Yazar "Kocabay, Samet" seçeneğine göre listele
Listeleniyor 1 - 10 / 10
Sayfa Başına Sonuç
Sıralama seçenekleri
Öğe An investigation of the probiotic properties of Lactobacillus fermentum(International Society of Academicians, 2020) Çetinkaya, Serap; Kocabay, Samet; Yenidunya, AliThe study assessed some of the probiotic characteristics of an isolate (AB4 26) of Lactobacillus fermentum. AB4 26 was isolated from a faecal sample of an infant, fed with breast milk. The results indicated that the isolate had acceptable survival rates in gastric juice both in the presence and absence of pepsin. It also displayed acceptable sensitivity rates to eleven different antibiotics. Hydrophobicity test showed that the isolate had a good capacity to adhere to xylene. It could also destroy sodium salts. AB4 26 displayed the least survival rates in bile salt. These initial findings could suggest that infant faeces and breast milk could serve as good sources of probiotic organisms.Öğe Characterization of thermostable beta-amylase isozymes from Lactobacillus fermentum(ELSEVIER SCIENCE BV, 2016) Kocabay, Samet; Cetinkaya, Serap; Akkaya, Birnur; Yenidunya, Ali FazilA 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.Öğe Gaita bakterilerinden ektraselüler amilaz üretimi, izalasyonu ve karakterizasyonu(Cumhuriyet Üniversitesi, 2015) Kocabay, Samet; Akkaya, Birnur; Yenidünya, Ali FazılAmilazlara olan ihtiyaç günümüz biyoteknolojisinde kullanım alanlarından dolayı artmaktadır. Bu ihtiyaçların karşılanması amacıyla bakteriyel amilazların izolasyonu saflaştırılması ve karakterizasyonu günümüzde ilgi odağı oluşturmaktadır. Gaita bakterilerinden ektraselüler ? - amilaz üreten bakterilerin hem fenotipik hem de genotipik karakterizasyonu yapılarak üretilen ? - amilaz enziminin karakterizasyonu gerçekleştirilmiştir. 16SrDNA gen bölgeleri dizilendiğinde Lactobacillus fermentum olduğu saptanmıştır. Gram pozitif, %3 NaCl içeren besi yerinde üreyebilen bir bakteridir. Üretilen amilaz enzimi 20 kDa ağırlığındadır. Enzimin çalışması için optimum pH 5.0 ve 10.0'dur ve sıcaklığı 45 ºC' ve 37 ºC olarak bulunmuştur. Anahtar kelimeler: amilaz, biyoteknoloji, gaita, ekstraselüler enzim, nişastaÖğe In Silico Studies of Synthetic Sulfatide as a Potential Drug Candidate Against Covid-19(2022) Kocabay, Samet; Alagöz, Mehmet; Bakır, Hıncal Gokhan; Akkaya, BirnurSulfatides 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.Öğe Inhibitory effects of carvacrol on glucansucrase from Streptococcus mutans and salivary α-amylase: in silico and in vitro studies(Tubitak Scientific & Technological Research Council Turkey, 2025) Kocabay, Samet; Alagoz, M. Abdullah; Akkaya, BirnurBackground/aim: Streptococcus mutans produces glucansucrase, an enzyme that converts sucrose into lactic acid, which lowers the pH in the oral environment and leads to tooth enamel demineralization, a key factor in dental caries. Additionally, glucansucrase facilitates the formation of extracellular polysaccharides, which promote bacterial adhesion to tooth surfaces. This study investigates the inhibitory effects of carvacrol, a natural compound, on glucansucrase activity both in vitro and in silico. Materials and methods: Glucansucrase enzyme was purified from S. mutans. The inhibitory effects of carvacrol against glucansucrase enzyme were investigated both in vitro and in silico. Results: In the presence of 50 mM carvacrol, glucansucrase and salivary amylase activities were reduced by 51.25% and 14.85%, respectively. Carvacrol did not significantly inhibit (4.73%) the salivary amylase enzyme at 10 mM. Glucansucrase activity decreased by 51.63% in the presence of 10 mM acarbose, which was used as a positive control in glucansucrase enzyme studies. Acarbose inhibited salivary amylase with 82.54% loss of enzyme activity in the presence of 1 mM acarbose. The docking score obtained for carvacrol was -5.262 kcal/mol, while that obtained for acarbose was -6.084 kcal/mol. We carried out molecular dynamics simulation studies for 100 ns to determine the stability of carvacrol in the active site of the protein. Carvacrol demonstrated stable binding to glucansucrase with hydrogen bonds and interactions at key residues (ASP477, GLN960, and ASP909), confirmed by molecular dynamics simulations. Carvacrol remained stable between 16 and 100 ns. Conclusion: Carvacrol selectively inhibits glucansucrase without significantly affecting salivary amylase, making it a more targeted inhibitor compared to acarbose, which inhibits both enzymes. Docking studies indicated that while carvacrol has a lower binding affinity than acarbose, its stable interaction with the enzyme suggests sustained inhibitory action. These findings highlight carvacrol as a promising natural compound for preventing dental caries, offering a more selective alternative to traditional inhibitors. Further in vivo studies are necessary to assess its therapeutic efficacy and safety in clinical applications for oral health.Öğe 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, BirnurDeaths 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. SarmaÖğe Preparation of sulfatide mimicking oleic acid sulfated chitosan as a potential inhibitor for metastasis(Elsevier, 2020) Kocabay, Samet; Akkaya, BirnurSulfatide 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.Öğe Probiotic Properties of a Lactobacillus fermentum Isolated from New-born Faeces(Japan Oil Chemists Soc, 2020) Kocabay, Samet; Cetinkaya, SerapLactic acid bacteria (LAB) have been demonstrated to have roles in many applications, ranging from lowering of cholesterol to immunological development. In this study, Lactobacillus fermentum was isolated from a new-born's faeces and its genotypic and probiotic characterizations were performed. Our results showed that the survival rate of isolated Lactobacillus fermentum was 39.39% at pH 2 and 81.34% in the stimulated gastric juice at pH 3. It also digested bile salts. Its surface hydrophobicity was found to be 57.59% in n-hexane. These findings indicated that the isolate can be a good probiotic candidate.Öğe 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 ZahirA 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.Öğe Yeni kitosan modifiye ürünlerinin eldesi ve biyolojik aktivitelerinin belirlenmesi(Sivas Cumhuriyet Üniversitesi, 2020) Kocabay, Samet; Akkaya, BirnurKitosan (Cs) doğada en çok bulunan polisakkaritlerden birisidir. Kaynak olarak yengeç, böceklerin dış iskeleti, mantarlar, bazı fungus ve yeşil alglerin hücre duvar yapılarında bulunan kitinden elde edilmektedir. Biyouyumluluk, antimikrobiyal, antifungal, antikoagülant ve antikanser özelliklerinden dolayı ilaç sanayisinden gıda endüstrisi uygulamaları için ilgi odağıdır. Bu nedenle metastazı önlemeye yönelik oleik asit sülfatlanmış kitosan (OlcShCs) hazırlanarak biyolojik ve kimyasal karakteristik özellikleri araştırıldı ve orijinal kitosan ile karşılaştırıldı. Bunun için kitosan ve türevi FTIR, NMR, DSC, TGA ve DTA analizleri yapıldı ve kimyasal karakterizasyonu yapıldı. Akabinde kitosan türevinin antimikrobiyal, antifungal ve antikanser aktiviteleri araştırıldı. CS ve OlcShCs'nin FT-IR spektrumları karşılaştırıldığında CS'nin karakteristik spekrumları; 1646 cm?1 C=O amide-I gerilmesi (stretching)), 1568 cm?1 N-H amide-II bağlanması ve 1374 cm?1 C-N amide-III gerilmesini göstermektedir. Modifikasyon sonrası açil olmayan birincil amin grubuna karşılık gelen 1568 cm?1 pik kaybolurken, 1634 cm-1'de açığa çıkmaktadır. Bu durum modifiye kitosanda amid bağının varlığını göstermektedir. Ayrıca 1732 cm-1 ester bağının karbonil grubunun karakteristik pikidir. Bu bağ kitosanın hidroksil grubu ile oleik asitin karboksil grubu arasında açığa çıkmaktadır. Dolayısıyla yapıda N-açilasyonun açığa çıktığını göstermektedir. 788 ve 1207 cm-1'de yeni açığa çıkan FT-IR bantları ise sırasıyla sülfo gruplarının C–O–S and O-S–O bağ gerginliğine karşılık gelmektedir. H1 NMR analiz sonucuna bakıldığında 2.4 ppm'deki pik N-asetil glukozamin grubunun N-asetil protonlarına karşılık gelmektedir. 3.6 ppm'deki pik ise deasetile glukozamin kalıntılarının H-2 protonuna denk gelmektedir. Kitosanın oleik asit ile kimyasal modifikasyonu [-CH2-CO] 1.4 ppm'deki pik ile doğrulandı. Cs molekülünün E. coli CICC 21524, B. subtilis ATCC 21332, S. epidermidis ATCC 12228, C. albicans ATCC 60193 türlerine karşı sırasıyla %99.18±3.09, %87.50 ± 0.48, %100 ± 0, %12.90 ±3.4 antimikrobiyal etkiye sahip olduğu görüldü. Aynı konsantrasyonda OlcShCs molekülünün E. coli CICC 21524, B. subtilis ATCC 21332, S. epidermidis ATCC 12228, C. albicans ATCC 60193 türleri üzerine sırasıyla antimikrobiyal etkisi %0 ±6.69, %6.66 ±1.25, %59.13 ±4.97, %21.26 ±2.17 olarak saptandı. HeLa kanser hücrelerine karşı sitotoksik etkisi 24 saat için IC50 değeri 81.57±5.30 ?g/ml bulundu. Sonuç olarak yeni sentezlediğimiz kitosan türevi molekül kitosana göre genel anlamda daha düşük antimikrobiyal etki gösterdiği, HeLa hücrelerine karşı kitosan türevinin sitotoksik etki gösterdiğinden dolayı potansiyel ilaç adayı olabilir.
