Fig. 4: Nomilin is a PXR agonist and the crystal structure for hPXRLBD-NCOA1676–700 bound to nomilin.
a Structure of nomilin and its analogues and hPXR reporter gene assay. The results represent three independent experiments. (One-way ANOVA test in deacetylnomilin and limonin; and Kruskal-Wallis test in nomilin, n = 3/each, the data were shown as means ± SEM. ***p < 0.001 compared to the control group). b TR-FRET assay. The TR-FRET ratio (520/495) was calculated by subtracting the background. c Dimeric human PXRLBD-NCOA1676-700 (in blue and red for protomer A and B, respectively) and co-activator peptide (in orange) fusion protein. The nomilin molecules are shown as stick models and coloured by element. d The space-filling model of protomer A was sliced to show the binding pocket for nomilin (shown as stick model) and some residues closely interacting with nomilin. H407 was shown in its two alternative conformations. e The omit Fo-Fc electron density maps for nomilin in protomer A (upper) and B (lower) are shown as mesh models and contoured to 1.0 σ. f A close view of the binding site of protomer A. The nomilin is shown as stick and space-filling models, with the surrounding residues shown as a stick model. g The schematic diagram for the hPXR-nomilin interaction network. h A comparison between binding pockets of hPXR LBD in complex with nomilin and rifampicin. Both hPXRs are shown as cartoon models in blue and grey for nomilin-bound and rifampicin-bound structures, respectively. The nomilin and rifampicin are shown as stick models coloured by element (green-red for nomilin and grey-red for rifampicin). The structure model of the hPXR-rifampicin complex was generated with coordinates from PDB ID 1SKX. i hPXR mutations change the effects of nomilin action. The plasmids were transfected into HEK293T cells, which were treated with nomilin or rifampicin for 24 h (two-tailed unpaired Student’s t-test, n = 3/each, the data were shown as means ± SEM, ***p < 0.001 vs. control group).
