A synthetic DNA base pair expands the genetic alphabet to enable the creation and scale-up of novel and diverse protein therapeutics with improved safety and efficacy profiles
SAN DIEGO, November 29, 2017 – Synthorx Inc. announced today that scientists at The Scripps Research Institute (TSRI) and the company, guided by Floyd Romesberg, Ph.D., have developed the first semi-synthetic organism that can store and retrieve increased genetic information. The semi-synthetic organism was made to maintain, replicate, transcribe, and translate a synthetic DNA base pair in order to incorporate various non-natural amino acids (nnAAs) into a full-length protein. This research, published today in Nature, breaks through technical barriers to creating more diverse proteins for improved drug characteristics as well as enabling cost-effective scale-up for drug development.
An expanded genetic alphabet allows for site-specific incorporation of different non-natural amino acids to create novel full-length and functional proteins. In the current paper, the scientists used the semi-synthetic organism to create a variant of green fluorescent protein (GFP) with non-natural amino acids incorporated at specific sites. The semi-synthetic organism was able to robustly produce the full-length variant protein with an efficiency similar to that with which the natural protein is produced.
Dr. Romesberg said, “This is the first time that proteins have been produced in any cell by the decoding of a six-letter genetic alphabet, instead of just the natural four-letter alphabet. The limited combinations of the natural DNA bases, A, T, G, and C, have restricted the types of new protein therapeutics that could be made. Adding X and Y to the genetic alphabet, we now have an expanded vocabulary to be able to generate a variety of new proteins that might be developed for a wide range of applications, including as new therapeutics.”
The regular ‘genetic alphabet’ of DNA constitutes of two base pairs (A–T and G–C). Dr. Romesberg and his team designed another base pair, d5SICSTP and dNaMTP (abbreviated X and Y), that was previously shown to be stably replicated and maintained by a single-celled organism. The four natural DNA bases are used to code for or “spell” proteins assembled from the 20 natural amino acids. With X and Y, it is now in principle possible to encode for an additional 152 novel amino acids to make proteins with unique pharmacological properties and to improve the safety and efficacy of protein therapeutics.
“Protein therapeutics have delivered tremendous value to patients, but have limitations that cannot be corrected utilizing the twenty natural amino acids,” said Laura Shawver, Ph.D., president and CEO of Synthorx. “Now that we have a semi-synthetic organism that can encode and translate expanded genetic information, we have an efficient system for the design and scale-up of novel protein therapeutics that impart improved pharmacological properties of biologics making them more efficacious, safer and more convenient for patients.”
To make the semi-synthetic organism, scientists modified Escherichia coli, a single-cell bacterium commonly used in the laboratory and manufacturing of protein therapeutics. Also added to the E. Coli was DNA that encoded mRNA with the AXC and GXC codons as well as DNA that encoded for the corresponding tRNAs, which combine during translation in the cell to produce proteins with non-natural amino acids at desired positions. In addition, the E. coli was previously engineered to express a nucleoside triphosphate transporter, which imports the needed precursors for the synthetic base pair from the media, as the cells cannot make X and Y themselves, which is a built-in safeguard.
Yorke Zhang, a graduate student in Dr. Romesberg’s lab and the first author on the paper explained, “The semi-synthetic organisms have a number of built in safeguards. What this research accomplishes that has not been possible before is to enable the efficient site-specific incorporation of multiple non-natural amino acids into proteins of any size, from small peptides to large biologics, and to efficiently and robustly manufacture these improved protein therapeutics at scale.”
Dr. Shawver concluded, “This research is a tremendous technological leap and will be extremely valuable to drug discovery and development. We can now design and build the protein therapeutics we want and create an entirely new generation of tailored medicines to improve how we treat disease.”
Synthorx Inc. is a biotechnology company using synthetic biology to discover and develop novel protein therapeutics. Synthorx’s expanded genetic alphabet platform has the unique ability to drive the site-specific incorporation of multiple synthetic amino acids into proteins thereby tuning receptor specificity important for improving efficacy and safety. In addition, their engineered organisms provide the ability to manufacture these improved proteins, called Synthorins, with the required fidelity and yield. Synthorx’s unique platform expands the chemical and structural repertoire of protein therapeutics and uncovers new ways to modulate pharmacological properties of biologics, not possible with other technologies. Synthorx is working internally and in collaboration with pharmaceutical companies toward the design and discovery of first-in-class drugs for a variety of therapeutic areas. Synthorx’s investors include RA Capital Management, Avalon Ventures, and Correlation Ventures. The company was founded based on important discoveries in Dr. Floyd Romesberg’s lab at The Scripps Research Institute. The company is headquartered in La Jolla, Calif.