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 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 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, ATİLLAPublication Metadata only New 1H-indole-2,3-dione 3-thiosemicarbazones with 3-sulfamoylphenyl moiety as selective carbonic anhydrase inhibitors(2022-05-01T00:00:00Z) Eraslan-Elma, Pinar; AKDEMİR, ATİLLA; Berrino, Emanuela; Bozdag, Murat; Supuran, Claudiu T.; Karali, Nilgun; AKDEMİR, ATİLLA1-Methyl/ethyl/benzyl-5-(un)substituted 1H-indole-2,3-diones (2, 3, and 4) were synthesized by reaction of 5-(un)substituted 1H-indole-2,3-diones (1) with methyl iodide, ethyl chloride, and benzyl bromide. (3-Sulfamoylphenyl)isothiocyanate (6) was obtained by the treatment of 3-aminobenzenesulfonamide (5) with thiophosgene. Compound 6 was reacted with hydrazine to yield 4-(3-sulfamoylphenyl)thiosemicarbazide (7). Novel 1-(un)substituted/methyl/ethyl/benzyl-5-(un)substituted 1H-indole-2,3-dione 3-[4-(3-sulfamoylphenyl)thiosemicarbazone] derivatives (8-11) were prepared by condensation of 7 and 1-4. The structures of the synthesized compounds were confirmed by elemental analysis and spectral data. Inhibition of the widely distributed cytosolic off-targets human carbonic anhydrases (hCAs) I and II, and two tumor-associated membrane-bound isoforms (hCAs IX and XII), by 8-11 was investigated. The hCA II inhibitory effects of all tested compounds were in the subnanomolar to low nanomolar levels (K-i = 0.32-83.3 nM), and generally high selectivity for hCA II isoenzyme over hCA I, IX, and XII isoenzymes was observed. The strongest inhibitors of hCA II, 1-benzyl-5-(trifluoromethoxy)-substituted 11c (K-i = 0.32 nM) and 1-ethyl-5-chloro-substituted 10e (K-i = 0.35 nM), were docked within the enzyme active site. Molecular modeling studies with the most effective hCA IX and XII inhibitors were also carried out.Publication Metadata only Target Recognition Molecules and Molecular Modeling Studies(2017-01-01) Bütün, Burcu; Akdemir, Atilla; BÜTÜN, BURCU; AKDEMİR, ATİLLAPublication Metadata only Exploring new Probenecid-based carbonic anhydrase inhibitors: Synthesis, biological evaluation and docking studies.(2015-09-01) MOLLICA, A; COSTANTE, R; Akdemir, ATİLLA; CARRADORI, S; STEFANUCCI, A; MACEDONIO, G; CERUSO, M; SUPURAN, CT; AKDEMİR, ATİLLA