Identification of Inhibitors of the Anti-Infective Target DXS Using Ligand-Based Virtual Screening

The enzymes of the methylerythritol phosphate (MEP) pathway are important drug targets given that pathogens such as Mycobacterium tuberculosis and Plasmodium falciparum use this pathway for the biosynthesis of the essential isoprenoid precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), while humans exclusively utilize an alternate pathway. The thiamine-diphosphate-dependent enzyme 1-deoxy-D-xylulose-5-phosphate synthase (DXS) catalyzes the primary and rate-limiting step of the MEP pathway. To expand the structural diversity and acquire potent and selective inhibitors of DXS, we performed a ligand-based virtual screening (LBVS) campaign supported shape similarity to screen the ZINC database, ranging from previously discovered DXS inhibitors as references. Biochemical evaluation of the top-scoring compounds against tubercle bacillus DXS and further rounds of LBVS using the simplest hits as references afforded inhibitors within the single-digit micromolar range. In addition to the promising biochemical activity, the hits are active in cellbased assays against Plasmodium falciparum and even drug-resistant strains of tubercle bacillus . Further, assays demonstrated their selectivity over mammalian thiamine-diphosphate-dependent enzymes, their lack of cytotoxicity and validated DXS because the intracellular target.