Abstract – Codomax has developed a codon engineering platform that enables bespoke, high-yield, cost- effective protein manufacturing by leveraging a newly discovered translational regulatory system in industrially relevant cell systems. Protein manufacturing has a current estimated market size of over $300 billion, distributed among the areas of antibodies and biologic therapeutics, biotechnology, industrial protein reagents, and food. However, protein production is often a time-, cost- and resource-intensive process. Some proteins are difficult to express in high yields due to the inability of the cell to translate the gene sequences efficiently. Candidate proteins may be abandoned at the research and development phase due to an inability to produce them in sufficient yields for cost-effective commercial-scale production. Traditional codon optimization, a widely used strategy, can result in only modest yield improvements because it is grounded in incomplete and incorrect models of protein translation that assume a static pool of tRNAs within a given organism. Codomax has discovered that cells regulate translation in response to stress by altering the tRNA pool to match the codons enriched in stress response mRNAs, which in turn enhances translation of the codon-biased mRNAs. Codomax’s platform leverages this mechanism by using systems-level approaches to measure the codons that are most frequently translated during the production of a recombinant protein, accounting for a specific cell type under specific growth conditions and using this information to choose the truly optimal codons. This solution increases recombinant protein production in cells and enhances the translation of mRNA therapeutics, helping to meet current protein manufacturing demands. Pilot studies of this approach in Pichia pastoris, one of the three major cell lines used in protein manufacturing, resulted in a 2.4-fold increase in protein production compared to genes already optimized by existing commercial algorithms. In this Phase I project, Codomax will build on these findings by undertaking two specific aims: (1) optimizing codons for interferon production in P. pastoris and demonstrating an increase in protein yield of at least 200% as well as the ability to retain 90% functionality in IFN-α-2b and IFNγ, and (2) establishing the feasibility of the platform to enable complex protein production using N-glycosylated IFN-beta-1a and human serum albumin as case studies. Successful completion of these aims will both demonstrate proof-of-concept of our platform to produce commercially relevant therapeutic proteins in higher yields than existing technologies and demonstrate the feasibility of using P. pastoris for manufacturing complex biologics. Resonating well with the Biden Administration’s National Biotechnology and Biomanufacturing Initiative, this project provides a strong foundation for Phase II plans to scale our technology for commercialization, given the growing clinical utility of interferon therapies and the applicability of our technology to any type of biologic therapeutic. Our technology will ultimately find broad application in enabling development of biologics and lowering commercialization costs.

Narrative – The protein manufacturing industry is hampered by the fact that some proteins are difficult to express in high yields due to poor translation. Codon optimization, a widely used strategy, can result in only modest yield improvements because it is currently grounded in incomplete and incorrect models of protein translation that assume a static pool of tRNAs within a given organism and static codon usage. Codomax has discovered that cells regulate translation in response to stress by altering the tRNA pool to match the codons enriched in stress response mRNAs, which in turn enhances translation of the codon-biased mRNAs. Our project will take advantage of codon-biased translation and develop a platform that enables bespoke, high-yield, cost-effective protein manufacturing by leveraging a newly discovered translational regulatory system in industrially relevant cell systems, removing a pain point from the protein manufacturing industry and allowing more candidate proteins to progress past the research and development phase.