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Öğe Characterization of short-length multi-walled carbon nanotubes and cytotoxicity on MDA-MB-231 and HUVEC cell lines(Springer Japan Kk, 2020) Dinc, Bircan; Unlu, Ayhan; Bektas, MuhammetMulti-walled carbon nanotubes (MWNTs) are suitable for delivering large biomolecules with lower cytotoxicity values and low prime cost. Surface modifications of MWNTs affect interaction with cells and proteins. Oxidation with strong acids decreases cytotoxicity of CNTs and increases protein-loading capacity. Here, after oxidation, TEM images revealed more aligned structure and carboxylated groups at the surface which decreases toxicity. Functionalized MWNTs showed more gradual degradation than the pristine MWNTs and mass loss increased by 2% in the same temperature range. Raman spectroscopy corrected graphitic structure with characteristic D and G bands at 1330 and 1579 cm(-1) and increased intensity after oxidation. FTIR spectroscopy peaks at 1443 cm(-1), 1560, 1640 cm(-1), 2100-2200 cm(-1) and 3426 cm(-1) are ascribed to C-O-C vibrational stretch, C=C bonds, vibration of C equivalent to C bonds and stretch of hydroxyl groups, respectively. The sonication-driven dispersion of in phosphate-buffered saline, distilled water and cell culture medium were detected by UV-vis-NIR spectroscopy, water-dispersed functionalized MWNTs revealed the highest absorbance value. Cytotoxicity of MWNTs was investigated before and after functionalization in breast cancer (MDA-MB-231) and human vein endothelial (HUVEC) cells. Relatively low-toxicity results were obtained in functionalized MWNTs and cellular uptake of MWNTs were corrected with fluorescent imaging of cells and cell lysates. Protein-loading capacity of fsMWNTs (functionalized short-length multi-walled carbon nanotubes) was evaluated by using bovine serum albumin (BSA) and with an equal amount of fsMWNTs and BSA; 36% binding yield was obtained. Protein corona after covalent functionalization potentially lowered cytotoxicity up to 6%.Öğe A Comparative Study of Short Multi-Walled Carbon Nanotubes with Different Bulk Densities(Maik Nauka/Interperiodica/Springer, 2022) Dinc, Bircan; Ustunsoy, Recep; Unlu, Ayhan; Meran, Mehdi; Karatepe, Nilgun; Bektas, MuhammetMulti-walled carbon nanotubes (MWNTs) were investigated before and after carboxylic acid functionalization. Here, the comparative analysis of MWNTs with different bulk densities reveals similar Raman and FTIR spectra before and after acid functionalization except for minor differences. However thermal analyses exhibited some basic differences for both MWNTs before and after acid treatment. We investigated the cytotoxicity of two MWNTs on HT-29 and HEK293-T cells through three different methods: MTT assay, DAPI staining, and xCELLigence real-time cell analyzing method. It was observed that high bulk density affects the cytotoxicity for both cell lines and in all methods. Because the acid treatment lowered the bulk density, after acid treatment, the MWNTs with the higher bulk density (C150P) elicited similar cytotoxicity compared to the lower one (C70P).Öğe Cross-reacting material 197 (CRM197) affects actin cytoskeleton of endothelial cells(General Physiol And Biophysics, 2017) Edis, Bilge Ozerman; Varol, Basak; Haciosmanoglu, Ebru; Unlu, Ayhan; Bektas, MuhammetCRM197, cross-reacting material 197, is a mutant of diphtheria toxin (DTx). CRM197 is used in pharmacology as a carrier protein. It has been recently shown that CRM197 causes breakdown in actin filaments. In order to show intracellular localization of CRM197 and visualize cell structure via actin cytoskeleton, endothelial cells were cultured and subjected to CRM197 in vitro. To address the interaction between CRM197 and actin both experimental and theoretical studies were carried out. Colocalization of CRM197 with actin filaments was determined by immunofluorescence microscopy. Following 24-hour incubation, the loss of cell-cell contact between cells was prominent. CRM197 was shown to bind to G-actin by gel filtration chromatography, and this binding was confirmed by Western blot analysis of eluted samples obtained following chromatography. Based on crystal structure, docked model of CRM197-actin complex was generated. Molecular dynamics simulation revealed that Lys42, Cys218, Cys233 of CRM197 interacts with Gly197, Arg62 and Ser60 of G-actin, respectively. CRM197 binding to G-actin, colocalization of CRM197 with actin filament, and actin cytoskeleton rearrangement resulting in the loss of cell-cell contact show that actin comes into sight as target molecule for CRM197.Öğe Cytotoxicity of doxrubicin loaded single-walled carbon nanotubes(Springer, 2018) Unlu, Ayhan; Meran, Mehdi; Dinc, Bircan; Karatepe, Nilgun; Bektas, Muhammet; Guner, F. SenihaCarbon nanotube (CNTs) is a new alternative for efficient drug delivery and it has a great potential to change drug delivery system profile in pharmaceutical industry. One of the important advantage of CNTs is their needle-like, cylindrical shape. This shape provides a high surface area for multiple connections and adsorption onto for millions of therapeutic molecules. CNTs can be internalized by cells via endocytosis, passive diffusion and phagocytosis and release the drug with different effects like pH and temperature. The acidic nature of cancer cells and the susceptibility of CNTs to release the drug in the acidic environment have made it a promising area of research in cancer drug delivery. In this research, we investigated cell viability, cytotoxicity and drug delivery in breast cancer cell line by designing non-covalent single walled carbon nanotubes (SWNT)-doxorubicin (DOX) supramolecular complex that can be developed for cancer therapy. Applied high concentrations of DOX loaded SWNTs changed the actin structure of the cells and prevented the proliferation of the cells. It was showed that doxorubicin loaded SWNTs were more effective than free doxorubicin at relatively small concentrations. Once we applied same procedure for short and long (short: 1-1.3 mu m; long: 2.5-4 mu m) SWNTs and compared the results, more disrupted cell structure and reduction in cell proliferation were observed for long CNTs. DOX is bounded more to nanotubes in basic medium, less bound in acidic environment. Cancer cells were also examined for concentration at which they were effective by applying DOX and it was seen that 3.68 mu M doxorubicin kills more than 55% of the cells.Öğe Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies(Taylor & Francis Inc, 2017) Salmas, Ramin Ekhteiari; Unlu, Ayhan; Bektas, Muhammet; Yurtsever, Mine; Mestanoglu, Mert; Durdagi, SerdarPoly(ADP-ribose) polymerase-1 (PARP-1) enzyme has critical roles in DNA replication repair and recombination. Thus, PARP-1 inhibitors play an important role in the cancer therapy. In the current study, we have performed combination of in silico and in vitro studies in order to discover novel inhibitors against PARP-1 target. Structure-based virtual screening was carried out for an available small molecules database. A total of 257,951 ligands from Otava database were screened at the binding pocket of PARP-1 using high-throughput virtual screening techniques. Filtered structures based on predicted binding energy results were then used in more sophisticated molecular docking simulations (i.e. Glide/standard precision, Glide/XP, induced fit docking - IFD, and quantum mechanics polarized ligand docking - QPLD). Potential high binding affinity compounds that are predicted by molecular simulations were then tested by in vitro methods. Computationally proposed compounds as PARP-1 inhibitors (Otava Compound Codes: 7111620047 and 7119980926) were confirmed by in vitro studies. In vitro results showed that compounds 7111620047 and 7119980926 have IC50 values of 0.56 and 63M against PARP-1 target, respectively. The molecular mechanism analysis, free energy perturbation calculations using long multiple molecular dynamics simulations for the discovered compounds which showed high binding affinity against PARP-1 enzyme, as well as structure-based pharmacophore development (E-pharmacophore) studies were also studied.
