Genetic Arrays for Antibiotic Target Identification

DESCRIPTION (provided by applicant): Discovery and development of new antibiotics is widely recognized as an urgent medical need. However, despite intensive R&D efforts at several major pharmaceutical companies, few promising antibacterial drug leads have emerged in recent decades. One factor responsible for disappointing productivity in this therapeutic area has been the lack of a comprehensive bacterial essential gene knowledge base. Currently available antibiotics target fewer than 20 of the estimated 300 essential gene products in bacteria. From the standpoint of lead-discovery strategy, a more significant factor has been the difficulty of experimentally linking antibacterial compounds to their specific cellular targets. Without a rapid way to make such a link, it is very difficult to advance antimicrobial compounds through the lead-development process. The goal of this Phase 1/11proposal is to construct an important new tool for antibacterial lead discovery that exploits the results of recent work carried out at Elitra Pharmaceuticals. We have systematically identified and validated the essential gene complement of a number of pathogenic bacteria, which has enabled us to construct a set of Staphylococcus aureus strains, referred to as the TargetArray, in which expression of a single essential gene in each strain has been down-regulated or up-regulated relative to the wild type. We have demonstrated that this S. aureus TargetArray is a powerful tool for determining the mechanisms of action (MOA) and targets of antibacterial compounds or natural product extracts that inhibit bacterial growth. We propose here to create a comprehensive Escherichia coli TargetArray by modulating expression of all essential genes in this bacterium. We will use this strain array in parallel with the S. aureus TargetArray to analyze >1000 antibacterial hit compounds/extracts active against Gram-negative and/or Gram-positive bacteria. The E. coli and S. aureus TargetArrays, when used in parallel, will provide corroborating as well as complementary results to accelerate the discovery of drug candidates targeting novel cellular targets. Under Phase I funding, we will create and validate a smaller version of the E. coli TargetArray as a proof-of-concept. Under Phase II funding, we will create and validate the full E. coli TargetArray and conduct a large-scale MOA analysis of antibacterial compounds/extracts identified in Elitra's screening programs.