Table 1.
Average RMSD and free energy of binding (kcal/mol) for re-docking of rosiglitazone (N = 5).
Table 2.
Average RMSD and free energy of binding from cross-docking for various ligands relative to each listed PDB ID (top row) (N = 3).
Table 3.
Full names and structures for compounds listed by ligand ID in Table 2.
Figure 1.
Predicted docked conformations for α-eleostearic (purple), punicic (cyan), calendic (orange), jacaric (green), and catalpic (gold) acids relative to the rosiglitazone-occupied portion of the binding cavity (mesh surface) in the rigid PPARγ structure model.
Key residues with which hydrogen bonding occurs are labeled. Atom-specific coloring: red = oxygen; gray = carbon; blue = nitrogen. Table 4 contains distance measurements for each docked pose.
Table 4.
Distance measurements (in Angstroms [Å]) for docked conjugated triene poses displayed in Figure 1.
Figure 2.
Ligand-binding (A) and reporter assay (B) results for ESA bound to PPARγ with rosiglitazone (Ros) as a positive control.
(A) Ligand binding was assessed as a measure of mean polarization for the displaced Fluormone™ molecule versus increasing concentrations of either ligand. (B) Reporter activity was measured as relative luciferase activity for various concentrations of ESA versus 1 µM Ros. Error bars represent standard deviation, while asterisks (*) indicate significance (p≤0.05) between the data sets.
Figure 3.
Effect of ESA on disease activity scores for PPARγ-expressing (A) and PPARγ-null (B) mice with experimental IBD.
PPARγ-null refers to lack of functional PPARγ product in colon epithelial and immune cells only. Data points represent averaged disease scores for each group with error bars representing standard deviation. Asterisk (*) indicates significance (p≤0.05).
Figure 4.
Effect of ESA on immune cell subsets of PPARγ-expression and PPARγ-null mice with experimental IBD.
Tissues examined included blood (A and D) and spleen (B, C, and E). Values represent least square means for percentage of gated cells with error bars to indicate standard error. Letters indicate significance (p≤0.05) where a shared letter indicates groups which are not statistically significantly different.
Figure 5.
Effect of ESA on histopathological lesions in colons from PPARγ-expressing and PPARγ-null mice with experimental IBD.
Epithelial erosion (Erosion) (A), immune cell infiltration (Infiltration) (B), and mucosal thickness (Thickness) (C) were assessed and averaged for all the DSS-treated group of samples. Data are presented as mean score with error bars to indicate standard deviation. Letters indicate significance (p≤0.05) where a shared letter indicates groups which are not statistically significantly different.
Figure 6.
Effect of ESA on colonic concentrations of IL-6 (A), VCAM-1 (B), and ICAM-1 (C) in PPARγ-expressing and PPARγ-null mice with experimental IBD.
The mean ratio of expression for each protein relative to constitutively expressed β-actin is shown with error bars to indicate standard deviation. Letters indicate significance (p≤0.05) where a shared letter indicates groups which are not statistically significantly different.
Figure 7.
Visual assessments of molecular surface differences that result in unsuccessful docking of specific ligand types to the selected PPARγ structure model.
Farglitazar is represented in both panels with atom-specific coloring. (A) 1ZGY and 1FM9 surface representations are green mesh and solid gray, respectively. The three poses predicted for farglitazar relative to 1ZGY are shown in magenta, cyan, and yellow. (B) Side chain rotamers for F282 and F363 are responsible for the differences in cavity surface at the rear of the cavity. Surface colors for 1ZGY and 1FM9 are the same as in (A). Atom-specific coloring: gray/black = carbon, blue = nitrogen, red = oxygen, white = hydrogen, and yellow = sulfur.