Development of gain of function enzyme mRNA therapeutics to overcome the challenges of protein replacement therapy

Designing proteins that "transcend nature" with AI, delivered into the body via mRNA

There are currently thousands of rare diseases in the world, and approximately 80% of these are hereditary diseases in which the gene for a specific protein is congenitally absent or mutated. "Protein replacement therapy," which supplements the missing protein from an external source, has become a widely used treatment for these conditions. The global market for such therapies exceeds one trillion yen and is expected to grow further in the coming years.

However, conventional protein replacement therapy faces significant barriers. One is that the activity and stability of the administered protein in the body are not always sufficient. Another is that large and frequent doses are required to achieve therapeutic effects, which places a physical and economic burden on patients and increases the risk of side effects. This project, undertaken jointly by RevolKa Ltd. (a startup founded at Tohoku University) and our research group, is an ambitious attempt to overcome these challenges through a combination of directed molecular evolution, AI, and mRNA (messenger RNA) medicine.

The defining feature of this research is that rather than simply supplementing the missing protein "as-is," we deliver it as a "Gain of Function (GOF)" protein engineered to surpass the capabilities of the natural sequence. Wild-type proteins found in nature are not necessarily optimized as therapeutics. In the treatment of hemophilia B, for example, a variant with 8-fold greater blood coagulation activity compared with the wild type has been discovered, and its use has been shown to dramatically improve therapeutic outcomes. By artificially modifying the amino acid sequence of a protein to greatly enhance its activity and stability in this way, it becomes possible to simultaneously reduce the required dosage and improve safety. This is our vision for the "next-generation biopharmaceutical."

However, finding a variant with the desired function from among the vast number of possible amino acid combinations is an extremely difficult task. This is where the "aiProtein®" technology developed at Tohoku University comes into its own. This technology integrates directed molecular evolution, which mimics evolution in a test tube, with advanced machine learning (AI). The AI learns the relationship between protein structure and function from a small amount of experimentally obtained data and then predicts the optimal sequence to try next. By leveraging this technology, it has become possible to precisely and quickly design "proteins in which multiple functional and physical properties (such as activity and stability)" are simultaneously optimized, something that was previously unattainable by conventional methods.

As a means of delivering the high-performance GOF enzymes that have been engineered into patients' bodies, this project focuses on mRNA. The mRNA technology that gained widespread attention through COVID-19 vaccines offers significant advantages when applied to therapeutics. Conventional recombinant protein preparations are manufactured by having cells produce proteins in large bioreactors, followed by complex purification processes. In contrast, mRNA therapeutics work by administering mRNA, the blueprint for the protein, and using the patient's own cells as the "manufacturing facility."

This also enables the supplementation of enzymes that only function inside cells, while reducing manufacturing costs and shortening development timelines. In essence, the approach involves sending the "ultimate blueprint" designed by AI as mRNA, so that highly effective therapeutics are produced directly inside the body. By combining this mRNA delivery technology with GOF enzymes, this project aims to achieve efficient therapeutic effects in the intracellular environment, which has been difficult to accomplish with conventional treatments.

"Design proteins that transcend nature and deliver them via mRNA." Through this innovative approach, we will propose a new therapeutic modality that enables what conventional protein replacement therapy cannot: "the exertion of therapeutic effects inside cells," "the avoidance of complex formulation development for protein drugs," and "long-term drug efficacy and the resolution of immunogenicity."