Fizik Bölümü / Department of Physics

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Now showing 1 - 5 of 391
  • Publication
    Open Access
    Molecular Docking Analysis of Used Drugs for the Treatment of Cancer
    (Süleyman Demirel Üniversitesi, 2021) Demirbağ, Aliye Demet; Çelik, Sefa; AKYÜZ, SEVİM; Özel, Aysen
    In this study, the lowest energy molecular structures were determined by conformational analysis of six drugs commonly used in cancer treatment, in order to use as initial data for docking simulations. Using the AutoDock Vina software, the interaction mechanisms of the 6 FDA approved drugs (Pemetrexed, Irinotecan, Tamoxifen, Gemcitabine, Topotecan and Temozolomide) with DNA were investigated. In addition, MM/PB(GB)SA calculations for the drug-DNA structures under investigation have been performed. The calculated binding affinities and binding free energies of interactions were showed the stability of the structures. It has been found that the active site where these molecules interact with DNA is the same and that their various interactions, primarily hydrogen bond, play an important role in this stability of the structures. Furthermore, the pharmacophoric features of the investigated molecules were determined.The aim of the work is to deeply investigate the binding properties of the title drugs with DNA.
  • Publication
    Open Access
    Synthesis, Molecular Modelling, FT-IR, Raman and NMR Characterization, Molecular Docking and ADMET Study of New Nickel(II) Complex with an N4-Tetradentate Thiosemicarbazone
    (Taylor and Francis Ltd., 2021) Eğlence-Bakır, Songül; Çelik, Sefa; Şahin, Musa; Ozel, Ayşen E.; AKYÜZ, SEVİM; Ülküseven, Bahri
    A new nickel(II) complex was synthesized by using S-propyl-thiosemicarbazide and 2-amino-3,5-dibromobenzaldehyde. The complex, obtained by the template effect of nickel ions, was structurally analysed by experimental and theoretical vibrational spectroscopy, NMR and density functional theory (DFT) calculations. By using DFT/B3LYP method with 6-311++G(d, p) basis set, the most stable molecular structure of the title molecule was calculated. The fundamental vibrational wavenumbers, IR and Raman intensities for the optimized structure of the molecule under investigation were determined and compared with the experimental vibrational spectra. The vibrational assignment was achieved using the calculated potential energy distributions of the vibrational modes. Moreover, the molecular electrostatic potential (MEP), the highest occupied molecular orbital (HOMO) and the lowest occupied molecular orbital (LUMO) energies were calculated, Molecular docking of the molecule was carried out against DNA in order to identify the potential inhibitory action of the title compound. The findings suggested that the aforementioned compound has a strong binding affinity to interact with DNA residues DT8, DC9, DG12, DG16, DA17, and DA18 through the intermolecular hydrogen bonds. Also the performed in silico ADMET analysis was the prediction of the synthesized molecule’s pharmacokinetic and toxicity profile expressing good oral drug like actions and non-toxic nature. The complex has been shown to have the possibility to become a model molecule for drug development processes. Communicated by Ramaswamy H. Sarma. © 2020 Informa UK Limited, trading as Taylor & Francis Group.
  • Publication
    Metadata only
    Blood Serum-Infrared Spectra-Based Chemometric Models for Auxiliary Diagnosis of Autism Spectrum Disorder
    (Elsevier, 2021) ILDIZ, GÜLCE ÖĞRÜÇ; Bayarı, Sevgi; Yorguner, Neşe; Fausto, Rui
    This chapter focuses on the use of chemometric models developed from infrared (IR) spectroscopic data of blood serum as an auxiliary tool for autism spectrum disorder (ASD) diagnosis. In the introductory sections the fundamentals of IR spectroscopy are shortly reviewed and brief descriptions of the different chemometric methods used in the case study described in the last section of the chapter are presented. The last section deals with the application of the described strategy to the diagnosis of ASD in children and adolescents. © 2021 Elsevier Inc. All rights reserved.
  • Publication
    Restricted
    Investigation of the Magnetocaloric Effect and the Critical Behavior of the Interacting Superparamagnetic Nanoparticles of La0.8Sr0.15Na0.05MnO3
    (Elsevier Science Sa, 2022) Tozri, A.; Alhalafi, Sh.; Alrowaili, Ziyad A.; Horchani, Mongi; Omri, Aref; Skini, R.; Ghorai, S.; Benali, A.; Costa, Benilde F. O.; ILDIZ, GÜLCE ÖĞRÜÇ
    We report on structural, magnetic properties of Na-doped La0.8Sr0.15Na0.05MnO3 (LSNMO) nanoparticles (NP) with size about 50 nm elaborated via sol-gel route. The chemical composition was verified using the energy dispersive X-ray analysis (EDAX) and by X-ray photoelectron spectroscopy (XPS). Magnetic characterizations demonstrate that LSMNO exhibits a coexistence of interacting superparamagnetic (ISPM) phase with blocking temperature T-B = 194 K and a ferromagnetic phase with Curie temperature T-C = 255.5 K. At low temperatures, the SPM state undergoes a collective freezing state at T-f = 46 K. the high-temperature regime (well above TC) reveals that NP-LSNMO has a strengthened Griffiths-like phase compared to their bulk counterpart. An itemized investigation of the critical behavior of the material was carried out in the vicinity of T-C. The critical exponents [beta = 0.546(7), gamma = 0.972(6), and delta = 2.94 (5)] were found to be in close agreement with of the mean-field theory. The maximum magnetic entropy change (-Delta(pk)(M)) is about 1.41 Jkg(-1) K-1 and the refrigeration capacity (RC) is 288 Jkg(-1) for a field change of 5 T at T = 215 K. This magnetocaloric response is reasonably high for nanomaterials and, together with its cost-effectiveness, makes NP LSMNO a potential candidate material for active magnetic refrigerators. Besides, the ISPM properties are desirable for hyperthermia applications. Our findings suggest that the magnetic inhomogeneity and the dipolar interaction between the SPM and FM phases in the range T-B < T < T-C are crucial factors in determining the magnetic properties of NP-LSNMO. (C) 2021 Elsevier B.V. All rights reserved.
  • Publication
    Open Access
    Evaluation of Anti-Cancer and Anti-Covid-19 Properties of Cationic Pentapeptide Glu-Gln-Arg-Pro-Arg, From Rice Bran Protein and Its D-Isomer Analogs Through Molecular Docking Simulations
    (Elsevier Science Inc., 2021) Gasymov, Oktay K.; Çelik, Sefa; Ağaeva, Gülşen; AKYÜZ, SEVİM; Keçel-Gündüz, Serda; Qocayev, Niftali M.; Özel, Ayşen E.; Ağaeva, Ülker; Bakhishova, Matanat; Aliyev, Jamil A.
    Bioactive peptides derived from food proteins are becoming increasingly popular due to the growing awareness of their health-promoting properties. The structure and mechanism of anti-cancer action of pentapeptide GluGln-Arg-Pro-Arg (EQRPR) derived from a rice bran protein are not known. Theoretical and experimental methods were employed to fill this gap. The conformation analysis of the EQRPR pentapeptide was performed first and the obtained lowest energy conformer was optimized. The experimental structural data obtained by FTIR and CD spectroscopies agree well with the theoretical results. D-isomer introduced one-by-one to each position and all D-isomers of the peptide were also examined for its possible anti-proteolytic and activity enhancement properties. The molecular docking revealed avid binding of the pentapeptide to the integrins alpha(5)beta(1) and alpha(IIb)beta(3), with K-d values of 90 nM and 180 nM, respectively. Moreover, the EQRPR and its D-isomers showed strong binding affinities to apo-and holo-forms of M-pro, spike glycoprotein, ACE2, and dACE2. The predicted results indicate that the pentapeptide may significantly inhibit SARS-CoV-2 infection. Thus, the peptide has the potential to be the leading molecule in the drug discovery process as having multifunctional with diverse biological activities.