title: Evaluation of in vitro PXR-based assays and in silico modeling approaches for understanding the binding of a structurally diverse set of drugs to PXR.
abstract: The pregnane X-receptor (PXR) is a promiscuous nuclear receptor primarily responsible for the induction of genes from the cytochrome P450 3A family. In this study, we used a previously described PXR/SRC tethered protein to establish two in vitro assays for identifying PXR ligands: automated ligand identification system (ALIS) and temperature-dependent circular dichroism (TdCD). Kd values determined by ALIS and TdCD showed good correlations with the EC50 values determined by a PXR luciferase reporter-gene assay for 37 marketed drugs. The same set of compounds was modeled into the PXR ligand-binding domain that takes into consideration the structural variations of five published X-ray structures of PXR-ligand complexes. Major findings from our in silico analysis are as follows. First, the primary determinants for non-binders of PXR are molecular size and shape of the compounds. Low molecular weight (MW<300) compounds were in general found to be non-binders, and those molecules that do not match the shape of the PXR ligand-binding site may also act as a non-binder. Secondly, the favorable hydrophobic interactions, mostly through aromatic π-π interactions, and the presence of suitable hydrogen bond(s) between the compounds and PXR are attributes of strong binders. Thirdly, the structures of the PXR binding domain possess the flexibility that accommodates structurally diverse compounds, while some of the strong binders may also adapt flexible conformations for fitting into the binding site. The results from this study provide a molecular basis for future efforts in reducing/abolishing the PXR-dependent CYP3A4 induction liability.
authors.affiliation: Merck Research Laboratories, K-15-2-2700, 2015 Galloping Hill Road, Kenilworth, NJ 07033, United States.
authors.forename: Li
authors.initials: L
authors.lastname: Xiao
authors.forename: Elliott
authors.initials: E
authors.lastname: Nickbarg
authors.forename: Wenyan
authors.initials: W
authors.lastname: Wang
authors.forename: Ann
authors.initials: A
authors.lastname: Thomas
authors.forename: Michael
authors.initials: M
authors.lastname: Ziebell
authors.forename: Winfred W
authors.initials: WW
authors.lastname: Prosise
authors.forename: Charles A
authors.initials: CA
authors.lastname: Lesburg
authors.forename: S Shane
authors.initials: SS
authors.lastname: Taremi
authors.forename: Valerie L
authors.initials: VL
authors.lastname: Gerlach
authors.forename: Hung V
authors.initials: HV
authors.lastname: Le
authors.forename: K-C
authors.initials: KC
authors.lastname: Cheng
mesh_terms: D002942:Circular Dichroism; D017930:Genes, Reporter; D056945:Hep G2 Cells; D006801:Humans; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008156:Luciferases / Q000096:biosynthesis / Q000235:genetics; D008958:Models, Molecular; D015394:Molecular Structure; D008970:Molecular Weight; D056918:Nuclear Receptor Coactivators / Q000737:chemistry; D004364:Pharmaceutical Preparations / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D000077297:Pregnane X Receptor; D011485:Protein Binding; D011987:Receptors, Steroid / Q000737:chemistry* / Q000235:genetics; D013329:Structure-Activity Relationship; D013696:Temperature
chemical_list: D008024:Ligands; D056918:Nuclear Receptor Coactivators; D004364:Pharmaceutical Preparations; D000077297:Pregnane X Receptor; D011987:Receptors, Steroid; D008156:Luciferases