(47a) De Novo Computational Design of Nanobodies and Scfvs

Here we present our methodology for the de novo design of antibody variable regions, including nanobodies and scFvs. We have previously developed and presented the Optimal Complementarity Determining Regions (OptCDR) method to design antibody CDRs to bind any specified antigen. OptCDR has now been expanded to design entire antibody variable domains (CDRs and framework) and this new method can be used to design either nanobodies (heavy chains by themselves) or scFvs (heavy and light chains). First, an optimal combination of CDR canonical structure backbones is selected to bind the specified antigen. Subsequently, the amino acid sequences of the selected CDRs and the variable domain(s) framework are filled in and then the sequence and structure of the entire variable domain(s) are refined using our previously developed Iterative Protein Redesign and Optimization procedure. Finally, the most energetically promising mutations are accumulated so that a library of a desired size may be generated. Several therapeutically relevant systems are used to demonstrate the efficacy of the method, including the peptides CD20 and CD33.