Enzymatic determinants of the substrate specificity of CYP2C9: role of B'-C loop residues in providing the pi-stacking anchor site for warfarin binding

Biochemistry. 1999 Mar 16;38(11):3285-92. doi: 10.1021/bi982161+.


Previous modeling efforts have suggested that coumarin ligand binding to CYP2C9 is dictated by electrostatic and pi-stacking interactions with complementary amino acids of the protein. In this study, analysis of a combined CoMFA-homology model for the enzyme identified F110 and F114 as potential hydrophobic, aromatic active-site residues which could pi-stack with the nonmetabolized C-9 phenyl ring of the warfarin enantiomers. To test this hypothesis, we introduced mutations at key residues located in the putative loop region between the B' and C helices of CYP2C9. The F110L, F110Y, V113L, and F114L mutants, but not the F114Y mutant, expressed readily, and the purified proteins were each active in the metabolism of lauric acid. The V113L mutant metabolized neither (R)- nor (S)-warfarin, and the F114L mutant alone displayed altered metabolite profiles for the warfarin enantiomers. Therefore, the effect of the F110L and F114L mutants on the interaction of CYP2C9 with several of its substrates as well as the potent inhibitor sulfaphenazole was chosen for examination in further detail. For each substrate examined, the F110L mutant exhibited modest changes in its kinetic parameters and product profiles. However, the F114L mutant altered the metabolite ratios for the warfarin enantiomers such that significant metabolism occurred for the first time on the putative C-9 phenyl anchor, at the 4'-position of (R)- and (S)-warfarin. In addition, the Vmax for (S)-warfarin 7-hydroxylation decreased 4-fold and the Km was increased 13-fold by the F114L mutation, whereas kinetic parameters for lauric acid metabolism, a substrate which cannot interact with the enzyme by a pi-stacking mechanism, were not markedly affected by this mutation. Finally, the F114L mutant effected a greater than 100-fold increase in the Ki for inhibition of CYP2C9 activity by sulfaphenazole. These data support a role for B'-C helix loop residues F114 and V113 in the hydrophobic binding of warfarin to CYP2C9, and are consistent with pi-stacking to F114 for certain aromatic ligands.

Publication types

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

MeSH terms

  • Arachidonic Acid / metabolism
  • Aryl Hydrocarbon Hydroxylases*
  • Binding Sites / genetics
  • Blotting, Western
  • Catalysis
  • Cytochrome P-450 Enzyme Inhibitors
  • Cytochrome P-450 Enzyme System / chemistry*
  • Cytochrome P-450 Enzyme System / genetics
  • Cytochrome P-450 Enzyme System / metabolism*
  • Diclofenac / metabolism
  • Kinetics
  • Lauric Acids / metabolism
  • Leucine / genetics
  • Mutagenesis, Site-Directed
  • Phenylalanine / genetics
  • Protein Structure, Secondary
  • Static Electricity
  • Steroid 16-alpha-Hydroxylase*
  • Steroid Hydroxylases / antagonists & inhibitors
  • Steroid Hydroxylases / chemistry*
  • Steroid Hydroxylases / genetics
  • Steroid Hydroxylases / metabolism*
  • Substrate Specificity / drug effects
  • Substrate Specificity / genetics
  • Sulfaphenazole / pharmacology
  • Warfarin / metabolism*


  • Cytochrome P-450 Enzyme Inhibitors
  • Lauric Acids
  • Sulfaphenazole
  • lauric acid
  • Diclofenac
  • Arachidonic Acid
  • Phenylalanine
  • Warfarin
  • Cytochrome P-450 Enzyme System
  • Steroid Hydroxylases
  • Aryl Hydrocarbon Hydroxylases
  • Steroid 16-alpha-Hydroxylase
  • Leucine