Phage display of human antibodies from a patient suffering from coeliac disease and selection of isotype-specific scFv against gliadin

Development of a potent recombinant scFv antibody against the SARS-CoV-2 by in-depth bioinformatics study: Paving the way for vaccine/diagnostics development

BACKGROUND

The SARS-CoV-2 has led to a worldwide disaster. Thus, developing prophylactics/therapeutics is required to overcome this public health issue. Among these, producing the anti-SARS-CoV-2 single-chain variable fragment (scFv) antibodies has attracted a significant attention. Accordingly, this study aims to address this question: Is it possible to bioinformatics-based design of a potent anti-SARS-CoV-2 scFv as an alternative to current production approaches?

METHOD

Using the complexed SARS-CoV-2 spike-antibodies, two sets analyses were performed: (1) B-cell epitopes (BCEs) prediction in the spike receptor-binding domain (RBD) region as a parameter for antibody screening; (2) the computational analysis of antibodies variable domains (VH/VL). Based on these primary screenings, and docking/binding affinity rating, one antibody was selected. The protein-protein interactions (PPIs) among the selected antibody-epitope complex were predicted and its epitope conservancy was also evaluated. Thereafter, some elements were added to the final scFv: (1) the PelB signal peptide; (2) a GSGGGGS linker to connect the VH-VL. Finally, this scFv was analyzed/optimized using various web servers.

RESULTS

Among the antibody library, only one met the various criteria for being an efficient scFv candidate. Moreover, no interaction was predicted between its paratope and RBD hot-spot residues of SARS-CoV-2 variants-of-Concern (VOCs).

CONCLUSIONS

Herein, a step-by-step bioinformatics platform has been introduced to bypass some barriers of traditional antibody production approaches. Based on existing literature, the current study is one of the pioneer works in the field of bioinformatics-based scFv production. This scFv may be a good candidate for diagnostics/therapeutics design against the SARS-CoV-2 as an emerging aggressive pathogen.

Development of a new recombinant antibody, selected by phage-display technology from a celiac patient library, for detection of gluten in foods

Gluten, a group of ethanol-soluble proteins present in the endosperm of cereals, is extensively used in the food industry due to its ability to improve dough properties. However, gluten is also associated with a range of gluten-related diseases (GRDs), such as wheat allergies, celiac disease, and gluten intolerance. The recommended treatment for GRDs patients is a gluten-free diet. To monitor adherence to this diet, it is necessary to develop gluten-detection systems in food products. Among the available methods, immunodetection systems are the most popular due to their simplicity, reproducibility, and accuracy. The aim of this study was to generate novel high-affinity antibodies against gluten to be used as the primary reactant in an enzyme-linked immunosorbent assay (ELISA) test. These antibodies were developed by constructing an immune library from mRNA obtained from two celiac patients with a high humoral response to gluten-related proteins. The resulting library (composed by 1.1x107) was subjected to selection against gliadin using phage display technology. Following several rounds of selection, the Fab-C was selected, and demonstrated good functionality in ELISA tests, presenting a limit of detection of 15 mg/kg for detection of gluten in spiked mixtures and food products. The methodology can discriminate gluten-free products according to the current legislation.

From Polyclonal Sera to Recombinant Antibodies: A Review of Immunological Detection of Gluten in Foodstuff

Gluten is the ethanol-soluble protein fraction of cereal endosperms like wheat, rye, and barley. It is widely used in the food industry because of the physical-chemical properties it gives to dough. Nevertheless, there are some gluten-related diseases that are presenting increasing prevalences, e.g., celiac disease, for which a strict gluten-free diet is the best treatment. Due to this situation, gluten labeling legislation has been developed in several countries around the world. This article reviews the gluten immune detection systems that have been applied to comply with such regulations. These systems have followed the development of antibody biotechnology, which comprise three major methodologies: polyclonal antibodies, monoclonal antibodies (mAbs) derived from hybridoma cells (some examples are 401.21, R5, G12, and α-20 antibodies), and the most recent methodology of recombinant antibodies. Initially, the main objective was the consecution of new high-affinity antibodies, resulting in low detection and quantification limits that are mainly achieved with the R5 mAb (the gold standard for gluten detection). Increasing knowledge about the causes of gluten-related diseases has increased the complexity of research in this field, with current efforts not only focusing on the development of more specific and sensitive systems for gluten but also the detection of protein motifs related to pathogenicity. New tools based on recombinant antibodies will provide adequate safety and traceability methodologies to meet the increasing market demand for gluten-free products.

Infectious disease antibodies for biomedical applications: A mini review of immune antibody phage library repertoire

Antibody phage display is regarded as a critical tool for the development of monoclonal antibodies for infectious diseases. The different classes of antibody libraries are classified based on the source of repertoire used to generate the libraries. Immune antibody libraries are generated from disease infected host or immunization against an infectious agent. Antibodies derived from immune libraries are distinct from those derived from naïve libraries as the host's in vivo immune mechanisms shape the antibody repertoire to yield high affinity antibodies. As the immune system is constantly evolving in accordance to the health state of an individual, immune libraries can offer more than just infection-specific antibodies but also antibodies derived from the memory B-cells much like naïve libraries. The combinatorial nature of the gene cloning process would give rise to a combination of natural and un-natural antibody gene pairings in the immune library. These factors have a profound impact on the coverage of immune antibody libraries to target both disease-specific and non-disease specific antigens. This review looks at the diverse nature of antibody responses for immune library generation and discusses the extended potential of a disease-specified immune library in the context of phage display.

Identification of host cell binding peptide from an overlapping peptide library for inhibition of classical swine fever virus infection

The envelope proteins of classical swine fever virus (CSFV) mediate the binding of CSFV to cell surface molecules and allow CSFV subsequent to enter host cells. However, the proteins binding to host cells and their binding sequences are uncertain. The results showed that the protein E1, E2, and Erns were displayed on the surfaces of T7 phages. The E2 and Erns phage clones showed high binding affinity to host cells, in which the E2 phage clone interacted more specifically with host cells than with other cells, while the Erns phage clone interacted with all tested cells. A 30-mer phage displaying peptide library was constructed and screened against immobilized host cells, in which each peptide was overlapped 10aa to another peptide and spanned all amino acid sequences of Erns and E2. Fifty-eight clones with specific binding to host cells were isolated. Amino acid sequence analyses for two phage clones (P2 and P6) demonstrated the strongest binding positions were at 101-130 (S2) in Erns, and 141-170 (S6) in E2, respectively. The synthetic peptides (S2 and S6) could inhibit the binding of phage clones (P2 and P6) and CSFV to cell. About 86.74 and 74.24% inhibition rates of CSFV infection were achieved at 55 μM of the synthetic peptides S2 and S6. The results also indicated that the S2 (LAEGPPVKECAVTCRYDKDADINVVTQARN) and S6 (AVSPTTLRTEVVKTFRRDKPFPHRMDCVTT) from CSFV were host cell binding peptides, and both of them had potential for research of CSFV entering host cells.

Development of an optimized protocol for studying the interaction of filamentous bacteriophage with mammalian cells by fluorescence microscopy

Filamentous bacteriophage has been proposed as a vehicle that can carry and deliver therapeutics into mammalian cells for disease treatment, thus a protocol for imaging phage-cell interaction is essential. Because high signal intensity is necessary to study the mechanism of interaction between filamentous bacteriophage and mammalian cells, it is important to optimize the procedure for fluorescence labeling of phage in order to understand such interaction. Here, we describe a procedure that gives intense fluorescence labeling and can show interactions between fd-tet bacteriophage selected from phage libraries and mammalian cells (SKBR-3 and MCF-10A). The indirect labeling of phage with dye-conjugated antibody and cytoskeleton associated proteins was significantly enhanced in the presence of a cross-linking reagent called dithiobissuccinimidylpropionate (DSP) as shown by qualitative and quantitative fluorescence microscopy. The use of DSP resulted in high signal intensity in fluorescence imaging of phage-cell complex. The DSP cross-linker is believed to preserve soluble unbound proteins for fluorescence imaging. The interaction between the phage and mammalian cells was further confirmed by scanning electron microscopy.

Survey of the year 2003 commercial optical biosensor literature

In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.