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Although compound 1 showed weak transactivation activity for PPARγ (Fig. 2), it displayed high affinity to PPARγ in a binding assay (Ref. 14,15).
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TM MX multilabel counter (Perkin-Elmer, Boston, MA, U.S.A.). DNA cotransfection experiments included 58 ng of reporter plasmid, 12 ng of CMX-β-galactosidase, and 18 ng of each receptor expression plasmid per well in a 96-well plate. Luciferase data were normalized to an internal β-galactosidase control and reported values are means of triplicate assays.
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34347373711
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note
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The relative efficacy of compound 17 was 86% of that of GW501516.
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29
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34347383578
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note
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The X-ray structure of PPARδ complexed with GW2433 (PDB code 1GWX) was used as the target structure for docking. Protein preparation, receptor grid generation and ligand docking were performed using the software Glide 3.5. Compound 17 was docked into the ligand binding site of PPARδ. The extra precision mode of Glide was used to determine favorable binding poses, which allowed the ligand conformation to be flexibly explored while holding the protein as a rigid structure during docking. The predicted complex structure was then fully energy-minimized with both the protein and the ligand allowed to move using Macromodel 8.1 software. The conformation of 17 in the PPARδ ligand binding site was minimized by MM calculation based upon the OPLS-AA force field with each parameter set as follows; solvent: water, method: LBFGS, Max # Iterations: 10,000, Converge on: Gradient, Convergence Threshhold: 0.05.
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