Enantiomer discrimination illustrated by the high resolution crystal structures of type 4 phosphodiesterase

J Med Chem. 2006 Mar 23;49(6):1867-73. doi: 10.1021/jm051273d.


Type 4 phosphodiesterase (PDE4) inhibitors are emerging as new treatments for a number of disorders including asthma and chronic obstructive pulmonary disease. Here we report the biochemical characterization on the second generation inhibitor (+)-1 (L-, IC50=0.4 nM) and its enantiomer (-)-1 (L-, IC50=43 nM) and their cocrystal structures with PDE4D at 2.0 A resolution. Despite the 107-fold affinity difference, both enantiomers interact with the same sets of residues in the rigid active site. The weaker (-)-1 adopts an unfavorable conformation to preserve the pivotal interactions between the Mg-bound waters and the N-oxide of pyridine. These structures support a model in which inhibitors are anchored by the invariant glutamine at one end and the metal-pocket residues at another end. This model provides explanations for most of the observed structure-activity relationship and the metal ion dependency of the catechol-ether based inhibitors and should facilitate their further design.

Publication types

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

MeSH terms

  • 3',5'-Cyclic-AMP Phosphodiesterases / antagonists & inhibitors
  • 3',5'-Cyclic-AMP Phosphodiesterases / chemistry*
  • Catalytic Domain
  • Crystallography, X-Ray
  • Cyclic N-Oxides / chemistry*
  • Cyclic Nucleotide Phosphodiesterases, Type 4
  • Enzyme Inhibitors / chemistry
  • Models, Molecular*
  • Molecular Structure
  • Protein Binding
  • Pyridines / chemistry*
  • Stereoisomerism


  • Cyclic N-Oxides
  • Enzyme Inhibitors
  • L 869298
  • Pyridines
  • 3',5'-Cyclic-AMP Phosphodiesterases
  • Cyclic Nucleotide Phosphodiesterases, Type 4

Associated data

  • PDB/2FM0
  • PDB/2FM5