An antibody engineering platform using amino acid networks: A case study in development of antiviral therapeutics

We present here a case study of an antibody-engineering platform that selects, modifies, and assembles antibody parts to construct novel antibodies. A salient feature of this platform includes the role of amino acid networks in optimizing framework regions (FRs) and complementarity determining regions (CDRs) to engineer new antibodies with desired structure-function relationships. The details of this approach are described in the context of its utility in engineering ZAb_FLEP, a potent anti-Zika virus antibody. ZAb_FLEP comprises of distinct parts, including heavy chain and light chain FRs and CDRs, with engineered features such as loop lengths and optimal epitope-paratope contacts. We demonstrate, with different test antibodies derived from different FR-CDR combinations, that despite these test antibodies sharing high overall sequence similarity, they yield diverse functional readouts. Furthermore, we show that strategies relying on one dimensional sequence similarity-based analyses of antibodies miss important structural nuances of the FR-CDR relationship, which is effectively addressed by the amino acid networks approach of this platform.