A biophysical assay targeting Gyrase RNA

PROJECT SUMMARY The world is rapidly heading towards a pre-1940’s scenario when it comes to fighting infectious disease. Antimicrobial resistance is a growing problem on a global scale, greatly hampering our abilities to quell worldwide epidemics such as tuberculosis and malaria, as well as the simple staphylococcus infection . The proposed project is significant because unless innovative strategies are developed to produce robust and effective new classes of antibiotics, health care costs will continue to climb and we will completely lose our ability to combat even the most common infection. Current antibiotic treatments originated predominantly from natural products produced by fungi and bacteria that were able to inhibit the growth of other organisms, usually by inhibiting cell wall synthesis or maintenance or by inhibiting protein synthesis. Since penicillin was first isolated by Fleming in 1929, most of the subsequent generations of antibiotics remain very similar to the original natural products, wit h functional groups modified to increase their activity across a broader range of pathogens and decrease their side effect profiles. Oxazolidones, glycopeptides, -lactams, and quinolones show some promise for the future, but Gram-negative bacterial infections still remain problematic. Cases of multidrug-resistant (MDR, resistance to 2-3 classes), extensive drug resistance (XDR, resistance to most classes except colistin or tigecycline) and even pan drug resistance (PDR, resistance to all classes) nosocomial bacterial infections have skyrocketed in recent years, and the emergence of pan drug-resistant isolates are making these infections increasingly difficult to treat. Hospital-acquired infections like these account for up to 4% of all hospital stays in the United States and are incredibly diverse in causative pathogen, antibiotic resistance profile, and severity. A significant cause of nosocomial infection is the Enterobacteriaceae family, which includes Gram-negative bacilli that can be commensal or pathogenic. Enterobacteriaceae have a widespread clinical and economic impact due to the diversity of infections they cause; this family causes many infections such as pneumonia, bloodstream infections (BSIs), urinary tract infections (UTIs), and intra- abdominal infections (IAIs). The World Health Organization (WHO) lists carbapenem-resistant Enterobacteriaceae (CRE) as having a critical need for novel antibiotics on their Priority Pathogens list. Because the mortality of these multi drug-resistant infections is between 30 and 50% and there is such difficulty in finding viable treatments, the need for novel therapeutics for these pathogens must be addressed. Nucleic acids are promising avenues for drug design, both as therapeutics and as targets. Targeting heavily conserved RNA sequences and structures, in bacteria (Enterobacteriaceae), and involved in proliferation and survival of bacteria, is a promising approach. Using our proprietary probes, assays and libraries, we propose to develop a screening assay for an essential gene in Enterobacteriaceae. Here we propose an innovative plan for identification of a novel class of ligands that are specific for an mRNA present in an essential gene in bacteria, and we propose a biophysical screening assay for identifying such ligands. First, as outlined in Specific Aim 1, we will characterize a model nucleic acid domain that will be synthesized commercially and identify specific and high-affinity aminosugar binders. We will then synthesize sequence-specific RNA binding ligands and screen this targeted library of conjugates for sequence-specific binding and gene inhibition. The mechanism of action will be confirmed using a reporter gene assay (Specific Aim 2). A successful application of the approach will allow us to identify and validate lead compounds for inhibition of bacterial growth in Phase II studies.