Molecular Modelling Analysis of the Metabolism of Zebularine
Zebularine (ZEB) is a pyrimidinone ribinucleoside that is a potent inhibitor of DNA methyltransferases. The inhibition of DNA methylation by ZEB is believed to result from the formation of a covalent adduct between the enzyme and ZEB-substituted DNA. Based on both in vitro and in vivo activity in mammalian cells, ZEB has been proposed for clinical evaluation as an oral antitumor agent. The compound is quite stable with half-lives of 44 and 68 h at pH 1.0 and 2.0, respectively and shows no evidence of decomposition after more than a week at pH 5. At pH 7.4, the half-life is 508 h. It has been suggested that the enhanced chemical stability of ZEB is responsible for its oral activity. Molecular modelling analyses based on molecular mechanics, semi-empirical (PM3) and DFT (at B3LYP/6-31G* level) calculations show that ZEB and all its metabolites have large LUMO-HOMO energy differences indicating that they will be kinetically inert, thus providing an explanation for the long half-lives at different physiologically relevant pHs. The high solvation energies of ZEB and its metabolites suggest that they can be easily excreted via the urine.
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