Natural products (NPs) derived from microbes, plants, and animals have proven to be our richest source of bioactive molecules for use as therapeutics. Even today, with the rate of novel NP discovery dramatically slowed, NPs form the basis of ~1/3 of the top 200 drugs currently sold worldwide and ~45% of the new chemical entities approved as drugs over the past 25 years. However, despite the proven potential of NPs, most pharmaceutical companies have shut down their NP discovery programs due to cost, inefficiency, lengthy timelines, and dwindling returns. A major limitation of traditional "grind an find" NP discovery is that the majority of biosynthetic clusters silent in standard laboratory conditions. Next-generation sequencing experiments analyzing whole genomes of NP-producing bacteria have demonstrated that only a fraction of the gene clusters encoded in a given bacterial genome are active and producing detectable molecules under standard laboratory fermentation conditions. The remainder are silent during laboratory fermentation and have not been accessible to researchers for further study. An enormous amount of therapeutic value may be contained in these silent gene clusters. Radiant Genomics, Inc. proposes to develop a high-throughput, phage-mediated pipeline for integrating constitutively activating transcription factors, such as the Streptococcus Antibiotic Regulatory Protein (SARP)-family of transcription factors, within a broad range of target strains to activate silent natural product gee clusters. To make this possible, we have developed extremely low-volume next generation sequencing preps to both minimize sequencing costs and increase throughput, bioinformatics methods to identify SARPs and other regulatory transcription factors, high- throughput cloning of genes into phage-based vectors, and phage-based transformation of Streptomyces strains, many of which are resistant to other methods of transformation The Natural Products Discovery Institute (NPDI) houses the former natural product collections of Merck and Schering-Plough has over 20,000 pure and carefully preserved Actinomycete bacteria. Already one of the largest and most diverse natural product collections in the world, the strains in these collections contains tens of thousands of silent gene clusters. This Phase I SBIR collaboration between Radiant Genomics and the NPDI will demonstrate that the Radiant technology platform can activate these silent gene clusters and produce novel natural products that have never been accessible to scientists before. A Phase II grant will fund the high-throughput activation of these silent clusters and the discovery, purification, dereplication and analysis of these completely novel natural products.
Public Health Relevance Statement: Public Health Relevance: Natural products from microbes, plants, and animals have been our richest source of therapeutic molecules. However, discovery of novel natural products has decreased dramatically as the traditional "grind and find" methods for natural product discovery have become limiting and outdated. Radiant Genomics, Inc. has developed an innovative pipeline to activate silent gene clusters found in a wide range of bacterial genomes to produce novel natural products never before accessible to scientists and researchers.
Project Terms: activating transcription factor; Animals; Antibiotics; Automation; Bacteria; Bacterial Genome; Bacteriophages; base; Bioinformatics; Biological Factors; Chemicals; Cloning; Collaborations; Collection; comparative; cost; DNA; Fermentation; Funding; gene cloning; Gene Cluster; genetic regulatory protein; Genetic Transcription; Genome; Genomic DNA; Genomics; Grant; High Pressure Liquid Chromatography; Housing; innovation; Institutes; Laboratories; Libraries; Mediating; Methods; Microbe; Mining; next generation sequencing; novel; Organism; Parents; Pharmaceutical Preparations; Pharmacologic Substance; Phase; phase 2 study; Plants; Preparation; programs; Property; Protein Family; Protocols documentation; public health relevance; Research Personnel; research study; Resistance; Sampling; Scientist; Small Business Innovation Research Grant; Source; Streptococcus; Streptomyces; Techniques; Technology; Therapeutic; Therapeutic Studies; TimeLine; transcription factor; vector
