Computational protocol: Physiological characterization of a novel PPAR pan agonist, 2-(4-(5,6-methylenedioxybenzo[d]thiazol-2-yl)-2-methylphenoxy)-2-methylpropanoic acid (MHY2013)

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Protocol publication

[…] The crystal structures of human PPARα, PPARβ/δ, and PPARγ were obtained from the Protein Data Bank (PDB ID: PPARα, 1K7L; PPARβ/δ, 1GWX; and PPARγ, 3DZY) and used as the targets in docking calculations. We used the AutoDock 4.2 program and the tool's manual because of its automated docking capabilities. To define the docking pockets of the three PPAR subtypes, we used a set of predefined active sites of human PPARs. Docking simulations were performed between the three PPAR subtypes and MHY2013. To prepare compounds for the docking simulation, we performed the following steps: [] 2D structures were converted into 3D structures, [] charges were calculated, and [] hydrogen atoms were added using the ChemOffice program (http://www.cambridgesoft.com). In addition, the LigandScout 3.0 program was used to generate a pharmacophore model and to predict possible hydrogen-bonding residues between the three PPAR subtypes and MHY2013. AMBER ff99SB force-field parameter was applied for calculating ligand molecules. The docking protocol was validated by docking co-crystallized ligand structure. Energy evaluations were 2500000 and population size was 150. […]

Pipeline specifications

Software tools AutoDock, LigandScout
Application Protein interaction analysis
Diseases Fatty Liver, Kidney Diseases, Metabolic Diseases, Dyslipidemias
Chemicals Bezafibrate