Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases

J Mol Biol. 2002 Aug 23;321(4):591-9. doi: 10.1016/s0022-2836(02)00676-9.


Mechanism-based inhibitors of enzymes, which mimic reactive intermediates in the reaction pathway, have been deployed extensively in the analysis of metabolic pathways and as candidate drugs. The inhibition of cytosine-[C5]-specific DNA methyltransferases (C5 MTases) by oligodeoxynucleotides containing 5-azadeoxycytidine (AzadC) and 5-fluorodeoxycytidine (FdC) provides a well-documented example of mechanism-based inhibition of enzymes central to nucleic acid metabolism. Here, we describe the interaction between the C5 MTase from Haemophilus haemolyticus (M.HhaI) and an oligodeoxynucleotide duplex containing 2-H pyrimidinone, an analogue often referred to as zebularine and known to give rise to high-affinity complexes with MTases. X-ray crystallography has demonstrated the formation of a covalent bond between M.HhaI and the 2-H pyrimidinone-containing oligodeoxynucleotide. This observation enables a comparison between the mechanisms of action of 2-H pyrimidinone with other mechanism-based inhibitors such as FdC. This novel complex provides a molecular explanation for the mechanism of action of the anti-cancer drug zebularine.

Publication types

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

MeSH terms

  • Antineoplastic Agents / chemistry
  • Antineoplastic Agents / metabolism*
  • Antineoplastic Agents / pharmacology*
  • Base Sequence
  • Crystallography, X-Ray
  • Cytidine / analogs & derivatives
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism
  • DNA Methylation / drug effects*
  • DNA-Cytosine Methylases / chemistry
  • DNA-Cytosine Methylases / metabolism*
  • Haemophilus / enzymology
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Structure
  • Nucleic Acid Conformation
  • Protein Conformation
  • Pyrimidine Nucleosides / chemistry
  • Pyrimidine Nucleosides / metabolism*
  • Pyrimidine Nucleosides / pharmacology*


  • Antineoplastic Agents
  • Pyrimidine Nucleosides
  • Cytidine
  • pyrimidin-2-one beta-ribofuranoside
  • DNA
  • DNA modification methylase HhaI
  • DNA-Cytosine Methylases

Associated data

  • PDB/1M0E