Antibody binding epitope Mapping (AbMap) of hundred antibodies in a single run

Abstract

Epitope mapping is essential for the understanding how an antibody works. Given millions of antibodies short of epitope information, there is an urgent need for high-throughput epitope mapping. Here we combined a commercial phage displayed random peptide library of 109 diversity with next generation sequencing to develop Antibody binding epitope Mapping (AbMap) technology. Over two hundred antibodies were analyzed in a single test and epitopes were determined for >50% of them. Strikingly, the antibodies were able to recognize different proteins from multiple species with similar epitopes. We successfully identified the epitopes of 14 anti-PD-1 antibodies, including Sintilimab (i.e., L128, A129 and P130), and confirmed that the binding epitopes of Nivolumab and Sintilimab are very close to the binding interface of PD-1 and PD-L1. The predicted conformational epitopes of Pembrolizumab and Nivolumab are consistent with their antibody-antigen co-crystal structures. AbMap is the first technology enables high-throughput epitope mapping. HighlightsO_LIThe first technology enables epitope mapping of two hundred antibodies in a single run C_LIO_LILinear epitope was determined for >50% of the antibodies C_LIO_LIDistinct epitopes of 14 anti-PD-1 antibodies, including Sintilimab, were determined C_LIO_LIThe predicted conformational epitopes of Pembrolizumab and Nivolumab are consistent with the known antibody-antigen co-crystal structures C_LI