Fig 2: C25-Modified rifabutin analogs cluster into groups (A) and (B) based on their PXR binding properties. T0901317 (10 μM) was utilized as the 100% normalization control.

Fig 3: Ligand-dependent perturbation of PXR α12 observed in MD simulations. Structural overlays of the α12 helix from the PXR LBD are shown for rifabutin (RFB) (A), compound 9 (B), and compound 7 (C). For each ligand, the published PXR LBD-rifampicin crystal structure (PDB ID: 1SKX, gray) was superimposed onto the initial (MD-start) and final (MD-end) frames from 200 ns MD simulations using Cα backbone alignment. This figure was created with UCSF ChimeraX (Version 1.11).

Fig 4: (A) Chemical structures of rifampicin and rifabutin. Relevant numbering is shown. (B) X-ray crystal structure of the PXR LBD (gray) in complex with rifampicin (yellow) (PDB ID: 1SKX). Residues 178–209, which comprise the α2 helix of PXR adjacent to rifampicin, are disordered and exhibit no clear electron density. The 4-methylpiperazine ring of rifampicin is likewise not resolved in the electron density. Hydrogen bonds between PXR residues Gln285, His407, and Arg410 (cyan) and the rifampicin ansa chain are shown with cyan dashed lines. This figure was created with UCSF ChimeraX (Version 1.11).

Fig 5: Comparison of experimental CYP3A4 induction and molecular docking results for rifabutin and analogs 1–11. The left panel displays normalized CYP3A4 induction levels shown as mean ± SD from Table . The middle panel shows the predicted docking scores (kcal/mol) for the lowest energy conformer of each compound. The right panel provides an interaction map of predicted molecular interactions within the PXR LBD, where purple squares indicate proposed hydrogen-bonding (H-bond) interactions and green squares indicate proposed hydrophobic interactions. Key residues evaluated include Gln285, His407, and Arg410 for H-bonding, and Trp299 and Phe288 for hydrophobic contacts. The horizontal dashed line separates the final four compounds (8–11) where the docking scores were not consistent with the experimental CYP3A4 induction data. This figure was created with Python (Version 3.9).