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SARIYAR AKBULUT, BERNA

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Mühendislik Fakültesi

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SARIYAR AKBULUT

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BERNA

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Open Access
Repurposing bioactive aporphine alkaloids as efflux pump inhibitors
(ELSEVIER, 2019-11) SARIYAR AKBULUT, BERNA; Avci, Fatma Gizem; Atas, Basak; Aksoy, Cemile Selin; Kurpejovic, Eldin; Toplan, Gizem Gulsoy; Gurer, Caglayan; Guillerminet, Maxime; Orelle, Cedric; Jault, Jean-Michel; Akbulut, Berna Sariyar
Extrusion of drugs or drug-like compounds through bacterial efflux pumps is a serious health issue that leads to loss in drug efficacy. Combinatorial therapies of low-efficacy drugs with efflux pump inhibitors may help to restore the activities of such drugs. In this quest, natural products are attractive molecules, since in addition to their wide range of bioactivities they may inhibit efflux pumps. The current work repurposed the bioactive alkaloid roemerine as a potential efflux pump inhibitor. In Bacillus subtilis, both Bmr and BmrA, belonging to the major facilitator and the ATP-binding cassette superfamilies, respectively, were found to be inhibited by roemerine. Scanning electron microscopy and RNA-Seq analyses showed that it potentiated the effect of berberine. Growth rates and checkerboard assays confirmed the synergy of roemerine and berberine and that roemerine prevented berberine efflux by inhibiting Bmr. Transport assays with inverted membrane vesicles prepared from Escherichia cob overexpressing BmrA showed that increasing roemerine concentration decreased the transport of doxorubicin, the BmrA substrate, confirming that roemerine may also be considered as an inhibitor of BmrA. Thus, these findings suggest that conjugation of roemerine to substrates of efflux pumps, Bmr and BmrA, may help to potentiate the activity of their drug substrates.
Open Access
Piperidine-based natural products targeting type IV pili antivirulence: a computational approach
(2023-03-01) SARIYAR AKBULUT, BERNA; ÖZBEK SARICA, PEMRA; Ozcan A., Keskin O., Sariyar Akbulut B., Özbek Sarica P.
© 2022 Elsevier Inc.Type IV (T4) pilus is among the virulence factors with a key role in serious bacterial diseases. Specifically, in Neisseria meningitidis and Pseudomonas aeruginosa, it determines pathogenicity and causes infection. Here, a computational approach has been pursued to find piperidine-based inhibitor molecules against the elongation ATPase of T4 pili in these two selected pathogens. Using the modeled structures of the PilF and PilB ATPases of N. meningitidis and P. aeruginosa, virtual library screening via molecular docking has returned inhibitor molecule candidates. The dynamics of the best three binders have further been investigated in detail via molecular dynamic simulations. Among these, ligands with COCONUT IDs CNP0030078 and CNP0051517 were found to have higher potential in the inhibition of ATPases based on molecular dynamic simulation analysis and biological activity information. The obtained results will guide future efforts in antivirulence drug development against T4 pili of N. meningitidis and P. aeruginosa.
Open Access
Identification of novel inhibitors of the ABC transporter BmrA
(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2020-12) SARIYAR AKBULUT, BERNA; Sercinoglu, Onur; Senturk, Duygu; Kaya, Fatma Ece Altinisik; Avci, Fatma Gizem; Frlan, Rok; Tomasic, Tihomir; Ozbek, Pemra; Orelle, Cedric; Jault, Jean-Michel; Akbulut, Berna Sariyar
The resistance of microbes to commonly used antibiotics has become a worldwide health problem. A major underlying mechanism of microbial antibiotic resistance is the export of drugs from bacterial cells. Drug efflux is mediated through the action of multidrug resistance efflux pumps located in the bacterial cell membranes. The critical role of bacterial efflux pumps in antibiotic resistance has directed research efforts to the identification of novel efflux pump inhibitors that can be used alongside antibiotics in clinical settings. Here, we aimed to find potential inhibitors of the archetypical ATP-binding cassette (ABC) efflux pump BmrA of Bacillus subtilis via virtual screening of the Mu.Ta.Lig. Chemotheca small molecule library. Molecular docking calculations targeting the nucleotide-binding domain of BmrA were performed using AutoDock Vina. Following a further drug-likeness filtering step based on Lipinski's Rule of Five, top 25 scorers were identified. These ligands were then clustered into separate groups based on their contact patterns with the BmrA nucleotide-binding domain. Six ligands with distinct contact patterns were used for further in vitro inhibition assays based on intracellular ethidium bromide accumulation. Using this methodology, we identified two novel inhibitors of BmrA from the Chemotheca small molecule library.
Open Access
A two-step purification platform for efficient removal of Fab-related impurities: A case study for Ranibizumab
(2023-11-01) PİNAR, ORKUN; SARIYAR AKBULUT, BERNA; KAZAN, DİLEK; Tatli O., Oz Y., Dingiloglu B., Yalcinkaya D., Basturk E., Korkmaz M., Akbulut L., Hatipoglu D., Kirmacoglu C., Akgun B., et al.
Antibodies (mAbs) and antibody fragments (Fabs) constitute one of the largest and most rapidly expanding groups of protein pharmaceuticals. In particular, antibody fragments have certain advantages over mAbs in some therapeutic settings. However, due to their greater chemical diversity, they are more challenging to purify for large-scale production using a standard purification platform. Besides, the removal of Fab-related byproducts poses a difficult purification challenge. Alternative Fab purification platforms could expedite their commercialization and reduce the cost and time invested. Accordingly, we employed a strong cation exchanger using a pH-based, highly linear gradient elution mode following Protein L affinity purification and developed a robust two-step purification platform for an antibody fragment. The optimized pH gradient elution conditions were determined on the basis of purity level, yield, and the abundance of Fab-related impurities, particularly free light chain. The purified Fab molecule Ranibizumab possessed a high degree of similarity to its originator Lucentis. The developed purification platform highly intensified the process and provided successful clearance of formulated Fab- and process-related impurities (∼98 %) with an overall process recovery of 50 % and, thus, might be a new option for Fab purification for both academic and industrial purposes.
Open Access
Curcumin displays enhanced solubility and antibacterial activities when complexed with the cell penetrating peptide pVEC
(2022-06-01) SARIYAR AKBULUT, BERNA; Koleoglu E., Acar T., DERMAN S., SARIYAR AKBULUT B.
Curcumin is among phytochemicals with increasing popularity; unfortunately, its therapeutic potential is restricted due to poor water solubility and bioavailability. The current work undertakes the effort to improve the therapeutic potential of curcumin by complexing it with a cell penetrating peptide using copper ions. A mononuclear complex was synthesized from copper(II) acetate and curcumin. Then this complex was conjugated to the cell penetrating peptide, pVEC. The structural characterization of the complexes was achieved using UV-Vis and Fourier transform infrared spectroscopies. Dynamic and electrophoretic light scattering measurements have confirmed the complexation of curcumin with the peptide to form nanoparticles. Both solubility and kinetic stability of curcumin greatly improved upon complex formation with pVEC through copper ions. Then the antibacterial activity of curcumin in the complex was tested. The amount of curcumin in the minimum inhibitory concentration was similar to 30, similar to 8, and similar to 15 fold lower, respectively for Escherichia coli, Bacillus subtilis, and Staphylococcus aureus when complexed with pVEC; however, this improvement was specifically noteworthy for the gram-negative E. coli since the contribution of pVEC in the complex to the observed activity was negligible in this bacterium. With enhanced solubility and stability, metallo curcumin conjugated pVEC complex possesses potential for different therapeutic applications.
Open Access
Tyrosinase-based production of L-DOPA by Corynebacterium glutamicum
(SPRINGER, 2021-12) SARIYAR AKBULUT, BERNA; Kurpejovic, Eldin; Wendisch, Volker F.; Akbulut, Berna Sariyar
An increase in the number of elderly people suffering from the symptoms of Parkinson's disease is leading to an expansion in the market size of 3,4-dihydroxyphenyl-l-alanine (l-DOPA), which is the most commonly used drug for the treatment of this disease. Need for better quality products through economically feasible and sustainable processes makes biotechnological approaches attractive. The current study is focused on heterologous expression of Ralstonia solanacearum tyrosinase in Corynebacterium glutamicum cells to produce l-DOPA during growth on glucose or glucose/xylose mixtures. Whole-cells pre-grown on glucose were further exploited for biotransformation of l-tyrosine to l-DOPA. To prevent l-DOPA oxidation, not only the most commonly used agent, ascorbic acid, but also for the first time, thymol was evaluated. The highest l-DOPA titer was 0.26 +/- 0.02 g/L at the end of growth on a mixture of 1% xylose and 3% glucose in the presence of 200 mu M thymol as the oxidation inhibitor. The ability to co-utilize glucose and xylose to reach this titer could make these cells ideal for l-DOPA production using hydrolyzed lignocellulosic biomass. When the pre-grown cells were further used for biotransformation, the highest l-DOPA yield was 0.61 +/- 0.02 g/gDCW with 4 mM ascorbic acid. Since l-tyrosine biotransformation is primarily dependent on tyrosinase activity, yield in this route could be improved by optimizing reaction conditions. As the industrial workhorse for amino acid production, these C. glutamicum cells will clearly benefit from strain development efforts and bioprocess optimization towards sustainable and economically feasible l-DOPA production.
Open Access
Carvacrol enhances the antimicrobial potency of berberine in bacillus subtilis
(2022-05-01) SAYAR, NİHAT ALPAGU; SARIYAR AKBULUT, BERNA; Atas B., Aksoy C. S., Avci F. G., SAYAR N. A., Ulgen K., ÖZKIRIMLI ÖLMEZ E., SARIYAR AKBULUT B.
The essential oil carvacrol from oregano displays a wide range of biological activities among which is found the inhibition of efflux pumps. Thus, using carvacrol, the current work undertook the effort to potentiate the antimicrobial activity of berberine, a natural product with limited antimicrobial efficacy due to its efflux. Following the selection of concentrations for the combinatorial treatments, guided by checkerboard microtiter plate assay and growth experiments, ethidium bromide accumulation assay was used to find that 25 mu g mL(-1) carvacrol displayed a weak efflux pump inhibitor character in Bacillus subtilis. Scanning electron microscopy images and cellular material leakage assays showed that carvacrol at this concentration neither altered the morphology nor the permeability of the membrane alone but when combined with 75 mu g mL(-1) berberine. Among the efflux pumps of different families found in B. subtilis, except for BmrA and Mdr, the increase in the expressional changes was striking, with Blt displaying similar to 4500-fold increase in expression under the combination treatment. Overall, the findings demonstrated that carvacrol potentiated the effect of berberine; however, not only multiple pumps but also different targets may be responsible for the observed activity.
Open Access
A method for the quantitative determination of glycerophospholipid regioisomers by UPLC-ESI-MS/MS
(SPRINGER HEIDELBERG, 2019-02) SARIYAR AKBULUT, BERNA; Wozny, Katharina; Lehmann, Wolf D.; Wozny, Manfred; Akbulut, Berna Sariyar; Bruegger, Britta
Diacyl glycerophospholipids (GPs) belong to the most abundant lipid species in living organisms and consist of a glycerol backbone with fatty acyl groups in sn-1 and sn-2 and a polar head group in the sn-3 position. Regioisomeric mixed diacyl GPs have the same fatty acyl composition but differ in their allocation to sn-1 or sn-2 of the glycerol unit. In-depth analysis of regioisomeric mixed diacyl GP species composed of fatty acyl moieties that are similar in length and degree of saturation typically requires either chemical derivatization or sophisticated analytical instrumentation, since these types of regioisomers are not well resolved under standard ultra-performance liquid chromatography (UPLC) conditions. Here, we introduce a simple and fast method for diacyl GP regioisomer analysis employing UPLC tandem mass spectrometry (MS/MS). This GP regioisomer analysis is based both on minor chromatographic retention time shifts and on major differences in relative abundances of the two fatty acyl anion fragments observed in MS/MS. To monitor these differences with optimal precision, MS/MS spectra are recorded continuously over the UPLC elution profile of the lipid species of interest. Quantification of relative abundances of the regioisomers was performed by algorithms that we have developed for this purpose. The method was applied to commercially available mixed diacyl GP standards and to total lipid extracts of Escherichia coli (E. coli) and bovine liver. To validate our results, we determined regioisomeric ratios of phosphatidylcholine (PC) standards using phospholipase A(2)-specific release of fatty acids from the sn-2 position of the glycerol backbone. Our results show that most analyzed mixed diacyl GPs of biological origin exhibit significantly higher regioisomeric purity than synthetic lipid standards. In summary, this method can be implemented in routine LC-MS/MS-based lipidomics workflows without the necessity for additional chemical additives, derivatizations, or instrumentation.
Open Access
Curvularia lunata: A fungus for possible berberine transformation
(2022-01-01) SARIYAR AKBULUT, BERNA; Yılmaz D., AVCI F. G., SARIYAR AKBULUT B.
Abstract: The prevalence of multidrug-resistant microorganisms results in an urgent need for the development of new antimicrobial agents or new treatment strategies. In this sense, plants serve different alternatives. Berberine, a plantderived compound, is one of the alkaloids known to display antimicrobial activity against several types of microorganisms, while its being a substrate of various efflux pumps causes a decrease in its efficacy. Biotransformation makes it possible to obtain novel or more effective compounds with only minor structural modifications using enzyme systems. In this study, biotransformation of berberine by Curvularia lunata was examined. The working concentration of berberine was determined by observing the microbial growth on agar plates. The concentration of residual berberine in the media was analyzed by HPLC. In addition, laccase and beta-glucosidase enzyme activities were followed for their possible roles during the biotransformation of berberine. The results show that at the end of 14 days, C. lunata consumed 99% and 87% of berberine with the initial concentrations of 0.35 mg/mL and 0.5 mg/mL, respectively. Enzyme activities were not affected significantly. Since the concentration of berberine decreased, the biotransformation of berberine by C. lunata could be mentioned. Monitoring of biotransformation products plays a crucial role in discovering novel antimicrobial compounds and new valuable molecules.
Open Access
Membrane Active Peptides and Their Biophysical Characterization
(MDPI, 2018-08-22) SARIYAR AKBULUT, BERNA; Avci, Fatma Gizem; Akbulut, Berna Sariyar; Ozkirimli, Elif
In the last 20 years, an increasing number of studies have been reported on membrane active peptides. These peptides exert their biological activity by interacting with the cell membrane, either to disrupt it and lead to cell lysis or to translocate through it to deliver cargos into the cell and reach their target. Membrane active peptides are attractive alternatives to currently used pharmaceuticals and the number of antimicrobial peptides (AMPs) and peptides designed for drug and gene delivery in the drug pipeline is increasing. Here, we focus on two most prominent classes of membrane active peptides