A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR

Mol Cell. 2003 Apr;11(4):1079-92. doi: 10.1016/s1097-2765(03)00104-7.


The farnesoid X receptor (FXR) functions as a bile acid (BA) sensor coordinating cholesterol metabolism, lipid homeostasis, and absorption of dietary fats and vitamins. However, BAs are poor reagents for characterizing FXR functions due to multiple receptor independent properties. Accordingly, using combinatorial chemistry we evolved a small molecule agonist termed fexaramine with 100-fold increased affinity relative to natural compounds. Gene-profiling experiments conducted in hepatocytes with FXR-specific fexaramine versus the primary BA chenodeoxycholic acid (CDCA) produced remarkably distinct genomic targets. Highly diffracting cocrystals (1.78 A) of fexaramine bound to the ligand binding domain of FXR revealed the agonist sequestered in a 726 A(3) hydrophobic cavity and suggest a mechanistic basis for the initial step in the BA signaling pathway. The discovery of fexaramine will allow us to unravel the FXR genetic network from the BA network and selectively manipulate components of the cholesterol pathway that may be useful in treating cholesterol-related human diseases.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence / genetics
  • Animals
  • Benzene Derivatives / chemical synthesis
  • Benzene Derivatives / pharmacology
  • Binding Sites / drug effects
  • Binding Sites / physiology
  • Chenodeoxycholic Acid / agonists*
  • Chenodeoxycholic Acid / analogs & derivatives*
  • Chenodeoxycholic Acid / metabolism
  • Colon / metabolism
  • Cross Reactions / genetics
  • DNA-Binding Proteins / agonists
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • Gene Expression Profiling
  • Gene Expression Regulation / genetics
  • Gene Targeting
  • Genomic Library
  • Hepatocytes / drug effects
  • Hepatocytes / metabolism*
  • Humans
  • Liver / metabolism
  • Molecular Conformation
  • Molecular Structure
  • Oligonucleotide Array Sequence Analysis
  • Protein Structure, Tertiary / drug effects
  • Protein Structure, Tertiary / genetics
  • RNA, Messenger / genetics
  • Receptors, Cytoplasmic and Nuclear
  • Signal Transduction / drug effects
  • Signal Transduction / physiology
  • Transcription Factors / agonists
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics


  • Benzene Derivatives
  • DNA-Binding Proteins
  • RNA, Messenger
  • Receptors, Cytoplasmic and Nuclear
  • Transcription Factors
  • fexaramine
  • farnesoid X-activated receptor
  • Chenodeoxycholic Acid

Associated data

  • PDB/1OSH
  • PDB/1OSK