Structural plasticity of malaria dihydroorotate dehydrogenase allows selective binding of diverse chemical scaffolds

J Biol Chem. 2009 Sep 25;284(39):26999-7009. doi: 10.1074/jbc.M109.028589. Epub 2009 Jul 28.


Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Antimalarials / chemistry
  • Antimalarials / metabolism
  • Antimalarials / pharmacology
  • Binding Sites
  • Crystallography, X-Ray
  • Dihydroorotate Dehydrogenase
  • Humans
  • Hydrogen Bonding
  • Malaria, Falciparum / parasitology
  • Malaria, Falciparum / prevention & control
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • Oxidoreductases Acting on CH-CH Group Donors / antagonists & inhibitors
  • Oxidoreductases Acting on CH-CH Group Donors / chemistry
  • Oxidoreductases Acting on CH-CH Group Donors / metabolism*
  • Plasmodium falciparum / drug effects
  • Plasmodium falciparum / enzymology*
  • Plasmodium falciparum / genetics
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Protozoan Proteins / antagonists & inhibitors
  • Protozoan Proteins / chemistry
  • Protozoan Proteins / metabolism*
  • Pyrimidines / chemistry
  • Pyrimidines / metabolism
  • Pyrimidines / pharmacology
  • Sequence Homology, Amino Acid
  • Structure-Activity Relationship
  • Triazoles / chemistry
  • Triazoles / metabolism
  • Triazoles / pharmacology


  • Antimalarials
  • Dihydroorotate Dehydrogenase
  • Protozoan Proteins
  • Pyrimidines
  • Triazoles
  • Oxidoreductases Acting on CH-CH Group Donors

Associated data

  • PDB/3I65
  • PDB/3I68
  • PDB/3I6R