In Situ Biofilm Affinity-Based Protein Profiling Identifies the Streptococcal Hydrolase GbpB as the Target of a Carolacton-Inspired Chemical Probe

Natural products are important precursors for antibiotic drug design. These chemical scaffolds serve as synthetic inspiration for chemists who leverage their structures to develop novel antibacterials and chemical probes. We have previously studied carolacton, a natural product macrolactone from<i>Sorangium cellulosum</i>, and discovered a simplified derivative, <b>A2</b>, that maintained apparent biofilm inhibitory activity, although the biological target was unknown. Herein, we utilize affinity-based protein profiling (AfBPP) <i>in situ</i> during biofilm formation to identify the protein target using a photoexcitable cross-linking derivative of <b>A2</b>. From these studies, we identified glucan binding protein B (GbpB), a peptidoglycan hydrolase, as the primary target of <b>A2</b>. Further characterization of the interaction between <b>A2</b> and GbpB, as well as PcsB, a closely related homologue from the more pathogenic <i>S. pneumoniae</i>, revealed binding to the catalytic CHAP (cysteine, histidine, aminopeptidase) domain. To the best of our knowledge, this is the first report of a small-molecule binder of a conserved and essential bacterial CHAP hydrolase, revealing its potential as an antibiotic target. This work also highlights <b>A2</b> as a useful tool compound for streptococci and as an initial scaffold for the design of more potent CHAP binders.