Person: AKDEMİR, ATİLLA
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Publication Metadata only Identification of novel α7 nicotinic receptor ligands by in silico screening against the crystal structure of a chimeric α7 receptor ligand binding domain.(2012-10-01) THOMPSON, AJ; de, Graaf; Akdemir, ATİLLA; de, Esch; KOOISTRA, AJ; EDINK, E; LUMMIS, SC; AKDEMİR, ATİLLAA hierarchical in silico screening procedure using the crystal structure of an agonist bound chimeric α7/Ls-AChBP protein was successfully applied to both proprietary and commercial databases containing drug-like molecules. An overall hit rate of 26% (pK(i) ≥5.0) was obtained, with an even better hit rate of 35% for the commercial compound collection. Structurally novel and diverse ligands were identified. Binding studies with [(3)H]epibatidine on chimeric α7/5-HT(3) receptors yielded submicromolar inhibition constants for identified hits. Compared to a previous screening procedure that utilized the wild type Ls-AChBP crystal structure, the current study shows that the recently obtained α7/Ls-AChBP chimeric protein crystal structure is a better template for the identification of novel α7 receptor ligands.Publication Metadata only Fragment growing induces conformational changes in acetylcholine-binding protein: a structural and thermodynamic analysis.(2011-04-13T00:00:00Z) SIXMA, TK; SMIT, AB; Akdemir, ATİLLA; de, Esch; LEURS, R; van, Muijlwijk-Koezen; van, Nierop; JANSSEN, E; van, Elk; ZUIDERVELD, O; NAHAR, T; RETRA, K; RUCKTOOA, P; EDINK, E; AKDEMİR, ATİLLAPublication Metadata only Abietane diterpenoids as butyrylcholinesterase inhibitors from Salvia species(2012-08-01) Topcu, GÜLAÇTI; Akdemir, ATİLLA; Öztürk, Mahmut Serdar; Boğa, Miray; Kola, U.; TOPÇU, GÜLAÇTI; AKDEMİR, ATİLLAPublication Metadata only rac- and meso-Cyclohexanoids: Their alpha-, beta-glycosidases, antibacterial, antifungal activities, and molecular docking studies(2020-01-10T00:00:00Z) Karakilic, Emel; Baran, Sule; Ogutcu, Hatice; AKDEMİR, ATİLLA; Baran, Arif; AKDEMİR, ATİLLAAn efficient and versatile synthesis method has been postulated for hydroxymethylated rac- and meso-cyclohexanoid derivatives. The synthesis of these stereoisomers was achieved easily with traditional methods using hexahydroisobenzofuran 6, prepared from commercially available cis-hydrophthalic anhydride. The study, involving diastereoselective epoxidation and cis-hydroxylation, was conducted to obtain epoxy-, cis-, and trans-diol-furans 7, 8, and 9. After sulfamic acid-catalyzed ring-opening reaction of the epoxide and furan rings, rac- and meso-tetraacetates 14, 15, and 16 were afforded. Hydrolysis of acetate groups with ammonia in absolute methanol yielded the desired tetrols rac-17, meso-18, and meso-19. All structures, after purification by chromatographic methods and elucidation by spectral techniques, were screened against alpha- and beta-glucosidases. Compounds 7, 8, 10, 17, 18, and 19 were also evaluated for their antibacterial and antifungal activity against some selected synthesized compounds with varying degrees of inhibitory effects on the growth of different pathogenic microorganisms by the well-diffusion method. In addition, Saccharomyces cerevisiae alpha-glucosidase molecular modeling studies were performed for all rac- and meso-compounds 7, 8, 10, 17, 18, and 19.Publication Metadata only Design and synthesis of new heterocyclic compounds containing 5-[(1H-1,2,4-triazol-1-yl)methyl]-3H-1,2,4-triazole-3-thione structure as potent hEGFR inhibitors(2023-01-01) KOLCUOĞLU Y.; BEKİRCAN O.; Fazli H.; Sahin E.; TÜRE A.; AKDEMİR A.; Hamarat Sanlier S.; AKDEMİR, ATİLLA© 2023 Informa UK Limited, trading as Taylor & Francis Group.EGFR is one of the important mediators of the signaling cascade that determines key roles in various biological processes such as growth, differentiation, metabolism and apoptosis in the cell in response to external and internal stimuli. In recent years, it has been proven that although this enzyme activity is tightly regulated in normal cells, if the enzyme activity cannot be controlled, it can lead to malignancy. EGFR is also considered a prominent macromolecule in targeted cancer chemotherapy. For this purpose, a comprehensive modeling studies were conducted against EGFR protein and novel molecules containing 5-[(1H-1,2,4-triazol-1-yl)methyl]-3H-1,2,4-triazole-3-thione structure were suggested to be synthesized. Among the synthesized molecules, compounds 7c, 8c, 8f and 8g were determined to have significant IC50 values. Compound 8g was found to have the IC50 value closest to the very well-known EGFR inhibitor Gefitinib with its noncompetitive inhibition form. K i value of compound 8g was calculated as 0.00232 µM. Communicated by Ramaswamy H. Sarma.Publication Metadata only Molecular modelling studies to understand the effects of bioactive compounds on DNA and gene expression(2015-11-24) AKDEMİR, ATİLLA; AKDEMİR, ATİLLAPublication Metadata only A novel library of saccharin and acesulfame derivatives as potent and selective inhibitors of carbonic anhydrase IX and XII isoforms.(2016-03-01) CERUSO, M; SECCI, D; De, Monte; MOLLICA, A; SOBOLEV, AP; Akdemir, ATİLLA; SUPURAN, CT; GUGLIELMI, P; De, Cosmi; CODISPOTI, R; CARRADORI, S; AKDEMİR, ATİLLAPublication Metadata only Acetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors.(2011-10-15T00:00:00Z) RUCKTOOA, P; JONGEJAN, A; Akdemir, ATİLLA; de, Esch; de, Graaf; LEURS, R; SMIT, AB; BERTRAND, D; SIXMA, TK; BERTRAND, S; ELK, RV; AKDEMİR, ATİLLAPublication Metadata only Design and synthesis of novel peptidomimetics for cancer immunotherapy(2020-07-01T00:00:00Z) Kose, Ceyda; Uysal, Esra; Yazici, Busra; Tugay, Zeynep; Yanik, Hamdullah; Tavukcuoglu, Ece; Gulyuz, Sevgi; AKDEMİR, ATİLLA; ESENDAĞLI, GÜNEŞ; Yilmaz, Ozgur; Alptürk, Onur; DİNGİŞ BİRGÜL, SERAP İPEK; AKDEMİR, ATİLLATumor cells benefit from some certain signals, which are referred to as -immune checkpoints-, to escape immune-mediated destruction. With that in mind, it is believed that the blockade of these points, such as programmed cell death Ligand-1 (PD-L1) and programmed cell death 1 (PD-1), can restore an adaptative immune response against tumoral cells. In this study, we have designed and synthesized some novel peptidomimetics with a 2-aminobenzathiazole scaffold, which targets the PD-1/PDL-1 pathway. In the viability assay, it was found that these compounds decreased the proliferation of peripheral blood mononuclear cells in the concentration of 10 uM. Overall, our results indicate that these novel compounds are potential checkpoint inhibitors for cancer immunotherapy.Publication Metadata only Synthesis of a new series of dithiocarbamates with effective human carbonic anhydrase inhibitory activity and antiglaucoma action.(2015-05-15) LANZI, C; SUPURAN, CT; MASINI, E; CARTA, F; VULLO, D; ISIK, S; SCOZZAFAVA, A; BOZDAG, M; Akdemir, ATİLLA; AKDEMİR, ATİLLA