Kip Dudgeon

General strategy for the generation of human antibody variable domains with increased aggregation resistance

The availability of stable human antibody reagents would be of considerable advantage for research, diagnostic, and therapeutic applications. Unfortunately, antibody variable heavy and light domains (VH and VL) that mediate the interaction with antigen have the propensity to aggregate. Increasing their aggregation resistance in a general manner has proven to be a difficult and persistent problem, due to the high level of sequence diversity observed in human variable domains and the requirement to maintain antigen binding. Here we outline such an approach. By using phage display we identified specific positions that clustered in the antigen binding site (28, 30–33, 35 in VH and 24, 49–53, 56 in VL). Introduction of aspartate or glutamate at these positions endowed superior biophysical properties (non-aggregating, well-expressed, and heat-refoldable) onto domains derived from common human germline families (VH3 and Vκ1). The effects of the mutations were highly positional and independent of sequence diversity at other positions. Moreover, crystal structures of mutant VH and VL domains revealed a surprising degree of structural conservation, indicating compatibility with VH/VL pairing and antigen binding. This allowed the retrofitting of existing binders, as highlighted by the development of robust high affinity antibody fragments derived from the breast cancer therapeutic Herceptin. Our results provide a general strategy for the generation of human antibody variable domains with increased aggregation resistance.

Aggregation, stability, and formulation of human antibody therapeutics

Many human monoclonal antibodies display poor biophysical properties, such as low stability and a propensity to aggregate. These unfavorable tendencies can be even more pronounced for human antibody fragments, which often require a considerable degree of optimization. In this review, we describe methods for analyzing aggregation and stability of human antibodies and antibody fragments. We also provide an overview of recent approaches to improve these properties through engineering and formulation.

Sequence determinants of protein aggregation in human VH domains

Human antibody variable heavy (VH) domains tend to aggregate upon denaturation, for instance, by heat or acid. We have previously demonstrated that domains resisting protein aggregation can be selected from CDR-only repertoires by phage display. Here we analysed their sequences to identify determinants governing protein aggregation. We found that, while many different CDR sequences conferred aggregation-resistance, certain physico-chemical properties were strongly selected for. Thus, hydrophobicity and beta-sheet propensity were significantly lower among the selected domains, whereas net negative charge was increased. Our results provide guidelines for the design of human VH repertoires with reduced levels of protein aggregation.

Expression of high-affinity human antibody fragments in bacteria

Here we describe protocols for the expression of human antibody fragments in Escherichia coli. Antigen-specific clones are identified by soluble fragment ELISA and concentrated by periplasmic preparation. They are then further purified by affinity chromatography. This article provides an overview of expression and purification strategies for human antibody fragments, as well as detailed protocols for the identification of high-affinity binders and for affinity maturation.

Fully Human VH Single Domains That Rival the Stability and Cleft Recognition of Camelid Antibodies.

Background: Camelid antibody domains are naturally stable and capable of cleft binding. Results: Protein engineering can endow human antibody domains with such properties. Conclusion: Our strategy does not require undesirable antibody framework changes. Significance: Robust building blocks for human therapeutic applications. Human VH single domains represent a promising class of antibody fragments with applications as therapeutic modalities. Unfortunately, isolated human VH domains also generally display poor biophysical properties and a propensity to aggregate. This has encouraged the development of non-human antibody domains as alternative means of antigen recognition and, in particular, camelid (VHH) domains. Naturally devoid of light chain partners, these domains are characterized by favorable biophysical properties and propensity for cleft binding, a highly desirable characteristic, allowing the targeting of cryptic epitopes. In contrast, previously reported structures of human VH single domains had failed to recapitulate this property. Here we report the engineering and characterization of phage display libraries of stable human VH domains and the selection of binders against a diverse set of antigens. Unlike “camelized” human domains, the domains do not rely on potentially immunogenic framework mutations and maintain the structure of the VH/VL interface. Structure determination in complex with hen egg white lysozyme revealed an extended VH binding interface, with complementarity-determining region 3 deeply penetrating into the active site cleft, highly reminiscent of what has been observed for camelid domains. Taken together, our results demonstrate that fully human VH domains can be constructed that are not only stable and well expressed but also rival the cleft binding properties of camelid antibodies.

Rapid prediction of expression and refolding yields using phage display

Aggregation limits the recombinant production of many commercially important proteins. We have recently identified mutations that control the aggregation behavior of human antibody variable domains (Dudgeon K., Rouet R., Kokmeijer I., Schofield P., Stolp J., Langley D., Stock D. and Christ D. (2012) Proc Natl Acad Sci USA, 109, 10879-10884. This has allowed the generation of a panel of human antibody variable heavy domains with a defined range of aggregation propensities. Here we utilize this unique resource to validate a previously reported heat-denaturation method on phage (Jespers L., Schon O., Famm K. and Winter G. (2004) Nat Biotechnol, 22, 1161-1165. Our experiments revealed that the method is not only robust in respect to denaturation conditions on phage, but also highly indicative of solution behavior. In particular, it is an excellent predictor of expression and refolding yields.

Generation of Human Single Domain Antibody Repertoires by Kunkel Mutagenesis

Human antibody single domains are a promising new class of antibody fragments. Here we describe methods for the cloning of human V(H) and V(L) genes into phage and phagemid vectors. Furthermore, we provide detailed protocols for the generation of single domain antibody libraries by Kunkel mutagenesis and the analysis of diversity by DNA sequencing and superantigen binding.

Identification of aggregation inhibitors of the human antibody light chain repertoire by phage display

Protein aggregation hinders the development of biologics and underpins the molecular basis of many human diseases. Considerable variation of aggregation propensity exists not only between different proteins, but also within a single homologous family, which complicates analyses. A classic example is observed among human antibody light chains, which aggregate in a clonally specific manner, driven by sequence diversity within their variable domains. Here, we utilise a library versus library strategy, based on phage display and a chemical library of FDA approved drugs, to overcome this limitation. Our approach allowed the identification of small molecule drugs that inhibit the aggregation of the human light chain repertoire. It also provides a general template for the small molecule targeting of diverse protein families.