FabI Inhibitors as Potent, Gut Microbiome-Sparing Antibiotics

PROJECT SUMMARY/ABSTRACT The percent of Gram-negative bacterial infections that are resistant to common antibiotics has increased at an alarming rate over the last decade, and there is now an acute need for the discovery of novel antibiotics effective against multidrug-resistant Gram-negative pathogens. We have made progress understanding the relationship between physicochemical traits and compound accumulation in Gram-negative bacteria, enabling us to convert several antibiotics with Gram-positive-only activity into versions that possess activity against key Gram-negative pathogens. Most advanced is our FabI inhibitor fabimycin; FabI inhibition is a novel strategy with no approved antibiotics that hit this target. The nature of the FabI enzyme is that it is only essential in certain pathogenic bacteria, chief among them E. coli, K. pneumoniae, and A. baumannii; thus while fabimycin is effective against large clinical isolate panels of these pathogens, it has no activity against beneficial commensal bacteria that reside in the gut. A Gram-negative active antibiotic that spared the gut microbiome is without precedent and would be a very significant development, given the well-documented deleterious effects of broad-spectrum antibiotics in causing gut dysbiosis. In addition, our X-ray structures of fabimycin bound to FabI reveal critical interactions between the ligand and the protein backbone, making bacterial resistance much more challenging to arise than if interactions were solely with amino acid sidechains. Indeed, fabimycin has a low frequency of resistance, and resistance in cell culture only evolves over a long period of time. Excitingly, fabimycin is also active in multiple mouse and rat infection models, including those of soft tissue infection, pneumonia, sepsis, and UTI. To become a true clinical candidate the Therapeutic Index (TI) of fabimycin needs to be widened. Herein we propose development of more potent versions of fabimycin through application of a recent understanding of the relationship between compound efflux and structure that has emerged from our laboratories. Applying these lessons to fabimycin will enable us to systematically reduce its efflux liability, leading to MIC values for optimized derivatives that are 5-fold more potent than fabimycin and will thus have the appropriate TI for advancement. We have assembled a team of experts with the full suite of tools needed for this work: medicinal chemistry, understanding of efflux, access to large panels of clinical isolates, sophisticated models of antibacterial efficacy in mice and rats, and detailed pharmacokinetics and toxicology in mice, rats, and dogs, and microbiome studies in mice and dogs. Our Critical Path provides specific criteria for compound advancement and we are guided by best practices for antibiotic drug development as deliniated by the FDA. Our plan is to select the lead candidate by the end of Year 2, and then spend the remaining three years building a sophisticated data package that will facilitate rapid translation of this antibiotic to the clinic.