Chemical Genetics and Biology of Antibiotic Discovery

To effectively address antibiotic resistance, we need to discover new antibiotics and targets. Our group is approaching antibiotic discovery in several ways with an emphasis of using Chemical Biology and Chemical Genetics strategies.

Five specific areas are being pursued:

1) Yeast chemical genetics to identify new antibiotic-target pairs
2) Genetic manipulation of antibiotic producing bacteria
3) Investigation of unconventional antibiotic targets such as virulence factors
4) Use of chemically modified antibiotics to identify targets and activities
5) Discovery of new natural product antibiotics

1) Yeast chemical genetics

We are using genome scale approaches and a chemical genetics approach to identify targets of antifungal agents. In this approach, we probe arrayed clones of yeast genes to identify the targets of small molecule antifungal agents and the molecular networks that they perturb.

2) Antibiotic biosynthesis and engineering

The majority of antibiotics in clinical use are natural products or their derivatives. The most abundant sources of these molecules are in fact bacteria themselves. We are studying the biosynthesis of glycopeptide antibiotics with a goal of using the producing organisms to engineer new molecules to increase the chemical diversity of this important class of compounds.

The biosynthetic machinery that is used to make antibiotics is encoded in genes that are clustered together on the genome. We have sequenced the biosynthetic genes encoding the glycopeptide antibiotic A47934 and are studying the enzymology of biosynthesis and using bacterial genetics and mutation, and in vitro semi-synthesis to generate new molecules.

3) Unconventional antibiotic targets

The problem of antibiotic resistance will not be overcome solely by studying resistance and new antimicrobial molecules are always needed. We are interested in identifying new approaches to kill fungal pathogens and Gram negative bacteria.

Antifungals

Infections caused by fungi are difficult treat as they are relatively rare and fungi, like humans, are eukaryotes. As a result, most of the biochemistry that has been successfully targeted in bacterial pathogens (protein and nucleic acid synthesis for example) is identical between fungi and humans; this makes specificity of antifungal agents a significant challenge. We have been focusing on fungi-specific targets in amino acid biosynthesis. These are not essential for cell growth on rich media, but are important for virulence. Using both traditional and high throughput methods, we have identified and characterized several new inhibitors of the enzymes required for Met biosynthesis.

Antibacterials: Gram negative bacteria

Gram negative bacteria are intrinsically resistant to many antibiotics as a result of the impermeability of the outer membrane that is characteristic of these bacteria. Mutations in the biosynthetic genes that are necessary for formation of the lipopolysaccharide (LPS) layer of the outer membrane are known to reduce pathogenicity of Gram negative pathogens and to sensitize them to antibiotics. Together with our collaborators, we are targeting the bacterial LPS using novel HTS approaches to identify inhibitors of LPS biosynthesis and function.

4) Chemically modified antibiotics

Using synthetic chemistry to modify antibiotics, we can generate new probes of antibiotic function e.g. fluorescent probes to identify site of action. Furthermore, we can generate new antibiotics with improved or altered function. These experiments provide us with expanded chemical diversity and new agents that may evade current resistance mechanisms.

5) New natural product antibiotics

Living organisms have proven to be the most reliable source of bioactive chemicals with antimicrobial activity. Environmental microbes continue to be outstanding resources for the identification of new chemical scaffolds that perturb microbial biology. We are searching for new bioactive agents derived from these sources as starting points for new antimicrobial agents.