The effects of type II binding on metabolic stability and binding affinity in cytochrome P450 CYP3A4

Arch Biochem Biophys. 2010 May;497(1-2):68-81. doi: 10.1016/ Epub 2010 Mar 25.


One goal in drug design is to decrease clearance due to metabolism. It has been suggested that a compound's metabolic stability can be increased by incorporation of a sp(2) nitrogen into an aromatic ring. Nitrogen incorporation is hypothesized to increase metabolic stability by coordination of nitrogen to the heme-iron (termed type II binding). However, questions regarding binding affinity, metabolic stability, and how metabolism of type II binders occurs remain unanswered. Herein, we use pyridinyl quinoline-4-carboxamide analogs to answer these questions. We show that type II binding can have a profound influence on binding affinity for CYP3A4, and the difference in binding affinity can be as high as 1200-fold. We also find that type II binding compounds can be extensively metabolized, which is not consistent with the dead-end complex kinetic model assumed for type II binders. Two alternate kinetic mechanisms are presented to explain the results. The first involves a rapid equilibrium between the type II bound substrate and a metabolically oriented binding mode. The second involves direct reduction of the nitrogen-coordinated heme followed by oxygen binding.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biochemical Phenomena*
  • Cytochrome P-450 CYP3A / metabolism*
  • Cytochrome P-450 Enzyme System / metabolism*
  • Heme / chemistry
  • Heme / metabolism*
  • Humans
  • Kinetics
  • Models, Chemical
  • Physical Phenomena*
  • Protein Binding


  • Heme
  • Cytochrome P-450 Enzyme System
  • Cytochrome P-450 CYP3A
  • CYP3A4 protein, human