1,2,4-Triazole-Based First-in-Class Non-Nucleoside Inhibitors of the Bacterial Enzyme MraY

MraY is an essential bacterial enzyme for peptidoglycan synthesis in cell walls and serves as a promising but unrealized target for developing effective antibacterial drugs. Nature has provided a remarkable array of nucleoside inhibitors of MraY, and researchers have skillfully refined these structures to develop inhibitors that effectively mimic natural products. Yet, both natural products and their synthetic variants often face challenges regarding inadequate in vivo efficacy, and the intricate nature of these structures complicates their synthesis and exploration of structure-activity relationships (SAR). Here, we present our findings on the discovery of first-in-class small molecule MraY inhibitors that are non-nucleoside-derived, based on 1,2,4-triazoles, using a structure-based drug design strategy. By leveraging the structural roadmap of the MraY binding site, we discovered the initial hit compound 1 with an IC₅₀ value of 171 μM in vitro against MraY from Staphylococcus aureus (MraY _SA ) that was refined to compound 12a, exhibiting an IC₅₀ value of 25 μM. Molecular docking studies against MraY _SA provided critical insights into how the binding interactions of compounds directly influence their activity. Furthermore, we report that these compounds show broad-spectrum antibacterial activity against critical pathogens such as Enterococcus spp., methicillin-resistant S. aureus (MRSA), vancomycin-resistant Enterococci (VRE) strains, Acinetobacter baumannii, and Mycobacterium tuberculosis. This study showcases novel non-nucleoside inhibitors as a compelling proof-of-concept for crafting the next generation of antibacterial agents targeting MraY.