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ERDEM, SAFİYE

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ERDEM

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SAFİYE

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Now showing 1 - 6 of 6
  • PublicationOpen Access
    Stable hemiaminals from axially chiral pyridine compounds
    (2023-01-01) ERDEM, SAFİYE; Tuncel S. T., Demir I., ERDEM S., Dogan I.
    © 2023 Wiley Periodicals LLC.In this study, we have synthesized a series of 3-(pyridin-2-yl)-2-(pyridin-2-ylimino)thiazolidin-4-ol derivatives regioselectively from 2-iminothiazolidin-4-ones using LiAlH4 at room temperature. Due to the presence of the restricted rotation around the N3-Caryl single bond, the formation of M/P isomers was observed. The OH group of the hemiaminal was found to orient itself on the same side with pyridyl nitrogen during this restricted rotation to form an intramolecular hydrogen bond, which was demonstrated by the computational DFT study. This orientation presumably inhibited the occurrence of dehydration and stabilized the molecule.
  • PublicationOpen Access
    In vitro and in silico investigation of inhibitory activities of 3-arylcoumarins and 3-phenylazo-4-hydroxycoumarin on MAO isoenzymes
    (2022-11-01) DANIŞ, ÖZKAN; DEMİR, SERAP; ERDEM, SAFİYE; OGAN, AYŞE; Yuce-Dursun B., DANIŞ Ö., Ozalp L., Sahin E., DEMİR S., ERDEM S., OGAN A.
    A series of 3-aryl coumarin derivatives and 3-phenylazo-4-hydroxycoumarin were evaluated for their monoamine oxidase (MAO) A and B inhibitory activity and selectivity by fluorometric enzymological assays. Among 21 coumarin derivatives, compound 21 (3-phenylazo-4-hydroxycoumarin) displayed a good inhibitory activity (0.12 +/- 0.02 mu M) and very high selectivity for MAO-B (SI > 833.33). The inhibition was determined as mixed-type and not time-dependent. Docking studies, molecular dynamics and molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) calculations were performed to elucidate in vitro results. Our results reveal that the insertion of an azo linker between coumarin and phenyl rings in 3-arylcoumarins enhances MAO-B selectivity enormously since such a linker leads to the perfect alignment of the coumarin ring in the aromatic cage and the phenyl ring in the entrance cavity of MAO-B active site. Hydrogen bond interactions with Cys172 in the active site entrance of MAO-B also contributes to the remarkably higher inhibitory activity and selectivity for MAO-B.
  • PublicationOpen Access
    How fullerene derivatives (FDs) act on therapeutically important targets associated with diabetic diseases
    (2022-01-01) ERDEM, SAFİYE; Fjodorova N., Novic M., Venko K., Drgan V., Rasulev B., SAÇAN M., ERDEM S., Tugcu G., Toropova A. P., Toropov A. A.
    Fullerene derivatives (FDs) belong to a relatively new family of nano-sized organic compounds. They are widely applied in materials science, pharmaceutical industry, and (bio) medicine. This research focused on the study of FDs in terms of their potential inhibitory effect on therapeutic targets associated with diabetic disease, as well as analysis of protein-ligand binding in order to identify the key binding characteristics of FDs. Therapeutic drug compounds when entering the biological system usually inevitably encounter and interact with a vast variety of biomolecules that are responsible for many different functions in organisms. Protein biomolecules are the most important functional components and used in this study as target structures. The structures of proteins [(PDB ID: 1BMQ, 1FM6, 1GPB, 1H5U, 1US0)] belonging to the class of anti-diabetes targets were obtained from the Protein Data Bank (PDB). Protein binding activity data (binding scores) were calculated for the dataset of 169 FDs related to these five proteins. Subsequently, the resulting data were analyzed using various machine learning and cheminformatics methods, including artificial neural network algorithms for variable selection and property prediction. The Quantitative Structure-Activity Relationship (QSAR) models for prediction of binding scores activity were built up according to five Organization for Economic Co-operation and Development (OECD) principles. All the data obtained can provide important information for further potential use of FDs with different functional groups as promising medical antidiabetic agents. Binding scores activity can be used for ranking of FDs in terms of their inhibitory activity (pharmacological properties) and potential toxicity. (c) 2022 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).
  • PublicationOpen Access
    Cheminformatics and Machine Learning Approaches to Assess Aquatic Toxicity Profiles of Fullerene Derivatives
    (2023-09-01) ERDEM, SAFİYE; Fjodorova N., Novič M., Venko K., Rasulev B., Türker Saçan M., Tugcu G., Sağ Erdem S., Toropova A. P., Toropov A. A.
    Fullerene derivatives (FDs) are widely used in nanomaterials production, the pharmaceutical industry and biomedicine. In the present study, we focused on the potential toxic effects of FDs on the aquatic environment. First, we analyzed the binding affinity of 169 FDs to 10 human proteins (1D6U, 1E3K, 1GOS, 1GS4, 1H82, 1OG5, 1UOM, 2F9Q, 2J0D, 3ERT) obtained from the Protein Data Bank (PDB) and showing high similarity to proteins from aquatic species. Then, the binding activity of 169 FDs to the enzyme acetylcholinesterase (AChE)—as a known target of toxins in fathead minnows and Daphnia magna, causing the inhibition of AChE—was analyzed. Finally, the structural aquatic toxicity alerts obtained from ToxAlert were used to confirm the possible mechanism of action. Machine learning and cheminformatics tools were used to analyze the data. Counter-propagation artificial neural network (CPANN) models were used to determine key binding properties of FDs to proteins associated with aquatic toxicity. Predicting the binding affinity of unknown FDs using quantitative structure–activity relationship (QSAR) models eliminates the need for complex and time-consuming calculations. The results of the study show which structural features of FDs have the greatest impact on aquatic organisms and help prioritize FDs and make manufacturing decisions.
  • PublicationOpen Access
    Newly synthesized piperazine derivatives as tyrosinase inhibitors: in vitro and in silico studies
    (2022-07-01) ERDEM, SAFİYE; DOKUZPARMAK Ç., ÖZ TUNCAY F., Ozdemir S. B., Kurnaz B., Demir I., ÇOLAK A., ERDEM S., YILDIRIM N.
    In this study, a series of new organic compounds with piperazine as a fundamental skeleton was synthesized and evaluated for their tyrosinase inhibitory potentials by in vitro and in silico studies. The in vitro studies have shown that compounds 10a and 10b bearing 1,2,4, triazole nucleus could be considered potent tyrosinase inhibitors with IC50 values of 31.2 +/- 0.7 and 30.7 +/- 0.2 mu M, respectively. 10b (K-i = 9.54 mu M, mixed type inhibition) with the lowest IC50 value among derivatives was selected to determine kinetic constants and inhibition types. Furthermore, molecular docking analysis was performed for all compounds and it was observed that 4b, 5a, 4c, and 10b showed promising inhibitory effect on tyrosinase activity. Based on docking results, ADME predictions and in vitro studies, 10b might be considered suitable oral drug candidates for further studies.
  • PublicationOpen Access
    Identification of some novel amide conjugates as potent and gastric sparing anti-inflammatory agents: In vitro, in vivo, in silico studies and drug safety evaluation
    (2023-08-05) KULABAŞ, NECLA; DANIŞ, ÖZKAN; OGAN, AYŞE; ERDEM, SAFİYE; KÜÇÜKGÜZEL, İLKAY; KULABAŞ N., Set İ., Aktay G., GÜRSOY Ş., DANIŞ Ö., OGAN A., Sağ Erdem S., Erzincan P., Helvacıoğlu S., Hamitoğlu M., et al.
    Today, usage of NSAIDs (nonsteroidal anti-inflammatory drugs) is very common. However, it has been proven by many studies that NSAIDs with free carboxylic acid group damage the GI (gastrointestinal) system. Our aim was to mask the acidic groups of NSAIDs to prevent or reduce their side effects while preserving their pharmacological effects. In this study, new amide derivatives of known NSAIDs, compounds 11–20, were synthesized to investigate their analgesic and anti-inflammatory effects using in vivo models. While compound 11 showed the most remarkable anti-inflammatory activity by 60.9% inhibition value at 200 mg/kg dose, compounds 11, 12, 15 and 18 had almost the same analgesic activity to that of acetylsalicylic acid (100 mg/kg) and flurbiprofen (100 mg/kg). In addition, all test compounds used at high dose (200 mg/kg, p.o) did not show any acute toxicity. COX-1 and COX-2 inhibition properties of all compounds were measured by biochemical methods and the interaction of the most active compounds with COX enzymes is elucidated by computer-assisted virtual screening methods. It was determined by in vitro enzyme inhibition studies that compound 11 and 13, synthesized from selective COX-1 inhibitors dexketoprofen and flurbiprofen, are selective COX-2 inhibitors. Moreover, compounds 11–13 were found to be non-mutagenic according to the mutagenicity assay using Salmonella TA98 and TA100 strains with and without metabolic activation. Finally, the prediction of ADMET profile and drug-likeness properties of compounds 11–20 were examined and the obtained results were evaluated.