Homology modeling and molecular dynamics of CYP1A1 and CYP2B1 to explore the metabolism of aryl derivatives by docking and experimental assays

Eur J Med Chem. 2010 Nov;45(11):4845-55. doi: 10.1016/j.ejmech.2010.07.055. Epub 2010 Aug 14.


Since many drugs are metabolized by cytochrome P450 (CYP450), biotransformation studies using these enzymes are valuable in drug development. In this work, the biotransformation by CYP1A1 and CYP2B1 of two acetylcholinesterase (AChE) inhibitors, 4-(4'-hydroxy-phenylamino)-4-oxo propanoic acid (A) and 1H-pyrrolidine-1-(4'-hydroxy-phenyl)-2,5-dione (B), was investigated through docking and molecular dynamics (MD) simulations and by experimental methods using rat liver microsomes pretreated with β-naphthoflavone and phenobarbital (CYP1A1 and CYP2B1 inducers, respectively). The target proteins were initially built by homology modeling, and the resulting three-dimensional structures were refined by MD to obtain fifteen snapshots of each P450 isoform. These snapshots were used to dock compounds A and B as well as the reference compound acetaminophen (APAP). We confirmed that APAP produces a toxic intermediate (N-acetyl-p-benzoquinone imine) upon interaction of its amide group with the heme iron of CYP1A1. However, neither A nor B presented this kind of interaction within any snapshot with CYP1A1. On the other hand, when APAP, A and B were docked on CYP2B1, their hydroxyl group was located near the heme iron on the snapshot at 3.5 ns. Furthermore, B maintained the same position on all snapshots of this isoform. Therefore, theoretical results suggests that A and B do not generate toxic metabolites. These data were supported by HPLC analysis showing only one metabolite from A and B, which was identified by GC-MS as the hydroxylated product. Altogether, our results suggest that neither test compound is toxic.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Chromatography, High Pressure Liquid
  • Cytochrome P-450 CYP1A1 / chemistry*
  • Cytochrome P-450 CYP1A1 / metabolism
  • Cytochrome P-450 CYP2B1 / chemistry*
  • Cytochrome P-450 CYP2B1 / metabolism
  • Gas Chromatography-Mass Spectrometry
  • Microsomes, Liver / drug effects
  • Microsomes, Liver / enzymology
  • Models, Molecular*
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Phenobarbital / pharmacology
  • Rats
  • Sequence Homology, Amino Acid
  • beta-Naphthoflavone / pharmacology


  • beta-Naphthoflavone
  • Cytochrome P-450 CYP1A1
  • Cytochrome P-450 CYP2B1
  • Phenobarbital