Recent advances in the peptidoglycan-targeting bacterial labeling with stem peptide-mimicking probes

Bacterial peptidoglycan is highly conserved across most bacterial species and serves as a critical target for antibiotic development. Its chemical structure and biosynthetic pathways have been extensively studied for decades. PGN cross-linking, mediated by two distinct classes of enzymes, D,D-transpeptidase and L,D-transpeptidase, occurs at the stem peptide and is essential for cell wall biosynthesis. However, the spatiotemporal dynamics of this process remain challenging to resolve, limiting our understanding of PGN’s synthesis and remodeling. In the past decade, stem peptide-mimicking chemical probes have emerged as a valuable tool for PGN-labeling and dynamic investigation of the cross-linking process. This review summarizes the different types of stem peptide-mimicking probes designed for labeling PGN via either D,D- or L,D-transpeptidase-mediated cross-linking, with a focus on their design rationale, functioning mechanisms, and research applications. The structural flexibility and diversity of these probes offer broad potential applications in PGN labeling, antibiotic development, and microbiota analysis in different biological contexts.