A similarity model for the human angiogenic factor, thymidine phosphorylase/platelet derived-endothelial cell growth factor.

Thymidine phosphorylase (EC 2.4.2.4), identical to the angiogenic factor, platelet-derived endothelial cell growth factor (PD-ECGF), is up-regulated in several tumour types. A similarity model of human thymidine phosphorylase was built, based on the crystal structure of the Escherichia coli enzyme. The high residue conservation between the two enzyme sources (39% sequence identity and 53% sequence similarity) aided model building. The human model was very similar to the E. coli enzyme's crystal structure, with the main tertiary structure difference being the destruction of helix 15 in E. coli by the presence of a loop in the human model. The model was used to rationalize the nature of the binding of the substrates thymine and thymidine, and of known inhibitors using a quantitative docking algorithm. Ab initio calculations on the nM inhibitor 5-chloro-6-(1-(2-iminopyrrolidinyl)methyl)uracil hydrochloride gave its conformation and distribution of charge. Subsequent quantitative docking studies have led to the suggestion, for the first time, that this inhibitor behaves as an oxycarbenium ion transition-state analogue, explaining its strong reported inhibition.