Accelerating Antibody Discovery with Cell-Free Systems

The COVID-19 pandemic has highlighted the need for rapid, high-throughput, and robust therapeutic antibody screening platforms. Advances in both synthetic selections and antibody repertoire mining have enabled the rapid identification of hundreds of candidate binders in a single experiment. However, the expression and evaluation of these candidate antibodies still remains a major bottleneck in the discovery pipeline due to labor intensive steps and process throughput mismatches. In this work, we present a newly developed workflow that leverages cell-free protein synthesis (CFPS) and an Echo^® 525 acoustic liquid handler to enable the expression and evaluation of hundreds of antibodies in a single experiment. Our workflow consists of a cell-free DNA assembly step to generate antibody expression templates, a modified E. coli CFPS system to express antibodies, and the AlphaLISA protein-protein interaction assay to evaluate binding. Each step of this workflow can be carried out entirely within 384-well plates without purification steps and without ever going into cells, making it easily end-to-end automatable. The resulting platform is capable of evaluating more than an order of magnitude more candidates in less than one third of the time when compared to state-of-the-art antibody discovery pipelines. To validate the platform, we express a diverse set of 122 published COVID-19 neutralizing antibody candidates in triplicate in a single experiment. We evaluated these antibodies by mapping their target epitopes and evaluating their ability to compete with ACE2, the SARS-CoV-2 target human receptor. Our results are largely consistent with published literature on the antibodies, and we were able to easily distinguish the best reported candidates based on our data. We expect that these advancements will accelerate antibody discovery and development not only for viral diseases like COVID-19, but for the entire antibody industry.