Antibody Discovery, Optimization, and Application: Translational Protein Engineering for Precision Medicine

Abstract

Next-generation, “omics-based”, translational research is rapidly characterizing genetically determined pathophysiology at an unprecedented depth. Through the application of high-throughput sequencing technologies and advanced immune engineering methods new insights into adaptive immunity has been generated at an extraordinary rate. However, despite rapid accumulation of new scientific insight, critical gaps in our scientific understanding of antibody-mediated molecular immunity limit the number of novel antibody-based medical interventions that translate past basic scientific discovery andinto clinical application. Here, this original work directly addresses outstanding gaps in our scientific knowledge of molecular humoral immunity through the discovery, optimization, enhancement, and biophysical characterization of monoclonal antibody proteins to inform the development of new precision medicines. Experimental monoclonal antibody genes, structure, and functions are assessed using a suite of immune engineering technologies, including: natively-paired antibody heavy:light chain complementary DNA libraries, in vitro mutagenesis, recombinant DNA vectors, functional yeast-surface display, fluorescence activated cell screening, high-throughput single-cell next-generation sequencing, and advanced biophysical characterization assays to translate basic research findings into new, clinically relevant, insights. Experimental application of these technologies using functional antibody:antigen screening methods produced the discovery of a novel SARS-CoV-2 neutralizing monoclonal antibody 910-30, and delineated antibody paired heavy:light chain sequence-structure-function signatures contributing to potent SARS-CoV-2 neutralization in public antibody responses. These findings have important applications for understanding communal immunity and developing effective intervention strategies during an acute global pandemic outbreak. This work also describes translational antibody protein engineering methods used to define precise, functionally optimized, genetic sequences from template monoclonal antibodies CIS43 and VRC34.01, which target the clinically relevant pathogens plasmodium falciparum and viral HIV-1, respectively. The antibody insights gained from functional optimization experiments were used to produce improved biomolecular blueprints defining structural mechanisms and forward pathways for highly protective humoral immunity against P. falciparum and HIV-1, respectively. Altogether, the scientific outcomes from this research have immediate clinical applications for the development of therapeutic, prophylactic, diagnostic and research reagents for COVID-19, HIV/AIDS, and malaria, as well as broad impact for the development of precision medicines against diseases of clinical relevance.