Targeting isoprenoid-precursor biosynthesis in Klebsiella pneumoniae: Design, synthesis and evaluation of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) inhibitors

Klebsiella pneumoniae is a critical-priority pathogen based on the 2024 WHO list and poses a significant threat to human health. The methylerythritol phosphate (MEP) pathway, crucial for isoprenoid biosynthesis in many pathogenic bacteria, including K. pneumoniae, represents a promising source of targets for antibacterial drug discovery. In this study, we targeted the enzyme 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from K. pneumoniae that catalyzes the initial step of the MEP pathway and, apart from broad-spectrum thiamine analogues, has no reported inhibitors to date. We identified thienopyrimidinone 6 as a promising initial hit against KpDXPS and conducted a structure-activity relationship (SAR) exploration to enhance potency, solubility and toxicity profiles. This effort led to the development of compounds 14 and 19, which exhibit improved solubility and reduced toxicity while maintaining inhibitory activity against KpDXPS. These findings provide a strong foundation for the development of novel anti-infective agents to address infections caused by K. pneumoniae.