Zebularine: A Novel DNA Methylation Inhibitor that Forms a Covalent Complex with DNA Methyltransferases

• Published in: Journal of molecular biology Vol. 321; no. 4; pp. 591 - 599
• Main Authors: Zhou, L., Cheng, X., Connolly, B.A., Dickman, M.J., Hurd, P.J., Hornby, D.P.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 23.08.2002
• Subjects: Antineoplastic Agents - chemistry; Antineoplastic Agents - metabolism; Antineoplastic Agents - pharmacology; base flipping; Base Sequence; Crystallography, X-Ray; Cytidine - analogs & derivatives; DNA - chemistry; DNA - genetics; DNA - metabolism; DNA methylation; DNA Methylation - drug effects; DNA methyltransferase; DNA-Cytosine Methylases - chemistry; DNA-Cytosine Methylases - metabolism; Haemophilus - enzymology; Hydrogen Bonding; M. HhaI; Models, Molecular; Molecular Structure; Nucleic Acid Conformation; Protein Conformation; Pyrimidine Nucleosides - chemistry; Pyrimidine Nucleosides - metabolism; Pyrimidine Nucleosides - pharmacology; zebularine; AzadC, 5-azadeoxycytidine; AdoHcy, S-adenosyl- l-homo-cysteine; zebularine; M. HhaI; C5 MTase, cytosine-[C5]-specific DNA methyltransferase; DNA methylation; DNA methyltransferase; FdC, 5-fluorodeoxycytidine; M. HhaI, C5 MTase from Haemophilus haemolyticus; base flipping; AdoMet, S-adenosyl- l-methionine
• ISSN: 0022-2836; 1089-8638
• 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.