Stepwise in vitro affinity maturation of Vitaxin, an alphav beta3-specific humanized mAb

Abstract

A protein engineering strategy based on efficient and focused mutagenesis implemented by codon-based mutagenesis was developed. Vitaxin, a humanized version of the antiangiogenic antibody LM609 directed against a conformational epitope of the alphav beta3 integrin complex, was used as a model system. Specifically, focused mutagenesis was used in a stepwise fashion to rapidly improve the affinity of the antigen binding fragment by greater than 90-fold. In the complete absence of structural information about the Vitaxin-alphav beta3 interaction, phage-expressed antibody libraries for all six Ig heavy and light chain complementarity-determining regions were expressed and screened by a quantitative assay to identify variants with improved binding to alphav beta3. The Vitaxin variants in these libraries each contained a single mutation, and all 20 amino acids were introduced at each complementarity-determining region residue, resulting in the expression of 2,336 unique clones. Multiple clones displaying 2- to 13-fold improved affinity were identified. Subsequent expression and screening of a library of 256 combinatorial variants of the optimal mutations identified from the primary libraries resulted in the identification of multiple clones displaying greater than 50-fold enhanced affinity. These variants inhibited ligand binding to receptor more potently as demonstrated by inhibition of cell adhesion and ligand competition assays. Because of the limited mutagenesis and combinatorial approach, Vitaxin variants with enhanced affinity were identified rapidly and required the synthesis of only 2,592 unique variants. The use of such small focused libraries obviates the need for phage affinity selection approaches typically used, permitting the use of functional assays and the engineering of proteins expressed in mammalian cell culture.

Figure 1

Titration of variants and Vitaxin Fab on immobilized α_vβ₃. Bacterial cell lysates containing Vitaxin (•), variants with improved affinity isolated from the primary libraries (S102, ▪; Y100, □; and Y101, ▵) or from the combinatorial libraries (clone 17, ▴), or an irrelevant Fab (○) were titrated on immobilized α_vβ₃ as described in Materials and Methods.

Figure 2

(A) Inhibition of fibrinogen binding to immobilized α_vβ₃. Immobilized α_vβ₃ was incubated with 0.1 μg/ml of biotinylated fibrinogen and various concentrations of Vitaxin (○), S102 (•), F32 (▵), or C59 (▴) for 3 h at 37°C. Unbound ligand and Fab were removed by washing, and bound fibrinogen was quantitated after incubation with NeutrAvidin alkaline phosphatase conjugate. (B) Correlation of affinity of variants with inhibition of fibrinogen binding. The concentration of variants required to inhibit the binding of fibrinogen to immobilized α_vβ₃ by 50% (IC₅₀) was plotted as a function of the affinity (K_d).

Figure 3

Inhibition of M21 human melanoma cell adhesion to fibrinogen. Cells and various concentrations of Vitaxin Fab (▴), S102 (○), G102 (•), or C37 (▵) were added to 96-well cell culture plates that had been coated with 10 μg/ml of fibrinogen. After incubating for 35 min at 37°C unbound cells were removed by washing, and adherent cells were quantitated by crystal violet staining.