Screening of biotin-binding FV-antibodies from autodisplayed FV-library on E. coli outer membrane

SARS-CoV-2 vaccine based on ferritin complexes with screened immunogenic sequences from the Fv-antibody library

In this study, the vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was developed using ferritin complexes with the immunogenic sequences screened against the SARS-CoV-2 spike protein (SP) from the Fv-antibody library. The Fv-antibody library was prepared on the outer membrane of E. coli by the expression of the VH region of immunoglobulin G (IgG) with a randomized complementarity-determining region 3 (CDR3). Four Fv-antibodies to the receptor-binding domain (RBD) were screened from the Fv-antibody library, which had a comparable binding constant (KD) between SARS-CoV-2 SP and the angiotensin-converting enzyme 2 (ACE2) receptor. The binding sites of screened Fv-antibodies on the RBD were analyzed using a docking analysis, and these binding sites were used as immunogenic sequences for the vaccine. The four immunogenic sequences were modified and co-expressed as a part of ferritin which was assembled into a ferritin complex. After the vaccination of ferritin complexes to mice, the anti-sera were analyzed to have a high enough titer. Additionally, the immune responses were found to be activated by vaccination, such as the expression of IgG subclasses and the increased level of cytokines. The neutralizing activity of the anti-sera was estimated using a cell-based infection assay based on pseudo-virus expressing the SP of SARS-CoV-2 variants.

Screened Fv-Antibodies against the Angiotensin-Converting Enzyme 2 (ACE2) Receptor Neutralizing the Infection of SARS-CoV-2

For the prevention of SARS-CoV-2 infection, four Fv-antibodies with binding affinity for the ACE2 receptor were screened from an Fv-antibody library. The screened Fv-antibodies were expressed as soluble proteins and estimated to have a high binding affinity, comparable to that between SARS-CoV-2 and the ACE2 receptor. The interaction between the Fv-antibodies and the ACE2 receptor was analyzed using docking simulation, and the significant binding affinity of the screened Fv-antibodies was attributed to the homology in amino acid sequence with the ACE2 receptor. The neutralizing activities of the Fv-antibodies were demonstrated using a cell-based infection assay based on four pseudo-virus types with SARS-CoV-2 variant spike proteins (Wild-type D614, Delta B.1.617.2, and Omicron BA.2, and Omicron BA.4/5).

A one-step immunoassay based on switching peptides for diagnosis of porcine epidemic diarrhea virus (PEDV) using screened Fv-antibodies

In this study, a one-step immunoassay for porcine epidemic diarrhea virus (PEDV) based on Fv-antibodies and switching peptides was developed, and the assay results of PEDV were obtained by just mixing samples without any further reaction or washing steps. The Fv-antibodies with binding affinity to the spike protein of PEDV were screened from the Fv-antibody library using the receptor-binding domain (RBD) of the spike protein as a screening probe. Screened Fv-antibodies with binding affinities to the RBD antigen were expressed, and the binding constants (KD) were calculated to be 83-142 nM. The one-step immunoassay for the detection of PEDV was configured as a displacement immunoassay using a fluorescence-labeled switching peptide. The one-step immunoassay based on switching peptides was performed using PEDV, and the limit of detection (LOD) values for PEDV detection were estimated to be Ct = 39.7-36.4. Compared with the LOD value for a conventional lateral flow immunoassay (Ct = 33.0), the one-step immunoassay showed a remarkably improved LOD for the detection of PEDV. Finally, the interaction between the screened Fv-antibodies and the PEDV RBD was investigated using docking simulations and compared with the amino acid sequences of the receptors on host cells, such as aminopeptidase N (APN) and angiotensin-converting enzyme-2 (ACE-2).

Monocarboxylate transporter-1 (MCT-1) inhibitors screened from autodisplayed FV-antibody library

Monocarboxylate transporter-1 (MCT-1) inhibitors were screened from the Fv-antibody library, which contained complementary determining region 3 with randomized amino acid sequences (11 residues) through site-directed mutagenesis. Fv-antibodies against MCT-1 were screened from the autodisplayed Fv-antibody library. Two clones were screened, and the binding affinity (KD) against MCT-1 was estimated using flow cytometry. The screened Fv-antibodies were expressed as soluble fusion proteins (Fv-1 and Fv-2) and the KD for MCT-1 was estimated using the SPR biosensor. The inhibitory activity of the expressed Fv-antibodies was observed in HEK293T and Jurkat cell lines by measuring intracellular pH and lactate accumulation. The level of cell viability in HEK293T and Jurkat cell lines was decreased by the inhibitory activity of the expressed Fv-antibodies. The binding properties of the Fv-antibodies to MCT-1 were analyzed using molecular docking simulations. Overall, the results showed that the screened Fv-antibodies against MCT-1 from the Fv-antibody library had high binding affinity and inhibitory activity against MCT-1, which could be used as potential therapeutic drug candidates for the MCT-1 inhibitor.

Identification of a potent PCNA-p15-interaction inhibitor by autodisplay-based peptide library screening

Proliferating cell nuclear antigen (PCNA) is an essential factor for DNA metabolism. The influence of PCNA on DNA replication and repair, combined with the high expression rate of PCNA in various tumours renders PCNA a promising target for cancer therapy. In this context, an autodisplay-based screening method was developed to identify peptidic PCNA interaction inhibitors. A 12-mer randomized peptide library consisting of 2.54 × 106 colony-forming units was constructed and displayed at the surface of Escherichia coli BL21 (DE3) cells by autodisplay. Cells exhibiting an enhanced binding to fluorescent mScarlet-I-PCNA were enriched in four sorting rounds by flow cytometry. This led to the discovery of five peptide variants with affinity to mScarlet-I-PCNA. Among these, P3 (TCPLRWITHDHP) exhibited the highest binding signal. Subsequent flow cytometric analysis revealed a dissociation constant of 0.62 μM for PCNA-P3 interaction. Furthermore, the inhibition of PCNA interactions was investigated using p15, a PIP-box containing protein involved in DNA replication and repair. P3 inhibited the PCNA-p1551-70 interaction with a half maximal inhibitory activity of 16.2 μM, characterizing P3 as a potent inhibitor of the PCNA-p15 interaction.

Monoamine Oxidase-A (MAO-A) Inhibitors Screened from the Autodisplayed Fv-Antibody Library

Serotonin-like mimotopes were screened from the Fv-antibody library to be used as inhibitors against monoamine oxidase A (MAO-A). The Fv-antibody [corresponding to the VH region of immunoglobulin G (IgG)] consists of three complementarity-determining regions and four frame regions. The Fv-antibody library was prepared by site-directed mutagenesis of CDR3, which consists of 11 amino acid residues. Three target clones were screened from the Fv-antibody library, and the binding affinity of the screened clones to the monoclonal anti-serotonin antibody was analyzed using fluorescence-activated cell sorting. The screened Fv-antibodies were expressed as soluble proteins fused with green fluorescence protein. Additionally, the screened CDR3 regions (11 residues) of the selected Fv-antibodies were synthesized as peptides with linking amino acid residues. The binding constants (KD) of the three serotonin-like mimotopes (Fv-antibodies and peptides) were estimated using a surface plasmon resonance biosensor. The inhibitory activity (IC50) of the serotonin-like mimotopes (Fv-antibodies and peptides) was estimated separately for MAO-A and MAO-B enzymes and compared with that of conventional inhibitors. Finally, the screened serotonin-like mimotopes were used to treat a cell line (SH-SY5Y, ATCC code: CRL-2266) expressing serotonin receptors. This was done to confirm the following two aspects: (1) the binding of mimotopes to the serotonin receptors on the cell surface and (2) the inhibitory activity of mimotopes against MAO-A enzymes in the cell lysates.

Modeling the kinetics of lymph node retention and exposure of a cargo protein delivered by biotin-functionalized nanoparticles

Generation of protective immunity through vaccination arises from the adaptive immune response developed primarily in the lymph nodes drained from the immunization site. Relative to the intramuscular route, subcutaneous administration allows for direct and rapid access to the lymphatics, but accumulation of soluble protein antigens within the lymph nodes is limited. Subunit vaccines also require immune stimulating adjuvants which may not accumulate in the same lymph nodes simultaneously with antigen. Herein we report the use of biotinylated poly (lactic-co-glycolic acid) nanoparticles (bNPs) to enhance delivery of a model protein antigen to the lymphatics. bNPs provide dual functionality as adjuvant and vehicle to localize antigens with stimulated immune cells in the same draining lymph node. Using streptavidin as a model antigen, which can be loaded directly onto the bNP surface, we evaluated the kinetics of lymph node occupancy and adaptive immune responses in wildtype C57BL/6 mice. Antigen exposure in vivo was significantly improved through surface loading onto bNPs, and we developed a working kinetic model to account for the retention of both particles and antigen in draining lymph nodes. We observed enhanced T cell responses and antigen-specific B cell response in vivo when antigen was delivered on the particle surface. This work highlights the advantage of combining intrinsic adjuvant and antigen loading in a single entity, and the utility of kinetic modeling in the understanding of particle-based vaccines. STATEMENT OF SIGNIFICANCE: Development of safe and effective subunit vaccines depends on effective formulations that render optimized exposure and colocalization of antigens and adjuvants. In this work, we utilize a nanoparticle system which features self-adjuvanting properties and allows for surface loading of recombinant protein antigens. Using in vivo imaging, we demonstrated prolonged co-localization of the antigen and adjuvant particles in draining lymph nodes and provided evidence of B cell activation for up to 21 days following subcutaneous injection. A pharmacokinetic model was developed as a step towards bridging the translational gap between particulate-based vaccines and observed outcomes. The results have implications for the rational design of particle-based vaccines.

Phage-targeting bimetallic nanoplasmonic biochip functionalized with bacterial outer membranes as a biorecognition element

The use of phages-a natural predator of bacteria-has emerged as a therapeutic strategy for treating multidrug-resistant bacterial infections; thus, the isolation and detection of phages from the environment is crucial for advancing phage therapy. Herein, for the first time, we propose a nanoplasmonic-based biodetection platform for phages that utilizes bacterial outer membranes (OMs) as a biorecognition element. Conventional biosensors based on phage-bacteria interactions encounter multiple challenges due to the bacteriolytic phages and potentially toxic bacteria, resulting in instability and risk in the measurement. Therefore, instead of whole living bacteria, we employ a safe biochemical OMs fraction presenting phage-specific receptors, allowing the robust and reliable phage detection. In addition, the biochip is constructed on bimetallic nanoplasmonic islands through solid-state dewetting for synergy between Au and Ag, whereby sensitive detection of phage-OMs interactions is achieved by monitoring the absorption peak shift. For high detection performance, the nanoplasmonic chip is optimized by systematically investigating the morphological features, e.g., size and packing density of the nanoislands. Using our optimized device, phages are detected with high sensitivity (≥∼104 plaques), specificity (little cross-reactivity), and affinity (stronger binding to the host OMs than anti-bacterial antibodies), further exhibiting the cell-killing activities.

Homogeneous One-Step Immunoassay Based on Switching Peptides for Detection of the Influenza Virus

In this study, a homogeneous one-step immunoassay based on switching peptides is presented for the detection of influenza viruses A and B (Inf-A and Inf-B, respectively). The one-step immunoassay represents an immunoassay method that does not involve any washing steps, only treatment of the sample. In this method, fluorescence-labeled switching peptides quantitatively dissociate from the antigen-binding site of immunoglobulin G (IgG). In particular, the one-step immunoassay based on soluble detection antibodies with switching peptides is called a homogeneous one-step immunoassay. The immunoassay developed uses switching peptides labeled with two types of fluorescence dyes (FAM and TAMRA) and detection antibodies labeled with two types of fluorescence quenchers (TQ2 for FAM and TQ3 for TAMRA). The optimal switching peptides for the detection of Inf-A and Inf-B have been selected as L1-peptide and H2-peptide. The interactions between the four kinds of switching peptides and IgG have been analyzed using computational docking simulation and SPR biosensor. The location of labeling for the fluorescence quenchers has been determined based on the distance between the fluorescence dyes of the switching peptides and the fluorescence quenchers, calculated on the basis of the efficiency of fluorescence quenching, using the Förster equation. To demonstrate the feasibility of the one-step immunoassay, binding constants (K_D) have been calculated for detection antibodies against Inf-A and Inf-B with target antigens (Inf-A and Inf-B) and switching peptides (L1- and H2-peptides), using an isotherm model. The immunoassay has been demonstrated to be feasible using antigens as well as real samples of Inf-A and Inf-B with a critical cycle number (Ct). The immunoassay has also been compared to other commercially available rapid test kits for Inf-A and Inf-B and found to be far more sensitive for detection of Inf-A and Inf-B over the entire detection range.

Antibody-Mediated Screening of Peptide Inhibitors for Monoamine Oxidase-B (MAO-B) from an Autodisplayed FV Library

Inhibitors for monoamine oxidase-B (MAO-B) were screened from an F_V library with a randomized complementarity-determining region 3 (CDR3) region using a monoclonal antibody against dopamine. As the first step, the F_V library was expressed on the outer membrane of E. coli by site-directed mutagenesis of the randomized CDR3 region. Among the F_V library, variants with a binding affinity to monoclonal antibodies against dopamine were screened and cloned. From the comparison of the binding activity of the screened clones to a control clone with a modified F_V antibody (only with CDR1 and CDR2), the CDR3 regions of screened clones were determined to directly interact with the monoclonal antibody against dopamine. These CDR3 sequences were then synthesized as mimotopes (mimicking peptides) of dopamine. The inhibitory activity of two mimotopes against MAO-B was analyzed using HeLa cells overexpressing MAO-B, as well as using activated human astrocytes; their inhibitory activity was compared to that of a commercial inhibitor of MAO-B, selegiline. The inhibition efficiency of the two mimotopes (in comparison with selegiline) was estimated to be 67.2% and 69.4% in the HeLa cells and 64.4% and 58.0% in the human astrocytes. The gene expression pattern in astrocytes after treatment with the two mimotopes was also analyzed and compared with that in the human astrocytes treated with selegiline. Finally, the interaction between two mimotopes and MAO-B was analyzed using docking simulation, and the candidate regions of MAO-B for the interaction with each mimotope were explored through the docking simulation.

One-step immunoassay for food allergens based on screened mimotopes from autodisplayed FV-antibody library

One-step immunoassay detects a target analyte simply by mixing a sample with a reagent solution without any washing steps. Herein, we present a one-step immunoassay that uses a peptide mimicking a target analyte (mimotope). The key idea of this strategy is that the mimotopes are screened from an autodisplayed F_V-antibody library using monoclonal antibodies against target analytes. The monoclonal antibodies are bound to fluorescence-labeled mimotopes, which are quantitatively released into the solution when the target analytes are bound to the monoclonal antibodies. Thus, the target analyte is detected without any washing steps. For the mimotope screening, an F_V-antibody library was exhibited on the outer membrane of E. coli with a diversity of >10⁶ clones/library using autodisplay technology. The targeted clones were screened from the autodisplayed F_V-antibody library using magnetic beads with immobilized monoclonal antibodies against food allergens. The analysis of binding properties of a control strain with mutant F_V -antibodies composed of only CDR1 and CDR2 demonstrated that the CDR3 regions of the screened F_V-antibodies showed binding affinity to food allergens. The CDR3 regions were synthesized into peptides as mimotopes for the corresponding food allergens (mackerel, peanuts, and pig fat). One-step immunoassays for food allergens were demonstrated using mimotopes against mackerel, peanut, and pig fat without any washing steps in solution without immobilization of antibodies to a solid support.

Fluorescein and Rhodamine B-Binding Domains from Autodisplayed Fv-Antibody Library

In this study, the binding domains for fluorescent dyes were presented that could be used as synthetic peptides or fusion proteins. Fv-antibodies against two fluorescent dyes (fluorescein and rhodamine B) were screened from the Fv-antibody library, which was prepared on the outer membrane of Escherichia coli using the autodisplay technology. Two clones with binding activities to each fluorescent dye were screened separately from the library using flow cytometry. The binding activity of the screened Fv-antibodies on the outer membrane was analyzed using fluorescent imaging with the corresponding fluorescent dyes. The CDR3 regions of the screened Fv-antibodies (11 amino acid residues) were synthesized into peptides, and each peptide was analyzed for its binding activity to each fluorescent dye using fluorescence resonance energy transfer (FRET) experiments. These CDR3 regions were demonstrated to have a binding activity to each fluorescent dye when the regions were co-expressed as a fusion protein with Z-domain.