A bissulfone-indole derived as potent Clp protein inhibitors: Design, synthesis, and mechanistic study for plant...

CRP-like protein (Clp) belongs to the cyclic AMP receptor protein (CRP) family of biomacromolecules. It plays a broad and active role in the production of bacterial virulence factors and is therefore regarded as an important potential target for the development of novel antibacterial agents. Based on this, in this study, we designed and synthesized a series of bissulfone-indole derivatives. Antibacterial activity screening revealed that compound A8 exhibited excellent activity both in vitro and in vivo against Xanthomonas oryzae pv. oryzae (Xoo), Xanthomonas oryzae pv. oryzicola (Xoc) and Xanthomonas axonopodis pv. citri (Xac). Subsequently, activity-based protein profiling (ABPP), mass spectrometry, microscale thermophoresis (MST), biomembrane interferometry (BLI), molecular docking, molecular dynamics simulation and construction of clp binding site mutant strains confirmed that Clp is the target of A8. Mechanistic studies revealed that A8 binds to and inhibits Clp, disrupting its interaction with the virulence regulator Pyk, thereby impairing bacterial motility and pathogenicity. Transcriptomic and metabolomic analyses revealed that A8 interferes with amino acid metabolism and metabolic homeostasis, thereby inhibiting bacterial growth and virulence. Furthermore, A8 exhibited low toxicity to non-target organisms and plants. These results provide a new perspective for the synthesis and development of Clp inhibitors.