Biyoinformatik ve Genetik Bölümü Koleksiyonu

Permanent URI for this collectionhttps://gcris.khas.edu.tr/handle/20.500.12469/46

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Citation - WoS: 21
Citation - Scopus: 24
Conductivity Percolation of Carbon Nanotubes (cnt) in Polystyrene (ps) Latex Film
(Canadian Science Publishing Nrc Research Press, 2010) Uğur, Şaziye; Pekcan, Mehmet Önder; Yargı, Önder; Pekcan, Önder
In this study the effect of multiwalled carbon nanotubes (MWNT) on film formation behaviour and electrical conductivity properties of polystrene (PS) latex film was investigated by using the photon transmission technique and electrical conductivity measurements. Films were prepared by mixing PS latex with different amounts of MWNTs varying in the range between 0 and 20 wt%. After drying MWNT content films were separately annealed above the glass transition temperature (T-g) of PS ranging from 100 to 270 degrees C for 10 min. To monitor film formation behavior of PS-MWNT composites transmitted light intensity I-tr was measured after each annealing step. The surface conductivity of annealed films at 170 degrees C was measured and found to increase dramatically above a certain fraction of MWNT (4 wt%) following the percolation theory. This fraction was defined as the percolation threshold of conductivity R-c. The conductivity scales with the mass fraction of MWNT as a power law with exponent 2.27 which is extremely close to the value of 2.0 predicted by percolation theory. In addition the increase in I-tr during annealing was explained by void closure and interdiffusion processes. Film formation stages were modeled and the corresponding activation energies were measured.
Citation - WoS: 6
Citation - Scopus: 8
Critical Phenomenon During Photoinitiated Gelation at Different Temperatures: a Photo-Dsc Study
(Elsevier Science, 2011) Dogruyol, Zekeriya; Pekcan, Mehmet Önder; Arsu, Nergis; Dogruyol, Sevnur Keskin; Pekcan, Önder
The behaviour of photoinitiated radical polymerization of an 80 wt% epoxy diacrylate (EA) and 20 wt% tripropyleneglycoldiacrylate (TPGDA) mixture with 2-mercaptothioxanthone (TX-SH) photoinitiator was studied at different temperatures by using photo-differential scanning calorimetric (Photo-DSC) technique. All photopolymerization reactions were carried out under the same conditions. It was observed that all conversion curves during gelation at different temperatures present nice sigmoidal behaviour which suggests the application of the percolation model. Observations around the critical time called the glass transition point (t(g)) taken to reach the maximum rate of polymerization (Rp(max)) show that the gel fraction exponent (beta) obeyed the percolation model. The produced beta values were found to be around 0.50 predicting that the system under consideration belongs to the same universality class. However. Rp(max) and the final conversion (C(s)) values were found to increase when the temperature was increased up to a certain value. On the other hand t(g) values decreased and became saturated as the temperature was increased. (C) 2011 Elsevier B.V. All rights reserved.
Citation - WoS: 0
Citation - Scopus: 15
Discovery of New Azoles With Potent Activity Against Candida Spp. and Candida Albicans Biofilms Through Virtual Screening
(Elsevier, 2020) Karakurt, Arzu; Eşsiz, Şebnem; Kart, Didem; Öztürk, Naile; Kaynak, F. Betül; Gencel, Melis; Taşkor, Gülce; Karakurt, Arzu; Saraç, Selma; Eşsiz, Şebnem; Dalkara, Sevim
Systemic candidiasis is a rampant bloodstream infection ofCandidaspp. andC. albicansis the majorpathogen isolated from infected humans. Azoles, the most common class of antifungals which sufferfrom increasing resistance, and especially intrinsically resistant non-albicans Candida(NAC) species, actby inhibiting fungal lanosterol 14a-demethylase (CYP51). In this study we identified a number of azolecompounds in 1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethanol/ethanone oxime ester structurethrough virtual screening using consensus scoring approach, synthesized and tested them for theirantifungal properties. We reached several hits with potent activity against azole-susceptible and azole-resistantCandidaspp. as well as biofilms ofC. albicans.5i's minimum inhibitor concentration (MIC) was0.125mg/ml againstC. albicans, 0.5mg/ml againstC. kruseiand 1mg/ml against azole-resistantC. tropicalisisolate. Considering the MIC values offluconazole against these fungi (0.5, 32 and 512mg/ml, respec-tively),5iemerged as a highly potent derivative. The minimum biofilm inhibitor concentration (MBIC) of5c,5j, and5pwere 0.5mg/ml (and5iwas 2mg/ml) againstC. albicansbiofilms, lower than that ofamphotericin B (4mg/ml), afirst-line antifungal with antibiofilm activity. In addition, the active com-pounds showed neglectable toxicity to human monocytic cell line. We further analyzed the dockingposes of the active compounds inC. albicansCYP51 (CACYP51) homology model catalytic site andidentified molecular interactions in agreement with those of known azoles with fungal CYP51s andmutagenesis studies of CACYP51. We observed the stability of CACYP51 in complex with5iin moleculardynamics simulations.©2019 Elsevier Masson SAS. All rights reserved.1. IntroductionSystemic candidiasis is a major public health issue, especiallywith immune-suppressed cases reaching high mortality rates. Themembers of the genusCandidaare the most frequently recoveredfrom human fungal infection andCandida albicans, so far, is theleading pathogen identified in nosocomial candidiasis [1]. Inaddition to increasing drug-resistant strains ofC. albicans, emer-gence of non-albicans Candidaspp. (NAC) complicate the treatmentof mycoses [2].C. tropicalisis among the NACs that show reducedsusceptibility tofirst-line antifungals reportedly leading to break-through fungemia among high-risk patients [3,4]. Also,C. kruseiisknown to be intrinsically resistant to a number of azoles includingfluconazole [5]. One of the several mechanisms of therapy-resistance is formation of biofilms, which are complex microor-ganism colonies enclosed in an exopolysaccharide matrix on bioticand non-biotic surfaces. Persistent biofilms make fungi much lesssusceptible to antifungal drugs compared to their planktonic formsfor a number of reasons [6e8]. Therefore it is essential to design*Corresponding author. Hacettepe University Faculty of Pharmacy, Departmentof Pharmaceutical Chemistry, 06100, Sihhiye, Ankara, Turkey.E-mail addresses:suat.sari@hacettepe.edu.tr,suat1039@gmail.com(S. Sari).Contents lists available atScienceDirectEuropean Journal of Medicinal Chemistryjournal homepage:http://www.elsevier.com/locate/ejmechhttps://doi.org/10.1016/j.ejmech.2019.06.0830223-5234/©2019 Elsevier Masson SAS. All rights reserved.European Journal of Medicinal Chemistry 179 (2019) 634e648
Citation - WoS: 55
Citation - Scopus: 70
Drug Design for Cns Diseases: Polypharmacological Profiling of Compounds Using Cheminformatic, 3d-Qsar and Virtual Screening Methodologies
(Frontiers Media Sa, 2016) Nikolic, Katarina; Yelekçi, Kemal; Mavridis, Lazaros; Djikic, Teodora; Vucicevic, Jelica; Agbaba, Danica; Yelekçi, Kemal; Mitchell, John B. O.
The diverse cerebral mechanisms implicated in Central Nervous System (CNS) diseases together with the heterogeneous and overlapping nature of phenotypes indicated that multitarget strategies may be appropriate for the improved treatment of complex brain diseases. Understanding how the neurotransmitter systems interact is also important in optimizing therapeutic strategies. Pharmacological intervention on one target will often influence another one, such as the well-established serotonin-dopamine interaction or the dopamine-glutamate interaction. It is now accepted that drug action can involve plural targets and that polypharmacological interaction with multiple targets, to address disease in more subtle and effective ways, is a key concept for development of novel drug candidates against complex CNS diseases. A multi-target therapeutic strategy for Alzheimer's disease resulted in the development of very effective Multi-Target Designed Ligands (MTDL) that act on both the cholinergic and monoaminergic systems, and also retard the progression of neurodegeneration by inhibiting amyloid aggregation. Many compounds already in databases have been investigated as ligands for multiple targets in drug discovery programs. A probabilistic method, the ParzenRosenblatt Window approach, was used to build a "predictor" model using data collected from the ChEMBL database. The model can be used to predict both the primary pharmaceutical target and off-targets of a compound based on its structure. Several multi-target ligands were selected for further study, as compounds with possible additional beneficial pharmacological activities. Based on all these findings, it is concluded that multipotent ligands targeting AChE/MAO-A/MAO-B and also D-1-R/D-2-R/5-HT2A-R/H-3-R are promising novel drug candidates with improved efficacy and beneficial neuroleptic and procognitive activities in treatment of Alzheimer's and related neurodegenerative diseases. Structural information for drug targets permits docking and virtual screening and exploration of the molecular determinants of binding, hence facilitating the design of multi-targeted drugs. The crystal structures and models of enzymes of the monoaminergic and cholinergic systems have been used to investigate the structural origins of target selectivity and to identify molecular determinants, in order to design MTDLs.
Citation - WoS: 18
Citation - Scopus: 18
Gelation Mechanisms
(World Scientific Publ Co Pte Ltd, 2012) Pekcan, Önder; Pekcan, Mehmet Önder; Kara, Selim
In this paper, we survey the gelation mechanisms for various polymeric systems which are classified by the type and the strength of the cross-linkages. These are the "irreversible" gels that are cross-linked chemically by covalent bonds and the "reversible" gels that are cross-linked physically by hydrogen or ionic bonds and by the physical entanglement of polymer chains. Some of the natural polymer gels fall into the class of physical gels, among which the red algae that has attracted attention for various applications is discussed in detail. Various composite gels, formed from mixture of physical and chemical gels are also discussed in the last section of the article. Theoretical models describe the gelation as a process of random linking of subunits to larger and larger molecules by formation of an infinite network, where no matter what type of objects are linked, there is always a critical "gel point" at which the system behaves neither as a liquid nor as a solid on any length scale. The Flory-Stockmayer theory and percolation theory provide bases for modeling this sol-gel phase transition. The experimental techniques for measuring the critical exponents for sol-gel phase transitions in different polymeric systems are introduced and the validation of various theoretical predictions are surveyed.
Citation - WoS: 15
Citation - Scopus: 18
Producing Critical Exponents From Gelation for Various Photoinitiator Concentrations; a Photo Differential Scanning Calorimetric Study
(Elsevier Science SA, 2012) Dogruyol, Zekeriya; Pekcan, Mehmet Önder; Arsu, Nergis; Dogruyol, Sevnur Keskin; Pekcan, Önder
Photoinitiated radical polymerization of an 80 wt% epoxy diacrylate (EA) and 20 wt% tripropyleneglycoldiacrylate (TPGDA) mixture with various 2-Mercaptothioxanthone (TX-SH) photoinitiator concentrations was studied by using photo-differential scanning calorimetric (Photo-DSC) technique. Photopolymerization reactions were carried out under the same conditions of temperature and light intensity. It was observed that all conversion curves during gelation at various photoinitiator concentration present nice sigmoidal behavior which suggests application of the percolation model. The critical time where polymerization reaches the maximum rate (Rp(max)) is called the glass transition point (t(g)). The gel fraction exponents beta were produced from the conversion curves around t(g). The observed critical exponents were found to be around 0.55 predicting that the gel system obeys the percolation model. Rp(max) and final conversion (C-5) values were found to be increased as the photoinitiator concentration was increased. On the other hand t(g) values decreased as photoinitiator concentration was increased indicating higher TX-SH concentration causes early glass transition during radical polymerization. (C) 2011 Elsevier B.V. All rights reserved.

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