The biotechnology and applications of antibody engineering

Unleashing the power of antibodies: Engineering for tomorrow's therapy

Antibodies play a crucial role in host defense against various diseases. Antibody engineering is a multidisciplinary field that seeks to improve the quality of life of humans. In the context of disease, antibodies are highly specialized proteins that form a critical line of defense against pathogens and the disease caused by them. These infections trigger the innate arm of immunity by presenting on antigen-presenting cells such as dendritic cells. This ultimately links to the adaptive arm, where antibody production and maturation occur against that particular antigen. Upon binding with their specific antigens, antibodies trigger various immune responses to eliminate pathogens in a process called complement-dependent cytotoxicity and phagocytosis of invading microorganisms by immune cells or induce antibody-dependent cellular cytotoxicity is done by antibodies. These engineered antibodies are being used for various purposes, such as therapeutics, diagnostics, and biotechnology research. Cutting-edge techniques that include hybridoma technology, transgenic mice, display techniques like phage, yeast and ribosome displays, and next-generation sequencing are ways to engineer antibodies and mass production for the use of humankind. Considering the importance of antibodies in protecting from a diverse array of pathogens, investing in research holds great promise to develop future therapeutic targets to combat various diseases.

Immunoprecipitation

Selective immunoprecipitation of proteins is a useful tool for characterizing proteins and protein-protein interactions. Clear step-by-step protocols are provided for preparing lysates of cells and yeast under a variety of conditions, for binding the antibody to a solid matrix, and for performing the actual immunoprecipitation. An additional method is provided for increasing the specificity of the technique by reprecipitating the antigen with the same or a different antibody. © 2016 by John Wiley & Sons, Inc.

Antibody Immobilization on Solid Surfaces: Methods and Applications

The correct immobilization of the antibody component is one of the most critical steps in the development of immunoassays, immunosensors and immunochromatography matrices. Advances in hybridoma technology and protein engineering have allowed traditional limitations of polyreactivity of antibody preparations, poor device stability and random orientation of binding pockets to be largely overcome, resulting in stable, sensitive, highly specific and enormously diverse immunoplatforms with applications in diagnostics, environmental monitoring, and food and public safety. In this Chapter we introduce antibody structure and antibody-derived fragments, describe the most common methods of their immobilization and discuss ‘traditional’ applications of immobilized antibodies such as enzyme immunoassays and immunoaffinity chromatography, as well as exciting emerging uses in immunosensors, microarrays and nanomedicine.

Recombinant antibodies specific for the Plasmodium falciparum histidine-rich protein 2

Early diagnosis and appropriate treatment are key elements of malaria control programs in endemic areas. A major step forward in recent years has been the production and use of rapid diagnostic tests (RDTs) in settings where microscopy is impracticable. Many current RDTs target the Plasmodium falciparum histidine-rich protein 2 (PfHRP2) released in the plasma of infected individuals. These RDTs have had an indisputably positive effect on malaria management, but still present several limitations, including the poor characterization of the commercial monoclonal antibodies (mAbs) used for PfHRP2 detection, variable sensitivity and specificity, and high costs. RDT use is further limited by impaired stability caused by temperature fluctuations during transport and uncontrolled storage in field-based facilities. To circumvent such drawbacks, an alternative could be the development of well-characterized, stabilized recombinant antibodies, with high binding affinity and specificity. Here, we report the characterization of the cDNA sequences encoding the Fab fragment of F1110 and F1546, two novels anti-PfHRP2 mAbs. FabF1546 was produced in the Escherichia coli periplasm. Its properties of binding to the parasite and to a recombinant PfHRP-2 antigen were similar to those of the parental mAb. As the affinity and stability of recombinant antibodies can be improved by protein engineering, our results open a novel approach for the development of an improved RDT for malaria diagnosis.

Phage display as a novel screening tool for primary toxicological targets

In the present study the use of phage display as a screening tool to determine primary toxicological targets was investigated. These primary toxicological targets are the targets in the cell with which a chemical compound initially interacts and that are responsible for consecutive (toxic) effects. Nickel was used as model compound for the present study. By selection of Ni-binding peptides out of a 12-mer peptide phage library, it was possible to identify primary toxicological targets of Ni (and other metals). The selected Ni-binding peptides showed similarities to important primary toxicological targets of Ni, such as the hydrogenase nickel incorporation protein (hypB) and the Mg/Ni/Co transporter (corA). This shows that phage display, which is already widely used in other research fields, also has potential in ecotoxicology, as a novel screening tool with which to determine primary toxicological targets of chemical compounds.

Immunoprecipitation

Immunoprecipitation is a technique in which an antigen is isolated by binding to a specific antibody attached to a sedimentable matrix. It is also used to analyze protein fractions separated by other biochemical techniques such as gel filtration or density gradient sedimentation. The source of antigen for immunoprecipitation can be unlabeled cells or tissues, metabolically or intrinsically labeled cells, or in-vitro-translated proteins. This unit describes a wide range of immunoprecipitation techniques, using either suspension or adherent cells lysed by various means (e.g., with and without detergent, using glass beads, etc.). Flow charts and figures give the user a clear-cut explanation of the options for employing the technology.

Immunoprecipitation

Immunoprecipitation is a technique in which an antigen is isolated by binding to a specific antibody attached to a sedimentable matrix. It is also used to analyze protein fractions separated by other biochemical techniques such as gel filtration or density gradient sedimentation. The source of antigen for immunoprecipitation can be unlabeled cells or tissues, metabolically or intrinsically labeled cells, or in vitro-translated proteins. This unit describes a wide range of immunoprecipitation techniques, using either suspension or adherent cells lysed by various means (e.g., with and without detergent, using glass beads, etc.). Flow charts and figures give the user a clear-cut explanation of the options for employing the technology.

Immunoprecipitation

Immunoprecipitation consists of multiple ordered steps: lysing the cell with detergent if the antigen (usually a protein) to be precipitated is membrane-bound; binding of a specific antigen to an antibody; precipitating the antibody-antigen complex; washing the precipitate; and dissociating the antigen from the immune complex. The dissociated antigen is then analyzed by electrophoretic methods. In this unit, the basic protocol details the immunoprecipitation of a radiolabeled antigen with a specific antibody (polyclonal or monoclonal) covalently linked to Sepharose. Preparation of Ab-Sepharose is described in the Support Protocol. The first two alternate protocols present methods for precipitating or isolating the soluble immune complexes formed between a specific antibody and a radiolabeled antigen. Immunoprecipitation is achieved with polyclonal anti-immunoglobulin (Ig) serum, anti-Ig-Sepharose, Staphylococcus protein A or Streptococcus protein G bound to Sepharose, or Staphylococcus aureus bacteria which contain protein A on the cell surface. The third alternate protocol should be used for immunoprecipitation of antigens that are nonspecifically associated with other proteins. The fourth alternate protocol describes immunoprecipitation of unlabeled protein antigens with Ab-Sepharose.

Immunoprecipitation

Immunoprecipitation is a technique in which an antigen is isolated by binding to a specific antibody attached to a sedimentable matrix. It is also used to analyze protein fractions separated by other biochemical techniques such as gel filtration or density gradient sedimentation. The source of antigen for immunoprecipitation can be unlabeled cells or tissues, metabolically or intrinsically labeled cells, or in vitro-translated proteins. This unit describes a wide range of immunoprecipitation techniques, using either suspension or adherent cells lysed by various means (e.g., with and without detergent, using glass beads, etc.). Flow charts and figures give the user a clear-cut explanation of the options for employing the technology.

Immunoprecipitation

Selective immunoprecipitation of proteins is a useful tool for characterizing proteins and protein-protein interactions. Clear step-by-step protocols are provided for preparing lysates of cells and yeast under a variety of conditions, for binding the antibody to a solid matrix, and for performing the actual immunoprecipitation. An additional method is provided for increasing the specificity of the technique by reprecipitating the antigen with the same or a different antibody.

Development of novel tumor imaging agents with phage-display combinatorial peptide libraries

RATIONALE AND OBJECTIVES

Current radiologic methods do not provide sufficient information for unambiguous diagnosis and prognosis of cancer. The present investigation sought to address this deficiency by developing a system for designing novel small molecules targeted against tumor-specific molecules for use as radionuclide imaging agents.

MATERIALS AND METHODS

Part of a tumor-specific receptor, purified recombinant epidermal growth factor receptor (EGFR), variant III, extracellular domain (rEGFRvIII-ecd), was used as the target in the selection of EGFRvIII-specific peptide ligands from random peptide bacteriophage (phage) display libraries. After three rounds of screening, phage isolates were tested for binding affinity with an enzyme-linked immunosorbent assay. Positive phage were sequenced, and the peptides were synthesized and tested for binding affinity with a surface plasmon resonance assay.

RESULTS

Affinity screening identified 49 peptide-expressing phage that showed enhanced binding to the variant receptor compared with wild-type EGFR. Free peptides from the two phage isolates exhibiting the most favorable binding were tested for target binding. One of these demonstrated a binding affinity for rEGFRvIII-ecd in the 30-nmol/L range.

CONCLUSION

These data suggest that phage display libraries may be very useful in the design of novel, high-affinity tumor imaging agents.

Class-directed structure determination: foundation for a protein structure initiative

The recent sequencing of many complete genomes, combined with the development of methods that allow rapid structure determination for many proteins, has changed the way in which protein structure determinations can be approached. One-by-one determinations of individual protein structures will soon be augmented by class-directed structure analyses in which a group of proteins is targeted and structures of representative members are determined and used to represent the entire group. Such a shift in approach would be the foundation for a broad protein structure initiative targeting classes of proteins important for biotechnology and for a fundamental understanding of protein function.

Generating monoclonal antibodies to neuronal antigens

Methods for generating monoclonal antibodies directed to the functional sites of neuronal antigens are reviewed. These methods include optimal antigen preparation and presentation as well as selective targeting and manipulation of the antigenic response. We describe our use of the immunosuppressant drug, cyclophosphamide, to produce a selective immune response to rare, poorly immunogenic, or actively suppressed antigens. These techniques allow us to generate antibodies to the functional sites of neuronal antigens, such as cell surface molecules. Such antibodies are directed to complex carbohydrates, proteins, protein complexes and glycolipids that form the active site of neuronal antigens. We can use these antibodies in the molecular dissection of functional active sites that are inaccessible to genetic manipulation. These techniques favor the generation of antibodies that can be used to understand and manipulate neuronal cellular activity.