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    Computational screening of dipeptidyl peptidase IV inhibitors from micoroalgal metabolites by pharmacophore modeling and molecular docking
    (Wiley, 2016) Selvaraj, Gurudeeban; Kaliamurthi, Satyavani; Cakmak, Zeynep E.; Cakmak, Turgay
    Dipeptidyl peptidase IV (DPP-IV) catalyzes conversion of GLP1 (glucagon like peptide 1) to inert structure, which results in insufficient secretion of insulin and increase in postprandial blood glucose level. The present study attempts to identify novel inhibitors from bioactive metabolites present in microalgae against DPP-IV through virtual screening, molecular docking, and pharmacophore modeling for the active target. Possible binding modes of all 60 ligands against DPP-IV receptor were constructed using MTiOpenScreen virtual screening server. Pharmacophore model was built based on identified 38 DPP-IV test ligands by using the web-based PharmaGist program which encompasses hydrogen-bond acceptors, hydrophobic groups, spatial features, and aromatic rings. The pharmacophore model having highest scores was selected to screen active DPP-IV ligands. Highest scoring model was used as a query in ZincPharmer screening. All identified ligands were filtered, based on the Lipinski's ruleof- five and were subjected to docking studies. In the process of docking analyses, we considered different bonding modes of one ligand with multiple active cavities of DPP-IV with the help of AutoDock 4.0. The docking analyses indicate that the bioactive constituents, namely, beta-stigmasterol, barbamide, docosahexaenoic acid, arachidonic acid, and harman showed the best binding energies on DPP-IV receptor and hydrogen bonding with ASP545, GLY741, TYR754, TYR666, ARG125, TYR547, SER630, and LYS554 residues. This study concludes that docosahexaenoic acid, arachidonic acid, beta-stigmasterol, barbamide, harman, ZINC58564986, ZINC56907325, ZINC69432950, ZINC69431828, ZINC73533041, ZINC84287073, ZINC69849395, and ZINC10508406 act as possible DPP-IV inhibitors.
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    Induction of triacylglycerol production in Chlamydomonas reinhardtii: Comparative analysis of different element regimes
    (Elsevier Sci Ltd, 2014) Cakmak, Zeynep E.; Olmez, Tolga T.; Cakmak, Turgay; Menemen, Yusuf; Tekinay, Turgay
    In this study, impacts of different element absence (nitrogen, sulfur, phosphorus and magnesium) and supplementation (nitrogen and zinc) on element uptake and triacylglycerol production was followed in wild type Chlamydomonas reinhardtii CC-124 strain. Macro- and microelement composition of C. reinhardtii greatly differed under element regimes studied. In particular, heavy metal quotas of the microalgae increased strikingly under zinc supplementation. Growth was suppressed, cell biovolume, carbohydrate, total neutral lipid and triacylglycerol levels increased when microalgae were incubated under these element regimes. Most of the intracellular space was occupied by lipid bodies under all nutrient starvations, as observed by confocal microscopy and transmission electron micrographs. Results suggest that sulfur, magnesium and phosphorus deprivations are superior to nitrogen deprivation for the induction triacylglycerol production in C. reinhardtii. On the other hand, FAME profiles of the nitrogen, sulfur and phosphorus deprived cells were found to meet the requirements of international standards for biodiesel. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved.