The binding of C5-alkynyl and alkylfurano[2,3-d]pyrimidine glucopyranonucleosides to glycogen phosphorylase b: Synthesis, biochemical and biological assessment

C5-alkynyl and alkylfurano[2,3-d]pyrimidine glucopyranonucleosides have been synthesized and studied as inhibitors of glycogen phosphorylase b (GPb). Kinetic experiments have shown that most of these compounds were low micromolar inhibitors of the enzyme. The best inhibitor was 1-(β-d-glucopyranosyl)-5-ethynyluracil (Ki=4.7μM). Crystallographic analysis of these compounds in complex with GPb revealed that inhibitors with a long C5-alkynyl group exploited interactions with β-pocket of the active site and induced significant conformational changes of the 280s loop compared to GPb in complex with compounds with a short C5-alkynyl group. The results highlight the importance in the length of the aliphatic groups used to enhance inhibitory potency for the exploitation of the hydrophobic β-pocket. The best of the inhibitors had also a moderate effect on glycogenolysis in the cellular lever with an IC50 value of 291.4μM. [Display omitted] ► Novel C5-alkynyl & furano[2,3-d]pyrimidine nucleosides have been designed and synthesized. ► All compounds except two were low μM inhibitors of the enzyme. ► Three ligands induced significant conformational changes in the 280s loop. ► The most potent inhibitor was able to inhibit GPb activity in HepG2 cells in culture.