Imidazole- and Benzimidazole-Based Inhibitors of the Kinase IspE: Targeting the Substrate-Binding Site and the Triphosphate-Binding Loop of the ATP Site

The enzymes of the mevalonate-independent biosynthetic pathway to isoprenoids are attractive targets for the development of new drug candidates, in particular against malaria and tuberculosis, because they are present in major human pathogens but not in humans. Herein, the structure-based design, synthesis, and biological evaluation of a series of inhibitors featuring a central imidazole or benzimidazole scaffold for the kinase IspE from E. coli, a model for the corresponding malarial enzyme, are described. Optimization of the binding preferences of the hydrophobic sub-pocket at the substrate-binding site allowed IC50 values in the lower micromolar range to be reached. Structure–activity relationship studies using a 1,2-disubstituted imidazole central core revealed that alicyclic moieties fit the sub-pocket better than