Integrated Human Practices

The Promise of Protein-based Technologies

The diverse capabilities of proteins in biological systems have presented unique opportunities in the development of many novel products, and useful technologies, particularly for the pharmaceutical industry. Most notably, of the top-selling non-vaccine drugs of 2016, six were protein-based therapeutics. Five of these six therapeutics were antibodies treating conditions ranging from cancer to diabetes.¹

Team UAlberta was greatly enticed by the potential of protein-based technologies, especially for therapeutic applications. However, as none of our members are experts in this field, we set out to gain insights from stakeholders and researchers connected to these technologies.

Dr. Mary Hitt

Associate Professor

Department of Oncology

University of Alberta

One of our most motivational conversations was with Dr. Mary Hitt, an Associate Professor at the University of Alberta’s Department of Oncology. In our interview with her, we talked about the role that proteins have in medicine. She identified antibodies and peptides as both falling under the category of protein-based therapeutics, though, noted that each has their own place when it comes to treatments.

Antibody-based therapeutics are a prevalent treatment method for a wide range of diseases. Peptide therapies, which are compositionally similar, are drastically smaller and have simpler structures. Dr. Hitt discussed how antibodies can do much more than peptides, and exhibit greater affinity and stability than peptides. However, Dr. Hitt did note that the faster degradation of peptides can be a potential advantage as peptide-based drugs would not linger in a patient’s system as long as antibodies do. They are also relatively easier to manufacture compared to antibodies.

As an example, Dr. Hitt spoke about using peptides for imaging. Peptides specific to different proteins, such as overexpressed receptors on cancer cells, could be used as imaging agents as their relatively fast degradation, coupled with sufficient affinity, allow them to be introduced into the body for use in imaging studies without the long-term effects that a more stable antibody could have.

Our interesting conversation with Dr. Hitt revealed many insights into the field of protein-based therapeutics. Though challenges were identified, the promise of peptide therapies and the potential of their wider applications drew our team to further investigate protein-based technologies in the context of peptides therapies.

Screening Protein-Protein Interactions

Civilization has been using compounds found in nature to treat our various ailments since ancient times. Historically, drug discovery has been mainly serendipitous, but much effort has gone into developing more deliberate and informed strategies. Currently, the development of many therapeutics, including protein-based technologies, use natural proteins or compounds as starting points. However, wild-type proteins are often in need of optimization for use outside of their natural context ². For proteins, this optimization is the realm of protein engineering, where the chemical and physical properties of proteins are optimized for use in industries such as manufacturing, medicine, and materials³.

Because our understanding of protein dynamics is still incomplete, optimizing proteins often relies on directed evolution. This process involves repeated cycles of mutating proteins and screening for improved variants to engineer protein-protein interactions with higher specificity and affinity. Due to the iterative mutagenesis required, directed evolution, and the screening associated with the process is extremely laborious.

Dr. Maya Shmulevitz

Assitant Professor

Department of Medial Microbiology and Immunology

University of Alberta

Dr. Maya Shmulevitz, a researcher in the University of Alberta’s Department of Medical Microbiology and Immunology, has previously worked with the yeast two-hybrid system for screening protein-protein interactions. The particular system she used was based the expression of antibiotic genes regulated by the reconstitution of the yeast transcriptional machinery via the interaction of proteins of interest. The stringency of the screen is modulated with antibiotic concentration. If proteins of interest interact sufficiently, they confer antibiotic resistance to yeast, which are then selected.

However, what Dr. Shmulewitz found when using this system was that it was difficult to determine how many from a library of positive results should be selected, especially when no reference to controls are available. When Dr. Shmulevitz reduced the stringency of her test, she found many false positives, but when the screen was too stringent, many possible interactions are lost.

Our main take away message from our conversation with Dr. Shmulevitz was that the choice of reporter genes in assays like the yeast two-hybrid system is crucial to the results of a particular screen. In her case, antibiotic resistance did not provide an outcome that can be used to readily discern the relative strengths of protein-protein interactions, nor can it be used to separate desirable candidates from false positives. Though, as assays testing for protein interactions are not numerous, it was apparent that there is room for the development of other alternative screening methods to address these issues. In response, Team UAlberta aimed our project in developing a system that can provide a relatively quantitative readout linked to the strength of protein-protein interactions.

References

1. The Top 15 Best-Selling Drugs of 2016 | The Lists | GEN Genetic Engineering & Biotechnology News - Biotech from Bench to Business | GEN. GEN (2017). Available at: http://www.genengnews.com/the-lists/the-top-15-best-selling-drugs-of-2016/77900868. (Accessed: 30th May 2017)

2. Brustad, E. M. & Arnold, F. H. Optimizing non-natural protein function with directed evolution. Curr. Opin. Chem. Biol. 15, 201–210 (2011).