Antibiotics from Soil DNA Clone Libraries: Selection of Anti-MRSA Lead Compounds

DESCRIPTION (provided by applicant): The objective of the proposed research is to identify new antibiotic lead compounds with high potential for drug development for the treatment of methicillin-resistant Staphylococcus aureus (MRSA). The starting materials are natural product mixtures produced by hit clones previously identified in eMetagen Corporation's large-insert soil metagenomic libraries. The project is a collaboration between eMetagen, an innovative biotechnology company focused on drug discovery and a respected group of natural products chemists at Harvard Medical School led by Prof. Jon Clardy and Dr. Frank C. Schroeder. eMetagen applies patented, cultivation-independent methods to obtain natural products from the "metagenome," or collective genome, of a soil microbial population. Traditional drug discovery methods require laboratory cultivation of microbes to be tested for desired activities, and soil microbes have been one particularly rich source of "druggable" natural products. Traditional methods have been used to discover over 7,000 antibiotics, with the result that it is now very difficult to isolate an organism or compound that has not been encountered before. However, the diversity of "uncultivable," (yet-to-be cultured) microorganisms is far greater than that of organisms grown in the laboratory. Microbial populations in soils are >99% composed of species that have never been grown in culture. eMetagen accesses biochemistry from the uncultured majority of soil bacteria to produce natural products never before tested for antibiotic or other drug activities. The starting materials for this project are 15 large-insert clones showing antimicrobial activities against MRSA. These clones were discovered during a project funded by an NIH/NIAID Small Business Biodefense Program Phase I STTR grant. At present, the antibiotics produced by these anti-MRSA clones have not been characterized. The specific aims of this Phase I SBIR project are: (1) adapt hit clones to operate with eMetagen's improved cloning and expression system and re-confirm their antibiotic activities, (2) prioritize hit clones according to indicators of their mechanisms of action and effectiveness against diverse MRSA isolates, (3) determine chemical structures of active components and identify New Chemical Entities (NCEs), eliminate from consideration non-NCEs and NCEs which are inappropriate as drugs, and (4) determine minimum inhibitory concentrations and evaluate remaining candidates to choose lead compound(s) for Phase II research. The overall result of this research will be one to three high-quality lead compounds to be further developed as antibiotic drugs. These metagenome-derived lead compounds may be very different from known antibiotics; their commercial development will depend upon details of their structures, to be determined during this SBIR Phase I project. The product of this Phase I research will be a lead compound for treating infections by drug-resistant Staphylococcus aureus, one of the most serious health problems in the US and worldwide. Infection with S. aureus is a leading cause of sepsis and bacteremia, as well as pulmonary, skin and soft tissue infections, in both hospital and community settings. The rise of multiply drug-resistant pathogens generally, and S. aureus in particular, alarms medical and public health practitioners.