Antibody geometry and form: three-dimensional relationships between anti-idiotypic antibodies and external antigens

Development of a highly sensitive immunoassay based on pentameric nanobodies for carcinoembryonic antigen detection

BACKGROUND

Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM-5) is a well-characterized biomarker for the clinical diagnosis of various cancers. Nanobodies, considered the smallest antibody fragments with intact antigen-binding capacity, have gained significant attention in disease diagnosis and therapy. Due to their peculiar properties, nanobodies have become promising alternative diagnostic reagents in immunoassay. However, nanobodies-based immunoassay is still hindered by small molecular size and low antigen capture efficacy. Therefore, there is a pressing need to develop novel nanobody-based immunoassays with superior performance.

RESULTS

A novel pentameric nanobodies-based immunoassay (PNIA) was developed with enhanced sensitivity and specificity for CEACAM-5 detection. The binding epitopes of three anti-CEACAM-5 nanobodies (Nb1, Nb2 and Nb3) were analyzed. To enhance the capture and detection efficacy of CEACAM-5 in the immunoassay, we engineered bispecific nanobodies (Nb1-Nb2-rFc) as the capture antibody, and developed the FITC-labeled pentameric nanobodies (Nb3-VT1B) as the detection antibody. The binding affinities of Nb1-Nb2-rFc (1.746 × 10-10) and Nb3-VT1B (1.279 × 10-11) were significantly higher than those of unmodified nanobodies (Nb1-rFc, 4.063 × 10-9; Nb2-rFc, 2.136 × 10-8; Nb3, 3.357 × 10-9). The PNIA showed a linear range of 0.625-160 ng mL-1 with a correlation coefficient R2 of 0.9985, and a limit of detection of 0.52 ng mL-1, which was 24-fold lower than the immunoassay using monomeric nanobody. The PNIA was validated with the spiked human serum. The average recoveries ranged from 91.8% to 102% and the coefficients of variation ranged from 0.026% to 0.082%.

SIGNIFICANCE AND NOVELTY

The advantages of nanobodies offer a promising alternative to conventional antibodies in disease diagnosis. The novel PNIA demonstrated superior sensitivity and high specificity for the detection of CEACAM-5 antigen. This bispecific or multivalent nanobody design will provide some new insights into the design of immunoassays for clinical diagnosis.

Advances in protein subunit vaccines against tuberculosis

Tuberculosis (TB), also known as the "White Plague", is caused by Mycobacterium tuberculosis (Mtb). Before the COVID-19 epidemic, TB had the highest mortality rate of any single infectious disease. Vaccination is considered one of the most effective strategies for controlling TB. Despite the limitations of the Bacille Calmette-Guérin (BCG) vaccine in terms of protection against TB among adults, it is currently the only licensed TB vaccine. Recently, with the evolution of bioinformatics and structural biology techniques to screen and optimize protective antigens of Mtb, the tremendous potential of protein subunit vaccines is being exploited. Multistage subunit vaccines obtained by fusing immunodominant antigens from different stages of TB infection are being used both to prevent and to treat TB. Additionally, the development of novel adjuvants is compensating for weaknesses of immunogenicity, which is conducive to the flourishing of subunit vaccines. With advances in the development of animal models, preclinical vaccine protection assessments are becoming increasingly accurate. This review summarizes progress in the research of protein subunit TB vaccines during the past decades to facilitate the further optimization of protein subunit vaccines that may eradicate TB.

The promise of the anti-idiotype concept

A basic tenet of antibody-based immunity is their specificity to antigenic determinates from foreign pathogen products to abnormal cellular components such as in cancer. However, an antibody has the potential to bind to more than one determinate, be it an antigen or another antibody. These observations led to the idiotype network theory (INT) to explain immune regulation, which has wax and waned in enthusiasm over the years. A truer measure of the impact of the INT is in terms of the ideas that now form the mainstay of immunological research and whose roots are spawned from the promise of the anti-idiotype concept. Among the applications of the INT is understanding the structural implications of the antibody-mediated network that has the potential for innovation in terms of rational design of reagents with biological, chemical, and pharmaceutical applications that underlies concepts of reverse immunology which is highlighted herein.

Generation of Anti-Idiotypic Antibodies that Mimic HBsAg and Vaccination against Hepatitis B Virus

The advent of hybridoma technology has opened up a new avenue in vaccine development, and antigen-mimicking properties of anti-idiotypic antibodies have provided promising alternatives in the generation of experimental anti-idiotypic vaccines. In the present study, mice were immunized with anti-hepatitis B virus (HBV) mouse monoclonal and anti-HBV goat polyclonal antibody to produce anti-idiotypic antibodies. Two mouse monoclonal antibodies (6C9, 6H9) were obtained from the fusions, and the immunogenic properties and specificity of antibodies were analyzed. BALB/c mice were immunized with varying concentrations of anti-idiotypic antibodies (25, 50, 75, and 100 micrograms of anti-Id), and it was shown that anti-idiotypic antibodies generated hepatitis B surface antigen (HBsAg), as well as a BSA-specific antibody response. A simple method for the purification of monoclonal antibodies by dialyzing antibody against water has also been reported.

A receptor that subserves reovirus binding can inhibit lymphocyte proliferation triggered by mitogenic signals

A novel surface receptor complex involved in inhibition of T-cell proliferation is described. Biochemical isolation revealed two non-covalently associated proteins of about M(r) 65,000 (p65) and 95,000 (p95). These polypeptides may be related. The p65 form is expressed after cellular activation and replication and is recognized by monoclonal antibody (mAb) 87.92.6 or reovirus hemagglutinin as unnatural ligands. The p95 species is associated with tyrosine kinase enzymatic activity. Receptor ligation results in rapid alteration of the phosphotyrosine content of cellular substrates, and this activity correlates with antiproliferative effects. The inhibition of proliferation is a time-dependent reversible arrest at the G1-S phase of the cell cycle. Activation through the T-cell receptor, protein kinase C, or addition of cytokines does not reverse the antiproliferative effect. This receptor complex may define novel features of T-cell proliferation.

Crystal structure of an idiotype-anti-idiotype Fab complex

Anti-idiotypic monoclonal antibody 409.5.3 is raised against an antibody that neutralizes feline infectious peritonitis virus. This antibody, used as an immunogen, elicits the production of anti-anti-idiotypic antibodies that in turn neutralize the virus. The crystal structure of the complex between anti-idiotypic Fab 409.5.3 and idiotypic Fab fragment of virus-neutralizing antibody has been solved by molecular replacement using real-space Patterson search and filtering by Patterson correlation-coefficient refinement. The structure has been refined to an R value of 0.21 based on 21,310 unique reflections between 40.0 and 2.9 A. The three-dimensional structure reveals extensive, specific interactions that involve 118 van der Waals contacts and at least 9 probable hydrogen bonds. The two Fabs are rotated 61 degrees with respect to each other around the approximate long axis of the complex and are within 26 degrees being aligned along their major axes.

Bactericidal activity of two IgG2a murine monoclonal antibodies with distinct fine specificities for group B Neisseria meningitidis capsular polysaccharide

To analyze the fine specificity of the protective IgG response for the capsule of group B Neisseria meningitidis (Men B) induced after immunization with live bacteria, two specific IgG2a monoclonal antibodies (mAb) have been generated from hyperimmunized Balb/c and NZB mice (101C11 and 30H12). They specifically recognize in direct and competitive binding assays the capsular polysaccharides of Men B and Escherichia coli k1 on condition that the length of the polysaccharidic chain is sufficient to make a conformational structure (more than 15 monomers of alpha (2-->8) linked N-acetyl neuraminic acid). They do not interact with group A and group C Neisseria meningitidis polysaccharides in ELISA. A chemical derivative of the Men B polysaccharide, the N-propionylated Men B polysaccharide, considered as mimicking a unique bactericidal epitope on the surface of Men B is recognized by 101C11 but not by 30H12. The two mAb have, in vitro, a specific bactericidal activity against live Men B which do not seem serotype specific. Moreover, the killing of Men B mediated by 30H12 can be neutralized by an anti-idiotypic mAb (216F11) generated from A/J mice, immunized with polymerized 30H12. These data show that at least two distinct bactericidal epitopes exist on the surface of the Men B capsule.

New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking

A novel algorithm is presented which models protein-protein interactions using surface complementarity. The method is applied to antibody-antigen docking. A steric scoring scheme, based upon a soft potential, is used to assess complementarity, and a simple electrostatic model is then used to remove infeasible interactions. The soft potential allows for structural changes that occur during docking. Biochemical knowledge is necessary to reduce the number of docking orientations produced by the method to a manageable size. The information used includes the known epitope residues and a single loose distance constraint. The method is applied to all three crystallographically determined antibody-lysozyme complexes, HyHEL-10, D1.3 and HyHEL-5. For the first time, a predicted antibody structure (that of D1.3) is used as a docking target. In the four systems modelled, the method identifies between 15 and 40 possible docking orientations. The root-mean-square (r.m.s.) deviation between these orientations and the relevant crystallographic complex is measured in the interface region. For all four complexes an orientation is found with r.m.s. deviation in the range 1.9 A and 4.8 A. The algorithm is implemented on a single instruction/multiple datastream (SI/MD) architecture computer. The use of a parallel architecture computer ensures detailed coverage of the search space, whilst still maintaining a search time of two days.

Anti-tumor necrosis factor receptor and tumor necrosis factor agonist activity by an anti-idiotypic antibody

Tumor necrosis factor (TNF) is a cytokine which, among other properties, is a principle mediator of inflammation and septic shock. It acts upon target cells by binding to specific cell surface receptors. A10G10 is a murine monoclonal antibody which recognizes human TNF and neutralizes its activity. A rabbit polyclonal antibody directed at the antigen-binding site of A10G10 was raised and affinity purified over an A10G10 column. The resultant anti-idiotypic antibody recognized not only A10G10 but also both TNF receptors. It showed TNF agonist activity in two different TNF bioassays, and competed with several anti-TNF receptor monoclonal antibodies and TNF itself for binding to cells. These results represent an example of a method for obtaining antibodies to a ligand-specific receptor in the absence of the receptor itself.

Loops and Secondary Structure Mimetics: Development and Applications in Basic Science and Rational Drug Design

One goal of protein design and structural biochemistry is the reduction of complex molecules to small functional units that are amenable to high resolution analysis and rapid modification. We have developed a variety of small molecules which biochemically and biologically mimic the combining sites of proteins of the immunoglobulin superfamily. The chemical and biological properties of peptide mimetics suggest that these analogs can be used as indicators for new pharmaceutical agents. Mimetics are powerful tools for the study of molecular recognition since they are small in size, maintain solubility in physiologic fluids and are amenable to detailed structural studies. As such, they represent a step toward the rational design of low molecular weight non-peptide pharmaceutical agents devoid of some of the shortcomings of conventional peptides. Here we discuss the rationale and approaches for the development of these molecules, and their current and future applications.