Structure-guided neutralizing antibodies developed using EpiVolve technology

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Abstract Current strategies for developing neutralizing Abs are not effective and typically involve screening IgGs from recovered patients. Pandemic viruses evolve for mutations that can shield their epitopes from host immune surveillance system, so a lot of important epitopes will be missed. Even after neutralizing Abs isolated are from human sample, they still need further characterization using epitope binning and determination of specificities to avoid off target effect. A systematic method for exploring the entire protein surface of a virus that can identify all potential sites on the virus which can affect its life cycle would have significant impact and is needed. We propose a structure-guided systematic Ab development pipeline to discover Abs that can fight infectious diseases. We propose using our novel site-directed Ab development technology, ‘EpiVolve’ (short for Epitope Evolution). EpiVolve will be used to develop site-specific Abs to solvent-exposed residues and the adjacent ‘context’ sequences. These Abs will be used for fighting infectious disease. The advantages of EpiVolve are a) overcoming immune tolerance and targeting virus’ human proteome-mimicking epitopes, b) precisely targeting any antigenic epitopes regardless of its immunogenicity, c) taking advantage of B cell expansion and somatic hypermutation to generate IgG clonotypes against one targeted residue, which allows an ability to generate both pan-variants Abs and polymorphism-specific Abs, and d) an ability for generating a neutralizing Ab discovery pipeline. We will model this on SARS-cov-2 virus in Phase I and Influenza A in Phase II. EpiVolve developed site-specific antibodies will target solvent-exposed residues on the protein surface. Structure-guided Ag design will empower the EpiVolve technology in this systematic analysis. For this proposal, we will present the current preliminary data on the pilot EpiVolve study on SARS- cov-2 Receptor Binding Domain (RBD), focused mainly on the host cell receptor ACE2 binding interface. For Phase I studies, we propose to complete the pilot study and extend the study to the whole protein surface of the RBD domain. Characterizing each Ab by its binding affinity and ability to neutralize SARS-cov-2 virus will be included in Phase I studies. For Phase II, we propose to apply the learnings from this Phase I study on another virus model of great importance, the Influenza A virus. Specifically targeting the solvent-accessible residues of the conserved Stem/Stalk region of the Hemagglutinin (HA) protein