Open Cell-Free Protein Synthesis Technology Is Ready To Assist With Peptides

By Ed Miseta, Chief Editor, Clinical Leader

Aaron Sato, VP of research, Sutro Biopharma

Dr. Aaron Sato has more than 10 years of research experience in antibody protein and peptide engineering. As the VP of research at Sutro Biopharma, he leads the team in the use of their bacterial extract system to produce high-value protein therapeutics, such as ADC, biospecifics, and naked antibodies. At the 2013 Oligonucleotide & Peptide Based Therapeutics Congress he will speak on his company’s open cell free protein synthesis technology. I recently spoke with him to better understand his company and technology.

Ed Miseta: Please explain the technology you call open cell-free protein synthesis.

Aaron Sato: Using a defined bacterial strain, we can generate a ribosomal prep with an intact Krebs cycle and oxidative phosphorylation pathway in inverted vesicles. This allows us to make proteins in a test tube outside of a cell and provide ribosomes, amino acids, DNA and energy that drive the synthesis of proteins.

We can use that reaction to make all kinds of different proteins. We can make antibodies. We can make difficult to express proteins. We can also express difficult to express peptides, including small cysteine knot peptides, which are traditionally difficult to make in some static systems.  We can also engineer chaperones into our extract that help with the assembly of peptides and proteins in our system.

Miseta: Is this technology the primary focus of Sutro Biopharma?

Sato: We are not a peptide company and the expression of peptide is one of many applications of our technology.  With that said, we are very interested in branching out in this area.  Besides peptides, we are currently focused on using our technology for making bispecific antibodies and site specific antibody drug conjugates.

Using an orthogonal non-natural synthetase-tRNA system, we can actually insert a non-natural amino acid into an antibody sequence or any other protein sequence. We use that non-natural amino acid as a handle to conjugate a linker-warhead using copper-free click and/or reverse diels-alder chemistries.  Besides linker warheads, you can also envision conjugating synthetic peptides and small molecules to antibodies and proteins.  Since peptides and small molecules have an inherent short half-life, peptide and small molecule antibody conjugates should allow one to increase peptide exposure as well as potentially protecting peptides from degradation.  I will present some of these examples in my upcoming presentation at your event.

Miseta: How is your process different from what has been done in the past?

Sato: Learning from the past, we worked to develop a technology that allowed us make proteins with incorporated non-natural amino acids, which can be conjugated to synthetic peptides and small molecules.  Our peptide/small molecule platform is a merger of recombinant expression (with non-natural amino acids) and synthetic chemistry, which gives us a great deal of flexibility in developing novel peptide/protein therapeutics.

Miseta: What are the primary benefits of your technology?

Sato: The primary benefit of our system is SPEED.  We can make proteins and structured peptides quickly and in parallel in plates.  If we are making peptides in our recombinant cell free system, we can conduct a large structure-activity screen for peptides. Once we have a lead we like, we can immediately scale it up into larger volumes, e.g. bioreactors, for testing in efficacy models, pharmacokinetics, and toxicology.  We also have a manufacturing facility where we can run these reactions on the 100L scale to get to gram quantities of peptides and proteins very quickly.

Miseta: How many proteins/peptides can you make in parallel?

Sato: Thousands. It is all a matter of just making the DNA. If we have a particular peptide that we like, we just have to make another DNA construct and express hundreds to thousands of different derivatives of the parental sequence.  You are only limited by your automation capability. We can do thousands of different peptide/protein derivatives and then test them all for binding, blocking, and other functional assays.

Miseta: How long has Sutro been working on this technology?

Sato: We are coming up to our 10th year anniversary but we have only been a full-fledged discovery company for the last couple of years. We started with a focus on making difficult to express proteins and transitioned into a discovery organization where we are now involved in discovering novel protein/peptide molecules using the protein technology.  We initially tried to focus on difficult to express proteins and we did a number of studies for different companies, but it never really led to any substantial deals. We pivoted about three years ago and looked at what customers really wanted and what they were working on. At that time, antibody drug conjugates and bispecifics seemed to be what big pharma and big biotech wanted.  As a result, we focused the technology on those areas but there are many other areas where we apply the technology, e.g. peptide theraputics.

Miseta: Anything else you can tell us about the technology?

Sato: The flexibility of the platform has really opened up the space, particularly for peptide discovery. It is a fascinating technology that I think could work well with traditional synthetic peptide chemistry.

Miseta: Looking ahead a few years, are there any opportunities you see emerging?

Sato: I think our technology has the capacity to couple synthetically derived materials to a recombinant protein that can be made in our system. That is a big area that I think has a lot of potential. I do not believe there are a lot of technologies that allow people to do that. We can use antibodies that bind with one target and peptides that bind to another and complement each other in a similar manner to a bispecific antibody.

We are very interested in getting to the peptide therapeutic field and interacting with different companies to get their feedback on how we can have the greatest impact.  We are always open to hearing about new concepts and new ways to use our technology to help peptide companies.

For more information on the Oligonucleotide & Peptide Based Therapeutics Congress: http://www.globalengage.co.uk/oligos-peptides.html