Inhibition of uridine phosphorylase by pyrimidine nucleoside analogs and consideration of substrate binding to the enzyme based on solution conformation as seen by NMR spectroscopy

Some 3′- and/or 5′-substituted pyrimidine nucleosides, as well as anhydropyrimidine nucleosides, which have no flexibility about the N-glycosidic bond were studied as inhibitors of thymidine phosphorylase and uridine phosphorylase. The conformation of some analogs was also investigated in order to obtain information on substrate binding to the enzyme. The above compounds, including the potential anti-(human immunodeficiency virus) agent, 3′-azido-2′,3′-dideoxy-5-methyluridine were not substrates for either thymidine phosphorylase or uridine phosphorylase. (The only exception was arabinofuranosyl-5-ethyluracil, which proved to be a poor substrate for uridine phosphorylase). The phosphorolysis of thymidine by thymidine phosphorylase was slightly or not at all altered by these pyrimidine nucloside analogs. The lowest Ki was obtained in the case of 3′-azido-2′,3′-dideoxy-5-methyluridine and the highest in the case of 2′-deoxylyxofuranosyl-5-ethyluracil, when studying the analogs with flexible structure as inhibitors of uridine phosphorylase. The Ki for 2,3′- and 2,5′-anhydro-2′-deoxy-5-ethyluridine was 5–6 orders of magnitude higher than that for 2,2′-anhydro-5-ethyluridine. Competitive inhibition was observed in all cases. For these three molecules computer-aided molecular modelling predicts the following glycosidic torsion angles X(O4,-C1,-N1-C2): 109° for 2,2′-anhydro-5-ethyluridine, and 78° and 71° for 2,3′- and 2,5′-anhydro-2′-deoxy-5-ethyluridine respectively. These values are corroborated by high-resolution 13C- and 1H-NMR studies. 2′-Deoxy-5-ethyluridine is predicted to have a syn conformation with X= 46° and ΔE about 2.5 kJ/mol over the minimum energy (in anti position, X=−147°). 1H and 13C data including homonuclear Overhauser enhancements complete the information about the solution conformation. Considering the Ki values obtained, it is likely that substrates of uridine phosphorylase will bind to the enzyme in the same conformation as 2,2′-anhydro-5-ethyluridine. The >30° deviation from the N-glycosidic torsion angle of 2,2′-anhydro-5-ethyluridine results in much higher Ki values.