Antibody Therapeutics Xchange - San Diego - 2025

Overcoming complex therapeutic challenges requires next-gen precision and targeting for maximum efficacy, something that is often addressed by pursuing de novo antibody design. However, in silico antibody discovery models need accurate, high-resolution empirical structural data to correctly predict effective epitope/paratope interactions, especially for de novo antibody design. Here, we introduce an innovative approach that utilizes high-throughput, high-resolution analysis of higher-order structure (HOS) through radical footprinting mass spectrometry, enabling rapid, accurate characterization of epitopes/paratopes, conformational changes, and higher-order structure to generate a bespoke database of large libraries of antibody/antigen interactions. 

We then use these data to inform selection of binders with the greatest therapeutic potential. Through a combination of high throughput structural screening and empirically-constrained computational modeling, we systematically engineered antibodies that bind to a critical epitope on Human Fibroblast Activating Protein (hFAP), a historically challenging target, with exceptional affinity and specificity.

The antibody response to vaccination and infection is key to immune defense and human antibody therapeutic development, offering a blueprint for targeted treatments. While B-cell sequencing aids human antibody discovery, it may miss the full diversity of circulating antibodies, as only 2-3% of B cells are in circulation, and not all produce antibodies. We demonstrate a mass spectrometry proteomics-based approach to sequencing neutralizing antibodies from serum of a patient vaccinated against SARS-CoV-2. Following de novo sequencing, we recombinantly expressed 12 antibodies. Six recombinant antibodies exhibited similar or higher binding affinities than the original natural polyclonal antibody and exhibited neutralizing capabilities.

Overcoming complex therapeutic challenges requires next-gen precision and targeting for maximum efficacy. Conventional discovery approaches fall short since they are not guided by structure and are thereby limited in their ability to target specific epitopes. We introduce a novel approach: by leveraging high-throughput, high-resolution structure determination, we systematically engineer high-affinity antibodies that selectively bind a target epitope— ensuring exceptional precision and efficacy against even unstructured, multimeric or otherwise structurally challenging targets.