The importance of a downstream process for the purification of immunoglobulin antibodies is increasing with the growing application of monoclonal antibodies in many different areas. Although protein A is most commonly used for the affinity purification of antibodies, certain properties could be further improved: higher stability in alkaline solution and milder elution condition. Herein, we present the development of Fc-specific repebody by modular engineering approach and its potential as an affinity ligand for purification of human immunoglobulin antibodies. We previously developed the repebody scaffold composed of Leucine-rich repeat (LRR) modules. The scaffold was shown to be highly stable over a wide range of pH and temperature, exhibiting a modular architecture. We first selected a repebody that binds the Fc fragment of human immunoglobulin G (IgG) through a phage display and increased its binding affinity up to 1.9 × 10(-7) M in a module-by-module approach. The utility of the Fc-specific repebody was demonstrated by the performance of an immobilized repebody in affinity purification of antibodies from a mammalian cell-cultured medium. Bound-antibodies on an immobilized repebody were shown to be eluted at pH 4.0 with high purity (>94.6%) and recovery yield (>95.7%). The immobilized repebody allowed a repetitive purification process more than ten times without any loss of binding capability. The repebody remained almost intact even after incubation with 0.5 M NaOH for 15 days. The present approach could be effectively used for developing a repeat module-based binder for other target molecules for affinity purification.

Bruton’s tyrosine kinase (Btk) is critical for B-cell maturation and activation. Btk loss-of-function mutations cause human X-linked agammaglobulinemia (XLA). In contrast, Btk signaling sustains growth of several B-cell neoplasms which may be treated with tyrosine kinase inhibitors (TKIs). Here, we uncovered the structural mechanism by which certain XLA mutations in the SH2 domain strongly perturb Btk activation. Using a combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), we discovered an allosteric interface between the SH2 and kinase domain required for Btk activation and to which multiple XLA mutations map. As allosteric interactions provide unique targeting opportunities, we developed an engineered repebody protein binding to the SH2 domain and able to disrupt the SH2-kinase interaction. The repebody prevents activation of wild-type and TKI-resistant Btk, inhibiting Btk-dependent signaling and proliferation of malignant B-cells. Therefore, the SH2-kinase interface is critical for Btk activation and a targetable site for allosteric inhibition.

No abstract

An immunoassay is the most widely used method for analyzing a variety of analytes based on antigen-antibody interactions in the biological and medical sciences. However, the use of secondary antibodies has certain shortcomings, such as a high cost, cross-reactivity, and loss of binding affinity during labeling. Herein, we present the development of repebodies specifically binding to immunoglobulin G with a different origin, which is a small-sized nonantibody scaffold composed of leucine-rich repeat (LRR) modules, for use in immunoassays and imaging. Repebodies specific for IgG from different species (i.e., mouse, human, and rabbit) were selected through a phage display, and their affinities were matured using a modular engineering approach. The respective repebodies were labeled with various signal generators such as horseradish peroxidase (HRP), a fluorescent dye, and quantum dots, and the resulting repebodies were used as alternatives to conventional secondary antibodies in typical immunoassays and imaging. The labeled repebodies enabled the detection of diverse target analytes with high sensitivity and specificity, showing a negligible cross-reactivity. Moreover, the repebodies labeled with different color-emitting quantum dots allowed the imaging of cell-surface receptors and proteins in a multiplex manner. The developed repebodies can be effectively used for sensitive immunoassays and multiplex imaging.

Precise binding mode identification and subsequent affinity improvement without structure determination remain a challenge in the development of therapeutic proteins. However, relevant experimental techniques are generally quite costly, and purely computational methods have been unreliable. Here, we show that integrated computational and experimental epitope localization followed by full-atom energy minimization can yield an accurate complex model structure which ultimately enables effective affinity improvement and redesign of binding specificity. As proof-of-concept, we used a leucine-rich repeat (LRR) protein binder, called a repebody (Rb), that specifically recognizes human IgG 1 (hIgG 1). We performed computationally-guided identification of the Rb:hIgG 1 binding mode and leveraged the resulting model to reengineer the Rb so as to significantly increase its binding affinity for hIgG 1 as well as redesign its specificity toward multiple IgGs from other species. Experimental structure determination verified that our Rb:hIgG 1 model closely matched the co-crystal structure. Using a benchmark of other LRR protein complexes, we further demonstrated that the present approach may be broadly applicable to proteins undergoing relatively small conformational changes upon target binding.