and growth factors, including fibroblast growth factors (FGF1 and FGF2), vascular endothelial growth factor (VEGF), hepatocyte growth factor, transforming growth factor beta and platelet-derived growth factor. These are the most important factors in metastasis due to the formation of new vascular structures caused by those elements. To reduce tumor growth and metastasis, various drugs have been designed by modifying chitosan and its derivatives. In this study, we used chitosan oligomer (A), sulfated chitosan oligomer (ShCsO) (B), heparin (C), phosphate monomer (D1) of PI-88 and sulfate monomer (D2) of PI-88 as heparanase inhibitors. We modified the chitosan oligomer with chlorosulfonic acid to synthesize ShCsO to investigate its inhibitory effects on human serum heparanase. Also examined were molecular docking; molecular dynamics (MD); adsorption, distribution, metabolism, elimination and toxicity (ADMET); and target prediction. ShCsO decreased enzyme activity at a concentration of 0.0001 mg/mL. The docking scores of A, B and C from in silico studies were -6.254, -6.936 and -6.980 kcal/mol, respectively, and the scores for the two different PI-88 monomers were -5.741 and -5.824 kcal/mol. These results show that ShCsO may be a potential drug candidate for treating cancer. Communicated by Ramaswamy H. Sarma
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    Preparation of sulfatide mimicking oleic acid sulfated chitosan as a potential inhibitor for metastasis
    (Elsevier, 2020) Kocabay, Samet; Akkaya, Birnur
    Sulfatide is associated with numerous health problems, affecting different parts of the human body, including the metastasis; however, the underlying mechanisms are yet to be fully elucidated. Sulfatide has been used to potential inhibitor for tumor cell metastasis. In the present study we synthesized oleic acid sulfated chitosan (OlcShCs). It shows structural similarity to sulfatide because of its functional groups (sulfate and fatty acyl chains). Chitosan has smart properties such as biocompatibility, biodegradability and non-toxicity. We have prepared oleic acid sulfated chitosan (OlcShCs) by chitosan modification to mimic sulfatide. Its structure was characterized by FT-IR, H-NMR, and thermogravimetric analysis. After characterization studies its antimicrobial, antifungal and cytotoxic properties were investigated. Oleic acid sulfated chitosan (OlcShCs) was tested for its anti-cancer potential against human cancer cell lines (HeLa (ATCC (R) CCL-2 (TM))) for 24 h, 48 h and 72 h using the MIT assays. This new material which is soluble at physiological conditions, is a potential candidate for further metastasis inhibition investigations. (C) 2019 Elsevier B.V. All rights reserved.
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    Production, purification, and characterization of metalloprotease from Candida kefyr 41 PSB
    (Elsevier Science Bv, 2017) Yavuz, Sevgi; Kocabay, Samet; Cetinkaya, Serap; Akkaya, Birnur; Akkaya, Recep; Yenidunya, Ali Fazil; Bakici, Mustafa Zahir
    A thermostable metalloprotease, produced from an environmental strain of Candida kefyr 41 PSB, was purified 16 fold with a 60% yield by cold ethanol precipitation and affinity chromatography (bentoniteacrylamide-cysteine microcomposite). The purified enzyme appeared as a single protein band at 43 kDa. Its optimum pH and temperature points were found to be 7.0 and 105 degrees C, respectively. K-m and V-max values of the enzyme were determined to be 3.5 mg/mL and 4.4 mu mol mL(-1) min(-1), 1.65 mg/mL and 6.1 mu mol mL(-1) min(-1), using casein and gelatine as the substrates, respectively. The activity was inhibited by using ethylenediamine tetraacetic acid (EDTA), indicating that the enzyme was a metalloprotease. Stability of the enzyme was investigated by using thermodynamic and kinetic parameters. The thermal inactivation profile of the enzyme conformed to the first order kinetics. The half life of the enzyme at 95, 105, 115, 125 and 135 degrees C was 1310, 610, 220, 150, and 86 min, respectively. (C) 2016 Elsevier B.V. All rights reserved.