UCSF

The development of engineered biologics as both tools and therapeutic molecules have transformed the scientific landscape tremendously. Due to their increased specificity, potency, bioavailability and decreased immunogenicity, antibodies have become a popular scaffold for drug development. In 2023, antibodies accounted for five of the top ten selling drugs in the US. In addition to their therapeutic purposes, the high specificity of antibodies allows them to be powerful tools for studying and modifying biological systems. Antibodies are now regularly used to modify cellular signaling pathways, block protein interactions, detect a specific antigen of interest, among many other applications.Though our body naturally produces antibodies to fight off infection, the ability to generate synthetic antibodies against a chosen antigen of interest gives scientists the opportunity to expand the scope of druggable targets. A library consisting of up to 1011 fully synthetic antibodies can be displayed on systems such as phage, yeast, or mammalian cells, then screened for binding against an immobilized antigen. If binders are identified from the pool, they are isolated and sequenced to obtain information about the antibody’s amino acid combination for further production and characterization. These antibodies can then be optimized and applied in various formats for downstream biological experiments. Here, I describe three approaches for using antibody and protein engineering to uncover novel information on biological systems at the protein or cellular level. First in chapter 1, we use naïve antibody discovery to identify functional antibody modulators of protein arginine deiminase (PAD4), a protein highly implicated in the development of autoimmune diseases. In chapter 2, we develop a PAD4 fusion protein to target the enzyme to HER2+ expressing cancer cells and identify the substrate scope of PAD4 at the cell surface. In the last chapter, we create an antibody-drug conjugate using site-specific bioconjugation for targeted degradation of challenging cell surface proteins.