PharmTech: What parts of the protein-expression process are still rate-limiting, and how do you see these challenges being addressed? What improvements do you expect to see in the future?

Squires: We anticipate that given the continued need for protein supply across the spectrum of applications, many of the existing weak links in protein expression will be strengthened. One of the most pressing unmet needs is production of small amounts of protein for research purposes. Often, dozens of proteins ranging from antigens for preclinical testing to related variants of a target protein for some form of differential testing are required. While only a small amount of protein, a few mg, is generally required for activity evaluation or crystallization for these types of studies, currently all of the cloning steps needed to get even that small amount of protein are identical to those required to assemble a strain or cell line for large-scale biopharmaceutical production. This is highly inefficient and a consistent bottleneck in the process. Clearly, there is a need to develop off-the-shelf solutions to fill this gap. New, precise, and more adaptable tools allowing more rapid cloning and characterization will need to be developed. These tools will necessarily include the development and adoption of more effective high-throughput processing methods. Improvements in genetic, analytical, and processing methods practiced in high throughput, parallel modes will enable the researcher to access more tools and reach a wider range of solutions more rapidly.

Clearly, for these approaches to have an impact, methods to allow the researcher to identify productive clones at the earliest possible stage must be developed. Better reporter systems that may enable screening, even at the colony or single cell level, would be very valuable. Processing to obtain small amounts of protein would then benefit from the development of more efficient purification tags. These may also be envisioned to include reliable expression reporter sequences, sequences that promote proper protein folding, and ideally be efficiently and universally removable. Pfenex is exploring this segment, adapting its expression platform strategy specifically for custom reagents. Development in this area would be of great benefit not only to the core of researchers producing proteins for research purposes but the benefits would be amply felt in the area of target protein expression as well.