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Exploiting translation elongation for improved biologics manufacturing

Award Information
Agency: Department of Health and Human Services
Branch: National Institutes of Health
Contract: 1R41TR004774-01
Agency Tracking Number: R41TR004774
Amount: $324,999.00
Phase: Phase I
Program: STTR
Solicitation Topic Code: NCATS
Solicitation Number: PA22-178
Timeline
Solicitation Year: 2022
Award Year: 2023
Award Start Date (Proposal Award Date): 2023-08-01
Award End Date (Contract End Date): 2024-07-31
Small Business Information
17 Briden St.
Worcester, MA 01605-2669
United States
DUNS: N/A
HUBZone Owned: No
Woman Owned: No
Socially and Economically Disadvantaged: No
Principal Investigator
 SHANE BYRNE
 (978) 424-5542
 shane@codomax.com
Business Contact
 JOSEPH REDDY
Phone: (352) 514-7669
Email: joe@reddy.bz
Research Institution
 MASSACHUSETTS INSTITUTE OF TECHNOLOGY
 
255 MAIN STREET NE18-901
CAMBRIDGE, MA 02142-1029
United States

 Nonprofit College or University
Abstract

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.

* Information listed above is at the time of submission. *

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