IspE kinase as an anti-infective target: Role of a hydrophobic pocket in inhibitor binding

Enzymes of the methylerythritol phosphate (MEP) pathway are potential targets for antimicrobial drug discovery. Here, we focus on 4-diphosphocytidyl-2-C-methyl-D-erythritol (IspE) kinase from the MEP pathway. We use biochemical and structural biology methods to investigate homologs from pathogenic microorganisms; Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii. We determined the X-ray crystal structures of IspE-inhibitor complexes and studied inhibitors’ binding modes targeting the substrate pocket. The experimental results indicate the need for distinct inhibitor strategies due to structural differences among IspE homologs, particularly for A. baumannii IspE, which displays a unique inhibitory profile due to a tighter hydrophobic subpocket in the substrate binding site. This study enhances our understanding of the MEP enzymes and sets the stage for structure-based drug design of selective inhibitors to combat pathogenic microorganisms. [Display omitted] •IspE kinase from MEP pathway studied in E. coli, K. pneumoniae, and A. baumannii•Complex crystal structures reveal distinct inhibitor binding modes in IspE homologs•A. baumannii IspE shows unique inhibitory profile due to tighter hydrophobic subpocket•Findings guide structure-based design of selective IspE inhibitors for pathogens Hamid et al. investigate IspE kinase homologs from pathogenic bacteria, revealing structural differences that necessitate distinct inhibitor strategies. Their findings highlight the importance of the substrate pocket’s hydrophobic subpocket for inhibitor design. This study offers valuable insights for developing potent and selective inhibitors targeting the MEP pathway in pathogenic microorganisms.