Effects of modifications in the pentose moiety and conformational changes on the binding of nucleoside ligands to uridine phosphorylase from Toxoplasma gondii
Abstract One hundred and fifty analogues of uridine, with various modifications to the uracil and pentose moieties, have been tested and compared with uridine with respect to their potency to bind to uridine phosphorylase (UrdPase, EC 220.127.116.11) from Toxoplasma gondii . The effects of the α- and β-anomers, the L - and D -enantiomers, as well as restricted syn and anti rotamers, on binding were examined. Pseudo-, lyxo-, 2,3t-́anhydro-2′-deoxy-, 6,5′-cyclo-, 6,3′-methano-, O 5′,6 -methano- and carbocyclic uridines did not bind to the enzyme. Ribosides bound better than the corresponding xylosides, which were better than the deoxyribosides. The binding of deoxyribosides was in the following manner: 2′,3′-dideoxynucleosides > 2′,5′-dideoxynucleosides > 2′-deoxyribosides > 3′- and 5′-deoxyribosides. α-2′-Deoxyribosides bound to the enzyme, albeit less tightly than the corresponding β-anomers. The acyclo- and 2,2′-anhydrouridines bound strongly, with the 2,2′-anhydro-derivatives being the better ligands. 2,5′-Anhydrouridine bound to UrdPase less effectively than 2,2′-anhydrouridine and acyclouridine. Arabinosyluracil was at best a very poor ligand, but bound better if a benzyl group was present at the 5-position of the pyrimidine ring. This binding was enhanced further by adding a 5-benzyloxybenzyl group. A similar enhancement of the binding by increased hydrophobicity at the 5-position of the pyrimidine ring was observed with ribosides, α- and β-anomers of the 2′-deoxyribosides, acyclonucleosides, and 2,2′-anhydronucleosides. Among all the compounds tested, 5-(benzyloxybenzyl)-2,2′-anhydrouridine was identified as the best ligand of T. gondii UrdPase with an apparent K i value of 60 ± 3 nM. It is concluded that the presence of an N -glycosyl bond is a prerequisite for a nucleoside ligand to bind to T. gondii UrdPase. On the other hand, the presence of a 2′-, 3′-, or 5′-hydroxyl group, or an N -glycosyl bond in the β-configuration, enhanced but was not essential for binding. Furthermore, the potency of the binding of 2,2′-anhydrouridines (fixed high syn isomers) in contrast to the weaker binding of the 6,1′-anhydro- or 2,5′-anhydrouridines (fixed syn isomers), and the complete lack of binding of the 6,5′-cyclo, O 5′,6 -methano- and 6,3′-methanouridines (fixed anti isomers) to T. gondii UrdPase indicate that the binding of ligands to this enzyme is in the syn/high syn conformation around the N -glycosyl bond. The results also indicate that the parasite but not the mammalian host UrdPase can participate in hydrogen bonding with N 3 of the pyrimidine ring of nucleoside ligands. T. gondii UrdPase also has a larger hydrophobic pocket adjacent to the C5 of the pyrimidine moiety than the host enzyme, and can accommodate modifications in the pentose moiety which cannot be tolerated by the host enzyme. Most prominent among these modifications is the absence and/or lack of the ribo orientation of the 3′-hydroxyl group, which is a requirement for a ligand to bind to mammalian UrdPase. These differences between the parasite and host enzymes can be useful in designing specific inhibitors or “subversive” substrates for T. gondii UrdPase.
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