Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases.
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.
Zhou
L
L
Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.
Cheng
X
X
Connolly
B A
BA
Dickman
M J
MJ
Hurd
P J
PJ
Hornby
D P
DP
D000970:Antineoplastic Agents / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology*; D001483:Base Sequence; D018360:Crystallography, X-Ray; D003562:Cytidine / Q000031:analogs & derivatives; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation / Q000187:drug effects*; D015257:DNA-Cytosine Methylases / Q000737:chemistry / Q000378:metabolism*; D006190:Haemophilus / Q000201:enzymology; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D011741:Pyrimidine Nucleosides / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology*
D000970:Antineoplastic Agents; D011741:Pyrimidine Nucleosides; D003562:Cytidine; C009131:pyrimidin-2-one beta-ribofuranoside; D004247:DNA; C037664:DNA modification methylase HhaI; D015257:DNA-Cytosine Methylases