Exosomes delivering a high-throughput-screened RNA polymerase inhibitor for highly effective therapy of multidrug-resistant bacterial infected pneumonia.

Abstract

Bacterial pneumonia remains a primary global health threat, necessitating the development of novel therapeutic strategies to overcome escalating antibiotic resistance. In this study, we identified a highly active bacterial RNAP inhibitor, the repurposed semi-synthetic anthracycline hydrochloride Epirubicin (EPI), via the in silico high-throughput screening of a commercial library containing 16,563 small molecules. We identified EPI as a potent multi-target antibacterial agent. Alongside its intrinsic DNA intercalation properties, EPI heavily interferes with RNAP by targeting conserved catalytic residues (LYS838 and ASP1003), destabilizing the RNAP structure through a mechanism distinct from rifampicin. <i>In vitro</i>, EPI (8 μg/mL) achieved 99% eradication of <i>S. aureus</i> and multidrug-resistant (MDR) <i>E. coli</i> within 12 h by disrupting carbohydrate metabolism and ATP synthesis. To enhance clinical efficacy, EPI was encapsulated in stem cell-derived exosomes (Exo/EPI). In murine pneumonia models, the Exo/EPI nanoplatform cleared 99% of bacteria within 12 h. Furthermore, the platform rapidly attenuated infection-induced pulmonary inflammation, evidenced by a marked reduction in inflammatory cell infiltration, while significantly accelerating structural lung tissue repair and preventing cellular apoptosis via organized collagen deposition. This integrated strategy of computational discovery and exosomes delivery provides a blueprint for developing multifunctional antimicrobials against MDR infections.