SBIR-STTR Award

This Small Business Technology Transfer (STTR) Phase I project brings together computational enzyme design with systems biology to create a fully integrated platform for novel pathway designs. The approach chosen will combine specific databases and a novel pathway synthesis tool. This computational tool will use the information present in the databases to automatically discover, or "design", novel pathways for fermenting natural renewable feedstock to virtually any chemical of human interest. In the Phase II Experimental Plan, the goal is to further advance the concept by developing a high-performance pathway prioritization module to estimate each designed pathway yield and impact on organism metabolism, and experimentally test the performance of the system. To our knowledge, the proposed research is the first attempt of combining computational enzyme design with computational pathway prospecting and modeling. The broader impact/commercial potential of this project, if successful, will be to engineer biosystems and cell factories for industrial applications, especially in the field of bio-based chemicals and biofuels. Most successes to date in the field of synthetic biology have involved recombining natural enzyme building blocks into novel pathways. However, recent developments in computational enzyme design make it possible to have designer enzymes to enhance nature's catalytic repertoire. Being able to have an automated, computer-aided design tool that leverages new capabilities to create novel metabolic pathways employing synthetic enzymes will bring us closer to truly synthetic biology.

The broader impact/commercial potential of this Small Business Innovation Research (SBIR) Phase II project is to develop a platform to rapidly design synthetic organisms to produce biochemicals, which will replace environmentally harmful, ecologically inefficient industrial chemical processes. The technology developed in this proposal will provide a competitive edge in the rapid engineering of synthetic organisms to produce biochemicals by fermentation that are currently produced from oil (reducing our CO2 emissions) or extracted from natural species (reducing our taxing load on existing ecosystems). This technology also has the potential to be used for the manufacture of drugs, and to engineer novel organisms to improve crop production and therefore help address the mounting challenges of providing food to a growing world population without tapping too much in Earth's resources. Commercially, the chemicals that will be enabled by application of the technology developed during the Phase I program open up billion dollar markets that are currently inaccessible to the chemical industry. This SBIR Phase II project proposes to develop a platform that combines computational enzyme design with systems biology to create a fully integrated system for the design and testing of novel cell factories for the production of bulk and fine chemicals. During the Phase I project, the company, in collaboration with the University of Washington, has successfully developed a high-performance software code to rapidly design novel metabolic pathways to produce any target chemical from central metabolism. In Phase II, the company will further advance the concept by (1) developing a high-performance pathway prioritization module to estimate each designed pathway yield and impact on organism metabolism in the context of whole-genome models and (2) use the software platform to design libraries of pathways for the production of a variety of specialty chemical targets that are commercially valuable and not known to be produced by fermentation at scale. Then, (3) using an experimental screening setup, the DNA for all the proposed pathways will be assembled screened at high-throughput for detectable production of the target chemicals.