An activity-based probe for antimicrobial target DXP synthase, a thiamin diphosphate-dependent enzyme

• Published in: Frontiers in Chemical Biology Vol. 3
• Main Authors: Coco, Lauren B., Freel Meyers, Caren L.
• Format: Journal Article
• Language: English
• Published: Frontiers Media S.A 01-01-2024
• Subjects: 1-deoxy-D-xylulose 5-phosphate synthase; activity-based probe; alkyl acetylphosphonate; antimicrobial target; thiamin-dependent enzyme; vitamin biosynthesis
• ISSN: 2813-530X; 2813-530X
• DOI: 10.3389/fchbi.2024.1389620

This work reports an alkyl acetylphosphonate (alkylAP) activity-based probe (ABP) for 1-deoxy-
d
-xylulose 5-phosphate synthase DXPS, a promising antimicrobial target. This essential thiamin diphosphate (ThDP)-dependent enzyme operates at a branchpoint in bacterial central metabolism and is believed to play key roles in pathogen adaptation during infection. How different bacterial pathogens harness DXPS activity to adapt and survive within host environments remains incompletely understood, and tools for probing DXPS function in different contexts of infection are lacking. Here, we have developed alkylAP-based ABP
1
, designed to react with the ThDP cofactor on active DXPS to form a stable C2α-phosphonolactylThDP adduct which subsequently crosslinks to the DXPS active site upon photoactivation. ABP
1
displays low micromolar potency against DXPS and dose-dependent labeling of DXPS that is blocked by alkylAP-based inhibitors. The probe displays selectivity for DXPS over ThDP-dependent enzymes and is capable of detecting active DXPS in a complex proteome. These studies represent an important advance toward development of tools to probe DXPS function in different contexts of bacterial infection, and for drug discovery efforts on this target.