This SBIR Phase I program will design and synthesize candidate inhibitors of bacterial RNA polymerases (RNAP) as an approach to the development of novel antibacterial agents for use in treatment of infectious diseases, including organisms such as B. anthracis and Y. pestis that are instruments of bioterrorism. RNA polymerase is critical to the transcription of DNA. Inhibition of bacterial RNAP is known to be an effective antibacterial strategy, but current agents (e.g., rifampin) are toxic and induce resistant strains via binding to a highly variable site of RNAP. The unique approach proposed here is based on a genomic analysis by a collaborator, Prof. R. Ebright, comparing human and bacterial RNA polymerases that has identified a novel drug target site at the nucleotide entry channel. This region is highly conserved in bacteria, but there are distinct differences to the human enzyme that suggest that inhibitors can be designed to be selective for bacteria, resulting in very broad spectrum antibacterial activity with low toxicity and low induction of resistant strains. The high conservation in this region suggests that an inhibitor binding at this site would kill bacteria that are, or have been manipulated, to be resistant to standard antibiotics. Known peptide-based inhibitors of eukaryotic RNAP include amanitin analogs, potent mushroom toxins that bind near the novel drug target site. The program proposed here will design and synthesize lead peptide mimetic compounds structurally related to the scaffold of amanitin, incorporating features that would be uniquely complementary to bacterial RNAP. The goals are (a) to identify a simplified core structure that retains affinity for RNAP, (b) to identify analogs with reduced affinity for the human RNAP, and (c) to define sites on the analogs to elaborate this core to obtain compounds with high affinity to bacterial RNAP. The biostructural information on RNAP, the amanitin-RNAP II complex, and sequence data for resistance mutants will be used to map the location of synthetic modifications and positions of diversity to use to develop lead inhibitors. With the results obtained from this program, future optimization of the lead structure to enhance potency, selectivity, bioavailability, and metabolic profile will lead to a drug for treatment of serious infections where currently available antibacterial drugs are ineffective, including bioterrorism agents.
