Design and optimization of antibodies with hydrophobic binding loops

Abstract

Antibodies commonly use hydrophobic residues within their solvent-exposed loops (also known as complementarity-determining regions or CDRs) to mediate binding to target antigens. We are investigating the potential of using combinations of hydrophobic and charged residues to design functional binding loops that endow antibodies with both high affinity and solubility. Our focus is on designing antibodies to recognize toxic aggregates of the hydrophobic Alzheimer's Aβ peptide. We seek to harness the homotypic interactions between hydrophobic peptide segments that mediate Aβ aggregation to promote antibody-antigen recognition. By grafting hydrophobic peptide segments from Aβ into the CDRs of small antibodies, we have generated functional sequence- and conformation-specific antibodies in a rational manner. Nevertheless, these hydrophobic CDRs can also promote antibody aggregation. To overcome the poor solubility of these hydrophobic antibodies, we have investigated a novel mutational strategy in which charged residues are inserted at the edges of the hydrophobic CDRs without removing any of the hydrophobic residues. Strikingly, the charged insertion mutations potently inhibit antibody aggregation without reducing binding affinity. Further analysis demonstrates that both the type of charge (positive versus negative) and the location of the charge are both crucial for imparting greater solubility. Our findings demonstrate that the sequence of CDR loops can be designed and modified in a systematic manner to optimize both antibody binding affinity and solubility.