Design and Evolution of Domain Antibodies Specific for Amyloid Proteins

Antibodies that recognize toxic aggregated proteins associated with neurodegenerative disorders (e.g., Parkinson’s and prion diseases) are valuable for therapeutic and diagnostic applications. We have developed a novel approach for designing domain antibodies specific for amyloid proteins that is inspired by the molecular interactions that mediate protein aggregation. We find that grafting hydrophobic peptides from several amyloidogenic polypeptides into the complementarity-determining regions of domain antibodies generates Grafted AMyloid-Motif AntiBODIES (gammabodies) that recognize aggregated proteins with high nanomolar binding affinities (Perchiacca et al., PNAS, 2012; Ladiwala et al., PNAS, 2012). Our recent work has focused on improving the design of gammabodies to achieve low nanomolar binding affinities. Toward this aim, we find that increasing the length of the grafted amyloidogenic peptides significantly increases binding affinity. Moreover, we have developed methods for designing long hydrophobic binding loops that maintain high antibody solubility and folding stability. We are currently coupling these systematic design methods with directed evolution methods to further increase the binding affinities and stabilities of amyloid-specific domain antibodies.