Since the dawn of the biotechnology industry almost half a century ago, the recombinant DNA playbook has been limited by one key issue: the genetic code is based on a chemical alphabet of only four natural nucleotides, which significantly restricts the potential functions and applications of the oligonucleotides. (DNA consists of the four natural nucleotides, A, C, G, and T; RNA is made up of A, C, G, and U).
With the surging interest in synthetic biology, there is enormous academic and commercial interest in expanding the genetic code. In addition, there’s a move to developing techniques that would enable the enzymatic synthesis and amplification of oligonucleotides site-specifically labeled with functional groups not present among the nucleotides of the natural genetic alphabet.
Synthorx is a clinical-stage biotechnology company that uses its proprietary, first-of-its-kind Expanded Genetic Alphabet platform technology to increase the genetic code by adding a novel DNA base pair to create optimized biologics. The company is focused on prolonging and improving the lives of people with cancer and autoimmune disorders.
Its lead product candidate THOR-707, a variant of interleukin-2 (IL-2), is in development for the treatment of solid tumors as a single agent and in combination with an immune checkpoint inhibitor. They are also pushing another IL-2 variant called THOR-809 that selectively expands regulatory T cells without activating and expanding effector T or natural killer cells in preclinical models. The company, which is headquartered in La Jolla, California, was founded based on seminal discoveries by Floyd Rosenberg, PhD, at The Scripps Research Institute.
We sat down with Marcos Milla, PhD, chief scientific officer, and Lauren Baker, VP of Scientific & Medical Affairs, to discuss the history and future direction of Synthorx’s Expanded Genetic Alphabet platform technology. We also covered the company’s development since its recent acquisition by Sanofi.
GEN Edge: What was the founding vision or mission for Synthorx when it was all started?
Milla: The essential structure behind genetic transmission is the double helix. A-T and G-C are pairing with each other and create a linear strip that encodes information that encodes the amino acids needed to put proteins together. During the revolution that led to recombinant DNA technologies and the advent of biologics and therapeutics, people started wondering why genetic information is based on a four-letter code? Why can’t you have a larger palate of amino acids available to put proteins together?
About 20 years ago, Floyd Rosenberg and workers at the Scripps Research Institute started doing old fashioned medicinal chemistry—make molecules and assay them for replication of a piece of DNA and see whether it works. By doing that agnostic approach without any preconceived pairing mode, surprisingly they arrived at [two novel nucleotides] X and Y. After a screening exercise that took a decade, they came up with this new base pair that is very nonconventional. AT and CG have conventional Watson and Crick hydrogen bonding, but with X and Y you just have Van der Waals hydrophobic interactions. Why this works where so many others fail is that by eliminating hydrogen bonding, you have a pair that pairs with high fidelity that cannot interact with ATGC. This drives the fidelity of replication of X and Y in plasmids.
This was the seed that created Synthorx. The company was started with a vision of using X and Y to blow up the number of codons to make proteins. With four bases, you can only have 64 codons encoding for 20 amino acids. Now with this extra base pair, you can go up to 172 codons. Now you can genetically encode many more amino acids in proteins to install new functionalities that diversified the chemistry available for structure-activity relationships to build protein biologics.
GEN Edge: How do you make this work? How do you make new proteins on an industrial scale?
Milla: From 2014 to about 2016, a small bench team of very talented scientists turned this into an E. coli organism that can integrate all of these to produce recombinant proteins containing new amino acids. Essentially, this E. coli strain is the same that has been used for decades now in biotechnologies to make products like insulin. This is a workhorse for recombinant protein production.
In 2016, Synthorx was wondering, what do we do with this very cool strain? The decision was made to go after cytokines because multiple cytokines have been shown to have very powerful anti-tumoral effects or effects in controlling autoimmunity. But no cytokine is a drug. Mother nature did not design cytokines to have the pharmacokinetic and pharmacodynamic properties of biologics. Early on it was decided to point the system towards the bioconjugation of cytokines.
But no cytokine has the right pharmacokinetics because they are all very smart proteins. Because they are so small, they go through the renal filter and are excreted in one to two hours. They do not stay in circulation for enough time to drive the strong expansion of target immune cells. What the Synthorx platform allows is to put a new amino acid in the protein that will act as a hook to install a bioconjugate at specific positions by click chemistry. Now that you can very easily install a bioconjugate only at one specified position that is genetically encoded is a game-changer.
The bioconjugate not only reprograms the pharmacology of the interaction of the cytokine with the receptor but also improves the pharmacokinetic properties to optimize the pharmacodynamic responses. The bioconjugate also shields potentially immunogenic epitopes from immunosurveillance. This is very important because if you’re installing a new amino acid, you want to make sure that it doesn’t drive the production of antibodies. With this, we decided to attack IL-2, and we were able to generate THOR-707, which we are pushing to clinical development with Sanofi.
Now we’re pushing THOR-809 to clinical development with Sanofi for autoimmune diseases to drive autoimmune tolerance. This is really a holy grail of pharmacology for autoimmune and inflammatory conditions. Any current agent for autoimmune diseases is based on symptomology or disease modification—nothing can really reset the immune system to the tolerant state and hold the immune system from reacting to auto-antigens. So, that’s the promise of autoimmune therapeutics—to bring it back to a tolerant state.
GEN Edge: Are there any other avenues besides immuno-oncology that you want to pursue eventually?
Milla: One of the options that Synthorx was contemplating was to go into materials. For instance, you can start modifying spider silk to make special suits that cannot be penetrated by bullets for the department of defense like a real Spiderman suit.
I think the decision to go after pharmaceuticals was very smart because there is a lot that you can do to improve biologics either in their pharmacokinetic properties or their pharmacology. Multi-specific biologics are the next wave of biologic therapeutics. It doesn’t just take one target, but it takes two or three targets to capture a complete pharmacological effect for oncology, immune diseases, and even neuroscience. The ability of building multi-specific biologics will take us to the next wave of improved agents to address disease.
But if you think of any biologic on the market, these agents are built the same way with current recombinant DNA technologies. Now, imagine that you can start putting new amino acids into proteins to click protein models together with the geometry that you optimally need to address receptor-receptor or ligand-receptor interactions between cells. This is really a quantum leap for biologics, and this is where we are going next.
GEN Edge: How has being acquired by Sanofi affected Synthorx? Has it changed the company?
Milla: When you are a self-standing company with a lot of pressure from investors and a limited budget, you have to be very thrifty. You have a lot of limitations in the way you can build programs and execute on a critical path and do those additional experiments that are more revealing of mechanism.
Now that we’re part of a company that has deep and broad resources, we have been enabled to add these additional gates to our next projects. Of course, the work on IL-2 is very exciting, but we’re already working on the next cytokines. There is this new space of exploring the geometry of protein conjugation to build different multi-specifics, all of that would be very hard to do in a space where you have to go back and convince the investors every quarter that what you do will hold water and result in a higher level of returns. It allows us to be a bit more audacious in probing into the dark matter.
Baker: One of the things that I’ve noticed is that in small companies, you get a lot of innovation and creativity, and in large companies, you can execute and build well. It seems almost like a certain of a perfect blend of the two, where there’s a real focus and there’s a synergy that exists with this collaboration. You have this approach where you’ve got this real innovation and ideas, and it comes together so very well.
GEN Edge: What major goals does Synthorx have for the next 1, 5, and 10 years?
Milla: THOR-707 is in clinical development, which of course is the primary objective of the entire Sanofi-Synthorx program—to hit THOR-707 as hard as possible. After that, there is THOR-809 that should be going into IND and human next year. Then we’re looking at a few cytokines. We’re going be in this space of reprogramming cytokines either for improved PK or receptor specificity, most of these for immune-oncology, but certainly, there are some additional opportunities in auto-immune diseases. So, I believe that this space of bioconjugating cytokines to make them into practical drugs that you can conveniently dose safely into patients is our first horizon.
GEN Edge: Where does Synthorx end and Sanofi start?
Milla: Chemistry, manufacturing, and control from development to approval are very complex to manage for a small company, and we lack the experience to navigate the regulatory space. One of our objectives is to transfer technology as quickly as possible to completely enable the late development and commercialization of THOR-707. We realized we can take this through proof of concept, but at the end of the day, if we’re serious about moving this as soon as possible to serve patients in need, we do need to find a partner because we are just under-delivering on the promise of this agent.
I believe that biotech has a very important role in innovation and in finding new answers, but at the end of the day, I believe that pharma will always have an essential role in picking the best solutions and turning them into industrial and commercial solutions that can be distributed en masse and that can work for patients all over the world.
Baker: It makes it scalable, which is the benefit of the collaboration with Sanofi.
GEN Edge: Has Synthorx been able to retain its identity or transform since the acquisition, or has the acquisition moved Synthorx into a completely different company?
Milla: It’s an ongoing experiment. Certainly, I am hell-bent on maintaining some of our do not take no for an answer mentality unless the data are telling you that the answer is no. We need to keep pushing against the envelope and work the 25th hour.
We have expectations from Sanofi to teach us the many directions in which we need to learn to become savvier in identifying and executing on the next projects. To have a synthetic biology drug that is in Phase 1 in patients is a special place to be. We will just have to see how the experiment continues.