Hybrid Antibiotics for Persistent Infections

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Abstract The goal of this project is to optimize and study the pharmacology of dual-targeting urea depsipeptide (UDEP)-rifamycin hybrid antibiotics. These new agents have encouraging potential to treat biofilm- associated and complicated Gram-positive infections including bacteremia, prosthetic joint infections, and infective endocarditis, which are difficult to cure with standard of care antibiotics such as vancomycin and cause significant mortality. Most antibiotics require active bacterial growth to work effectively. Some bacteria evade killing by traditional antibiotics by growing slowly or not at all, allowing for survival even at high drug concentrations for prolonged periods. These surviving cells contribute to antibiotic tolerance and resistance, cause recurrent infections, prolong antibiotic therapy, and increase associated patient care costs. Recently, we have been using structure-based design to optimize the pharmacology of UDEP antibiotics, which overcome antibiotic tolerance by target non-dividing bacteria. UDEPs activate the ClpP protease causing uncontrolled proteolysis, killing stationary phase, dormant, antibiotic-tolerant cells, and biofilms. Rifampin, currently prescribed in combination with other antibiotics to treat M. tuberculosis (MTB) and prosthetic joint infections (PJI), also has activity against non-dividing cells by inhibiting DNA-dependent RNA polymerase and blocking RNA elongation during transcription. In addition to sharing activity against slowly-growing bacteria, UDEPs and rifampin also share the requirement to be used in combination with other antibiotics to prevent resistance development. We hypothesized that synthesizing a dual- targeting UDEP-rifampin hybrid antibiotic would result in significantly less resistance development and have the potential to achieve unprecedented activity against biofilms and difficult-to-treat infections. A single molecule has many advantages over a combination, for example, there is no need to match the pharmacokinetics, and dosing is simpler. In this proposal, we plan to carefully optimize UDEP-Rifamycin hybrid antibiotics using a detailed synthesis and testing cascade to ensure agents are developed that have potent activity against persisters in vitro and in vivo, and a safe pharmacological profile. The mode of action of the emerging leads will be carefully profiled to study their target engagement, resistance development, effects on growing and non-growing cells.