‘Knobs-into-holes’ engineering of antibody C_H3 domains for heavy chain heterodimerization

TLDR

Knobs‑into‑holes was first proposed by Crick in 1952 as a model for packing amino‑acid side chains between adjacent alpha‑helices. The study demonstrates knobs‑into‑holes as a novel, effective strategy for engineering antibody heavy‑chain heterodimers. They engineered a knob (T366Y) in the CH3 domain of a CD4‑IgG immunoadhesin and a complementary hole (Y407T) in a humanized anti‑CD3 antibody, enabling heterodimerization. Knobs‑into‑holes engineering yielded an anti‑CD3/CD4‑IgG hybrid comprising up to 92% of the purified pool versus 57% with wild‑type domains, demonstrating its effectiveness for creating Fc‑containing bifunctional therapeutics.

Abstract

'Knobs-into-holes' was originally proposed by Crick in 1952 as a model for the packing of amino acid side chains between adjacent alpha-helices. 'Knobs-into-holes' is demonstrated here as a novel and effective design strategy for engineering antibody heavy chain homodimers for heterodimerization. In this approach a 'knob' variant was first obtained by replacement of a small amino acid with a larger one in the CH3 domain of a CD4-IgG immunoadhesin: T366Y. The knob was designed to insert into a 'hole' in the CH3 domain of a humanized anti-CD3 antibody created by judicious replacement of a large residue with a smaller one: Y407T. The anti-CD3/CD4-IgG hybrid represents up to 92% of the protein A purified protein pool following co-expression of these two different heavy chains together with the anti-CD3 light chain. In contrast, only up to 57% of the anti-CD3/CD4-IgG hybrid is recovered following co-expression in which heavy chains contained wild-type CH3 domains. Thus knobs-into-holes engineering facilitates the construction of an antibody/immunoadehsin hybrid and likely other Fc-containing bifunctional therapeutics including bispecific immunoadhesins and bispecific antibodies.