Differential regulation of CYP3A4 promoter activity by a new class of natural product derivatives binding to pregnane X receptor

• Published in: Biochemical pharmacology 2013-09, Vol.86 (6), p.824-835
• Main Authors: Banerjee, Monimoy, Chen, Taosheng
• Format: Article
• Language: English
• Subjects: agonists; antagonists; Binding Sites; Biological Products - chemistry; Biological Products - pharmacology; Cell Line; computer software; cytochrome P-450; Cytochrome P-450 CYP3A - genetics; Cytochrome P-450 CYP3A - metabolism; Databases, Chemical; Drug metabolism; drugs; enzymes; Epithelial Cells - cytology; Epithelial Cells - drug effects; Epithelial Cells - metabolism; Escherichia coli - genetics; Escherichia coli - metabolism; fluorescence; Gene Expression Regulation - drug effects; Genes, Reporter; Gibbs free energy; Hep G2 Cells; High-Throughput Screening Assays; human cell lines; Humans; Luciferases; Molecular docking; Molecular Docking Simulation; Natural product derivative; pharmacokinetics; Pregnane X Receptor; Promoter Regions, Genetic; Protein Binding; PXR; Receptors, Steroid - agonists; Receptors, Steroid - antagonists & inhibitors; Receptors, Steroid - genetics; Receptors, Steroid - metabolism; Recombinant Proteins - agonists; Recombinant Proteins - antagonists & inhibitors; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; screening; Structure-Activity Relationship; structure-activity relationships; tryptophan; X-ray diffraction
• ISSN: 0006-2952; 1873-2968
• DOI: 10.1016/j.bcp.2013.07.023

The pregnane X receptor (PXR) regulates drug metabolism by regulating the expression of drug-metabolizing enzymes such as cytochrome P450 3A4 (CYP3A4), which is involved in the metabolism of >50% of clinically prescribed drugs. The activity of PXR can be controlled by the binding of small molecule agonists or antagonists. Because of its unique ligand binding pocket, PXR binds promiscuously to structurally diverse chemicals. To study the structure–activity relationship, novel modulators for PXR are needed. Here we report the virtual screening of ∼25,000 natural product derivatives from the ZINC database using the Molecular Operating Environment docking software tool against the PXR-rifampicin complex X-ray crystal structure. Our screening resulted in identification of compounds based on the lowest S score, which measures Gibbs free energy. Interestingly, we found that the compounds that bind directly to PXR, as revealed in an intrinsic tryptophan fluorescence assay, modulate CYP3A4 promoter activity differentially in HepG2 cells. Mutational analysis and docking studies showed that these compounds bind broadly in the ligand binding pocket but interact with different amino acid residues. We further investigated the mechanism of binding by analyzing the functional groups that are important for distinguishing agonists from antagonists. The approach we used to identify novel modulators that bind to PXR can be useful for finding novel modulators of PXR.