(175ak) Therapeutic Applications of an Algorithm for Ultra-Rapid Binding Interaction Engineering

Proteins mediate all the fundamental processes of life on earth, and the ways in which they do so have been the focus of biomedical research for over 50 years. Protein-based materials have the potential to solve a vast array of technical challenges.¹ A growing field is the use of proteins as therapeutic agents, including both naturally and computationally developed proteins.

Antibodies are one of the most important therapeutic protein classes, with global sales of $75 billion in 2013.² Antibodies/Immunoglobulins (Ig) are essential immune proteins for defending the body against invading pathogens. They do this by recognizing the sites and binding to markers and carrying out effector functions which activate the immune system of the organism in various ways. However, designing antibodies in the laboratory can be time consuming, expensive and can end up being inefficient in binding with the specific epitope. Thus, to find a solution to this problem, antibodies and antibody-like scaffolds are being designed computationally and tested in the laboratory. These include nanobodies (Nb), single chain variable fragments (scFv), fibronectin domains (Fn3), etc. These alternative scaffolds offer several advantages such as higher tumor penetration and lower cost of design, while retaining high binding affinity and specificity.

In order to rapidly design these proteins, our lab developed an Algorithm for Ultra-rapid Binding Interaction Engineering (AUBIE). It is used for the fast and de novo generation of high affinity antibody and alternative scaffold structures. Here, we present the results of applying AUBIE to designing several varieties of binding proteins against various antigenic epitopes. Results include: antibodies that bind the same epitope on HER2 as Herceptin, a multi-billion dollar medication; antibodies that bind an alternative epitope on HER2 that can be cross-linked with Herceptin to increase receptor internalization; Fn3 domains that bind Campylobactor jejuni membrane proteins for use in biosensors; Fn3 domains to distinguish between methicillin-resistant Staphylococcus aureus and non-antibiotic resistant S. aureus; and Nbs that bind Interleukin-3 for targeting cancer vaccines. These results demonstrate how AUBIE can be quickly used for designing highly-promising binding proteins for a variety of biomedical applications.

References

1. Po-Ssu Huang, Scott E. Boyken & David Baker, The coming of age of de novo protein design. doi: 10.1038/nature19946, Nature 320-327 (2016)

2. Kevin C. Entzminger, et al. De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide. doi: 10.1038/s41598-017-10737-9, Scientific Reports 1-11 (2017)