• Soman as a wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations 

  Authors:Bennion, Brian J.; Eşsiz-Gökhan, Şebnem; Lau, Edmond Y.; Fattebert, Jean-Luc; Emigh, Aiyana; Lightstone, Felice C.
  Publisher and Date:(Amer Chemical Soc, 2014)

  
  
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  A mathematical characterization of the gel point in sol-gel transition 

  Authors:Bilge, Ayşe Hümeyra; Pekcan, Önder
  Publisher and Date:(IOP Publishing Ltd, 2015)

  We model the sol-gel transition in terms of Susceptible-Infected-Removed (SIR) and Susceptible-Exposed-Infected-Removed (SEIR) models and compare with experimental results. We show, numerically, that the "gel point" described as the onset of the gelation phenomena and measured experimentally, corresponds to an accumulation point of the extreme values of the derivatives of the gelation curve. We define the "critical point of a sigmoidal curve" as the limit of the points where the derivatives reach ...

  
  
• Effect of temperature and graphene oxide on the swelling of PAAm-GO composite gels 

  Authors:Osma, Büşra; Akın Evingür, Gülşen; Pekcan, Önder
  Publisher and Date:(Avestia Publishing, 2019)

  Graphene oxide (GO) is a two dimensional carbon material with similar one-atom thickness, and is a light material having extremely high strength and thermal stability [1]. Thus, GO is an efficient filler for the enhancement of the electrical, mechanical and thermal properties of composite materials [2]. We focused on GO as a nanofiller in polyacrylamide hydrogels and PAAm-GO composites to investigate the effect of temperature and graphene oxide on the swelling. Polyacrylamide (PAAm) hydrogels have ...

  
  
• EFFECT OF CONTENT AND TEMPERATURE ON THE PHASE TRANSITIONS OF POLYMER COMPOSITES DOPED BY KAPPA CARRAGEENAN AND ALGINATE 

  Authors:Evingür, Gülşen Akın; Pekcan, Önder
  Publisher and Date:(Elsevier Academic Press Inc, 2016)

  
  
• The modifier effects of chymotrypsin and trypsin enzymes on fluorescence lifetime distribution of "N-(1-pyrenyl)maleimide-bovine serum albumin" complex 

  Authors:Özyiğit, İbrahim Ethem; Karakuş, Emine; Pekcan, Önder
  Publisher and Date:(Pergamon-Elsevier Science LTD, 2016)

  Chymotrypsin and trypsin are the well known proteolytic enzymes, both of which are synthesized in the pancreas as their precursors the inactive forms; chymotrypsinogen and trypsinogen and then are released into the duodenum to cut proteins into smaller peptides. In this paper, the effects of activities of chymotrypsin and trypsin enzymes on fluorescence lifetime distributions of the substrat bovine serum albumin (BSA) modified with N-(1-pyrenyl)maleimide (PM) were examined. In the labeling study ...

  
  
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  Drug Design for CNS Diseases: Polypharmacological Profiling of Compounds Using Cheminformatic, 3D-QSAR and Virtual Screening Methodologies 

  Authors:Nikolic, Katarina; Mavridis, Lazaros; Djikic, Teodora; Vucicevic, Jelica; Agbaba, Danica; Yelekçi, Kemal; Mitchell, John B. O.
  Publisher and Date:(Frontiers Media Sa, 2016)

  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 ...

  
  
• Design, Synthesis and hMAO Inhibitory Screening of Novel 2-Pyrazoline Analogues 

  Authors:Evranos-Aksöz, Begüm; Uçar, Gülberk; Yelekçi, Kemal
  Publisher and Date:(Bentham Science Publ Ltd, 2017)

  Aim and Objective: MAO inhibitors have a significant effect on the nervous system since they act in regulation of neurotransmitter concentrations. Neurotransmitter levels are critical for a healthy nervous system. MAO inhibitors can be used in the treatment of neurological disorders such as depression, Parkinson's disease and Alzheimer's disease, as the increase or decrease of some neurotransmitter concentrations is associated with these neurological disorders. This study was conducted to discover ...

  
  
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  Exploration of the binding pocket of histone deacetylases: the design of potent and isoform-selective inhibitors 

  Authors:Uba, Abdullahi Ibrahim; Yelekçi, Kemal
  Publisher and Date:(Tübitak Scientific & Technical Research Council Turkey, 2017)

  Histone deacetylases (HDACs) are enzymes that act on histone proteins to remove the acetyl group and thereby regulate the chromatin state. HDACs act not only on histone protein but also nonhistone proteins that are key players in cellular processes such as the cell cycle, signal transduction, apoptosis, and more. "Classical" HDACs have been shown to be promising targets for anticancer drug design and development. However, the selectivity of HDAC inhibitors for HDAC isoforms remains the motivation ...

  
  
• New Human Monoamine Oxidase A Inhibitors with Potential Anti-Depressant Activity: Design, Synthesis, Biological Screening and Evaluation of Pharmacological Activity 

  Authors:Evranos-Aksöz, Begüm; Uçar, Gülberk; Tas, Sadık Taşkın; Aksöz, Erkan; Yelekçi, Kemal; Erikci, Açelya; Sara, Yıldırım; İskit, Alper Bektaş
  Publisher and Date:(Bentham Science Publ Ltd, 2017)

  Aim and Objective: Depression is a momentous disease that can greatly reduce the quality of life and cause death. In depression, neurotransmitter levels such as serotonine, dopamine and noradrenaline are impaired. Monoamine oxidases (MAO) are responsible for oxidative catalysis of these monoamine neurotransmitters. Because of this relation, MAO-A inhibitors show antidepressant activity by regulating neurotransmitter levels. This study was carried out to investigate the design, synthesis and activity ...

  
  
• Investigation of intrinsic dynamics and allosteric coupling in human beta 2-adrenergic receptor 

  Authors:Özcan, Özer; Özgür, Canan; Doruker, Pemra; Akten, Ebru Demet
  Publisher and Date:(Springer, 2017)

  
  
• Pharmacophore-based virtual screening for identification of potential selective inhibitors of human histone deacetylase 6 

  Authors:Uba, Abdullahi Ibrahim; Yelekçi, Kemal
  Publisher and Date:(Elsevier Sci Ltd, 2018)

  Histone deacetylase (HDAC) 6 plays a role in oncogenic transformation and cancer metastasis via tubulin deacetylation, making it a critical target for anticancer drug design. However, lack of selectivity shown by many of the current HDAC6 inhibitors in clinical use and trials prompts the continuous search for selective inhibitors. Here, 10 pharmacophore hypotheses were developed based on the 3D common features of training set of 20 HDAC inhibitors in clinical use and trials. The hypotheses were ...

  
  
• The design of potent HIV-1 integrase inhibitors by a combined approach of structure-based virtual screening and molecular dynamics simulation 

  Authors:Samorlu, Augustine S.; Yelekçi, Kemal; Uba, Abdullahi Ibrahim
  Publisher and Date:(Taylor & Francis Inc, 2019)

  
  
• A new thiadiazine derivative induces oxidative stress dependent JNK pathway activation and cell death in hepatocellular carcinoma 

  Authors:Kahraman, Deniz Cansen; Bilget Güven, Ebru; Tozkoparan, Birsen; Çetin Atalay, Rengül
  Publisher and Date:(Amer Assoc Cancer Research,, 2019)

  
  
• Intermolecular interactions in human HDAC8 crystal structures and the stability of binding modes of co-crystallized inhibitors 

  Authors:Yelekçi, Kemal; Uba, Abdullahi
  Publisher and Date:(Amer Chemical Soc, 2019)

  
  
• Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors 

  Authors:Uba, Abdullahi Ibrahim; Yelekçi, Kemal
  Publisher and Date:(Taylor & Francis Inc, 2019)

  Histone deacetylases (HDACs) are implicated in the pathology of various cancers, and their pharmacological blockade has proven to be promising in reversing the malignant phenotypes. However, lack of crystal structures of some of the human HDAC isoforms (e.g., HDAC10) hinders the design of the isoform-selective inhibitor. Here, the recently solved X-ray crystal structure of Danio rerio (zebrafish) HDAC10 (Protein Data Bank (PDB) ID; 5TD7, released on 24 May 2017) was retrieved from the PDB and used ...

  
  
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  Antifungal screening and in silico mechanistic studies of an in-house azole library 

  Authors:Sarı, Suat; Kart, Didem; Sabuncuoğlu, Suna; Doğan, İnci Selin; Özdemir, Zeynep; Bozbey, İrem; Gencel, Melis; Reynisson, Johannes; Karakurt, Arzu; Saraç, Selma; Dalkara, Sevim
  Publisher and Date:(Wiley, 2019)

  Systemic Candida infections pose a serious public health problem with high morbidity and mortality. C. albicans is the major pathogen identified in candidiasis; however, non-albicans Candida spp. with antifungal resistance are now more prevalent. Azoles are first-choice antifungal drugs for candidiasis; however, they are ineffective for certain infections caused by the resistant strains. Azoles block ergosterol synthesis by inhibiting fungal CYP51, which leads to disruption of fungal membrane ...

  
  
• Synthesis, biological evaluation and molecular docking studies of bis-chalcone derivatives as xanthine oxidase inhibitors and anticancer agents 

  Authors:Burmaoğlu, Serdar; Özcan, Şeyda; Balcıoğlu, Sevgi; Gencel, Melis; Noma, Samir Abbas Ali; Eşsiz, Şebnem; Ateş, Burhan; Algül, Öztekin
  Publisher and Date:(Academic Press Inc Elsevier Science, 2019)

  In this study, a series of B-ring fluoro substituted bis-chalcone derivatives were synthesized by Claisen-Schmidt condensation reactions and evaluated for their ability to inhibit xanthine oxidase (XO) and growth inhibitory activity against MCF-7 and Caco-2 human cancer cell lines, in vitro. According to the results obtained, the bis-chalcone with fluoro group at the 2 (4b) or 2,5-position (4g) of B-ring were found to be potent inhibitors of the enzyme with IC50 values in the low micromolar range. ...

  
  
• A NEW THIADIAZINE DERIVATIVE INDUCES OXIDATIVE STRESS DEPENDENT CELL DEATH IN HEPATOCELLULAR CARCINOMA STEM CELLS 

  Authors:Kahraman, Deniz Cansen; Bilget Güven, Ebru; Aytaç, Peri; Tozkoparan, Birsen; Çetin Atalay, Rengül
  Publisher and Date:(Wiley, 2019)

  
  
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  Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10 

  Authors:Uba, Abdullahi Ibrahim; Yelekçi, Kemal
  Publisher and Date:(Taylor & Francıs Inc, 2020)

  Histone deacetylase (HDAC) 10 has been implicated in the pathology of various cancers and neurodegenerative disorders, making the discovery of novel inhibitors of the isoform an important endeavor. However, the unavailability of crystallographic structure of human HDAC10 (hHDAC10) hinders structure-based drug design effort. Previously, we reported the homology modeled structure of human HDAC10 built using the crystallographic structure of Danio rerio (zebrafish) HDAC10 (zHDAC10) (Protein Data Bank ...

  
  
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  Synthesis, in silico studies and cytotoxicity evaluation of novel 1,3,4-oxadiazole derivatives designed as potential mPGES-1 inhibitors 

  Authors:Erensoy, Gizem; Ding, Kai; Zhan, Chang-Guo; Elmezayen, Ammar; Yelekçi, Kemal; Duracık, Merve; Özakpınar, Özlem Bingol; Küçükgüzel, İlkay
  Publisher and Date:(MARMARA UNIV, 2020)

  A series of new 1,3,4-oxadizole derivatives containing thioether group, has been synthesized to investigate their mPGES-1 inhibitory activities. The synthesized compounds were also evaluated for their anticancer and COX-1/2 inhibitory activities. All compounds were checked for their purity using TLC and HPLC analyses. The melting points, elemental analysis, FT-IR, H-1-/C-13-NMR and LR-MS data were utilized for structural characterization. The most potent derivative was 2-[5-{[2-methyl-5-(propan- ...

  
  

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