Identification of potential pharmacological and toxicological targets differentiating structural analogs by a combination of transcriptional profiling and promoter analysis in LS-180 and Caco-2 adenocarcinoma cell lines

Pharmacogenet Genomics. 2006 Aug;16(8):579-99. doi: 10.1097/01.fpc.0000220561.59972.7a.


Detecting and understanding the potential for off-target pharmacological effects is critical in the optimization of lead compounds in drug discovery programs. Compound-mediated activation of the pregnane X receptor (PXR; NR1I2), a key regulator for drug metabolism genes, is often monitored to avoid potential drug-drug interactions. Two structural analogs, MRL-1 and MRL-2, were determined to be equivalent PXR activators in trans-activation assays. To differentiate these two PXR activators, their transcriptional effects were examined in PXR-sufficient (LS180) and PXR-deficient (Caco-2) adenocarcinoma cell lines. Both compounds regulated drug-management genes (e.g. CYP3A4, CYP2B6, UGT1A1 and ABCB1) in LS180 cells, but not in PXR-deficient Caco-2 cells. The potency of MRL-1 and MRL-2 on PXR activation was again equivalent as revealed by a set of 113 genes that were regulated by four prototypical PXR agonists (rifampicin, ritonavir, troglitazone and dexamethasone) in the LS180 cells. The specificity of the PXR signature genes was supported by the enrichment of putative PXR binding sites uncovered by sequence-based promoter analyses. Interestingly, an additional off-target activity of MRL-2 was suggested where sterol response element binding protein binding sites were found enriched in a subset of PXR signature genes. These genes, involved in cholesterol and fatty acid synthesis, were significantly regulated by ritonavir, chlorpromazine and MRL-2, which were linked to the manifestation of phospholipidosis. The present study demonstrates the utility of our approach in the differentiation and selection of lead compounds for drug development.

MeSH terms

  • Benzopyrans / pharmacology
  • Caco-2 Cells
  • Cells, Cultured
  • Combinatorial Chemistry Techniques / methods*
  • Drug Screening Assays, Antitumor / methods
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation
  • Humans
  • Inactivation, Metabolic / genetics
  • Intestines / drug effects
  • Models, Biological
  • Pregnane X Receptor
  • Promoter Regions, Genetic*
  • Receptors, Steroid / metabolism*
  • Rifampin / pharmacology
  • Substrate Specificity / genetics
  • Transcriptional Activation / drug effects


  • 7-(3-(2-chloro-4-(2,2,2-trifluoroethoxy)phenoxy)propoxy)-3,4-dihydro-2-methyl-2H-benzopyran-2-carboxylic acid
  • 7-(3-(2-chloro-4-(4-fluorophenoxy)phenoxy)propoxy)-2-ethyl-3,4-dihydro-2H-benzopyran-2-carboxylic acid
  • Benzopyrans
  • NR1I2 protein, human
  • Pregnane X Receptor
  • Receptors, Steroid
  • Rifampin