A fast and efficient procedure to produce scFvs specific for large macromolecular complexes

Isolation of phage-antibodies against Eimeria species that infect chickens

Eimeria is one of the most economically important pathogens in poultry production. Diagnosis of infection has the potential to inform treatment and prevention strategies. Here, phage display technology was used to isolate single chain antibodies (scFvs) that had a broad specificity against oocysts from the seven pathogenic species of Eimeria found in poultry. Three such scFvs, representing 2 scFv HCDR3 motifs, were isolated by random picks of clones isolated after five rounds of iterative enrichment (panning) of phage against the seven Eimeria species. Phage-antibody binding to Eimeria oocysts was also interrogated using next generation sequencing of the HCDR3 region of scFv genes contained with phage particles. This analysis demonstrated that the most abundant scFv found after 5 rounds of panning accounted for over >90 % of scFvs. Furthermore, the three scFvs isolated from random picks of clones were the only antibodies that were enriched through each round of panning. They were also seen to be enriched through the stages of phage panning that included binding to the Eimeria oocysts (selection phase) and to be selected against during the stages that consisted solely of phage propagation (growth only phase). The NGS data was further analysed to identify an additional scFv that demonstrated specific enrichment against 3 Eimeria species at the third round of panning and had the same pattern of enrichment during the selection and growth phases of panning. Rescue and analysis of this phage-scFv demonstrated a binder with broad specificity for Eimeria species. The four antibodies with broad specificity detected all seven Eimeria species in immunoassays. The binding of one such scFv that recognised all species was further validated by fluorescent microscopy.

Revolutionizing snakebite care with novel antivenoms: Breakthroughs and barriers

Snakebite envenoming (SBE) is a global public health concern, primarily due to the lack of effective antivenom for treating snakebites inflicted by medically significant venomous snakes prevalent across various geographic locations. The rising demand for safe, cost-effective, and potent snakebite treatments highlights the urgent need to develop alternative therapeutics targeting relevant toxins. This development could provide promising discoveries to create novel recombinant solutions, leveraging human monoclonal antibodies, synthetic peptides and nanobodies. Such technologies as recombinant DNA, peptide and epitope mapping phage display etc) have the potential to exceed the traditional use of equine polyclonal antibodies, which have long been used in antivenom production. Recombinant antivenom can be engineered to target certain toxins that play a critical role in snakebite pathology. This approach has the potential to produce antivenom with improved efficacy and safety profiles. However, there are limitations and challenges associated with these emerging technologies. Therefore, identifying the limitations is critical for overcoming the associated challenges and optimizing the development of recombinant antivenoms. This review is aimed at presenting a thorough overview of diverse technologies used in the development of recombinant antivenom, emphasizing their limitations and offering insights into prospects for advancing recombinant antivenoms.

Parallel evaluation of cell‑based phage display panning strategies: Optimized selection and depletion steps result in AML blast‑binding consensus antibodies

Phage display technology (PD) is a powerful technique for the generation of tumor-targeting antibodies. However, there are a number of different selection methods established in different laboratories around the world. Cell-based PD panning methods using primary tumor cells are particularly heterogeneous between laboratories, which can lead to inconsistent results. Therefore, the present study evaluated different cell-based PD selection methods regarding their potential to generate acute myeloid leukemia (AML) blast-binding antibodies. In addition to this evaluation, the present study improved the PD procedure by optimizing selection as well as depletion strategies. To the best of our knowledge, the current study demonstrated for the first time that antigen diversity during the depletion step is of importance for the enrichment of tumor-targeting phage antibodies. It is demonstrated that medium levels of depletion antigen diversity led to the most promising antibody candidates. In addition, it was determined that purification of blast cells from patients with AML by immunomagnetic separation ameliorated the selection of AML-binding phages during panning. Furthermore, suggesting a common design-related mechanism using a ‘single-pot’ PD library, such as the well-known Tomlinson single-chain fragment variable (scFv) library, the present study identified specific binding consensus phage particles in independent panning procedures. By means of these optimized strategies, four promising AML blast-binding phage particles were isolated and soluble scFv-Fc (scFv cloned to a fragment crystallizable of an IgG2a mouse antibody) fusion proteins were produced. These scFv-Fc antibodies bound the surface of AML blasts and were successfully internalized into their cytoplasm, indicating that they are potential immunoconjugate candidates for AML immunotherapy.

A rapid novel strategy for screening of antibody phage libraries for production, purification, and functional characterization of amber stop codons containing single-chain antibody fragments

Phage display antibody (PDA) libraries, allows the rapid isolation and characterization of high specificity monoclonal antibodies for therapeutic and diagnostic applications. However, selection of positive binding clones from synthetic and semi-synthetic libraries has an inherent bias towards clones containing randomly generated amber stop codons, complicating the identification of high affinity binding antibodies. We screened Tomlinson I and J library against receptor binding domain (RBD) of SARS CoV2, eight clones which showed positive binding in phage ELISA, contained one or more amber stop codons in their single-chain antibody fragment (scFv) gene sequences. The presence of amber stop codons within the antibody sequence causes the premature termination of soluble form of scFv expression in nonsuppressor Escherichia coli strain. In the present study, we have used a novel strategy that allows soluble expression of scFvs having amber stop codon in their gene sequences (without phage PIII protein fusion), in the suppressor strain. This strategy of introduction of Ochre (TAA) codon at the junction of scFv and PIII gene, speeds up the initial screening process which is critical for selecting the right scFvs for further studies. Present strategy leads to the identification of a scFv, B8 that binds specifically with nanomolar affinity toward SARS CoV 2 RBD, which otherwise lost in terms of traditional methodology.

Phage antibody library screening for the selection of novel high-affinity human single-chain variable fragment against gastrin receptor: an in silico and in vitro study

BACKGROUND

As a membrane G protein coupled receptors (GPCRs) family, gastrin/cholecystokinin-2 receptor (CCK2R) plays a key role in the initiation and development of gastric cancer.

OBJECTIVES

Targeting CCK2R by immunotherapeutics such as single-chain variable fragments (scFvs) may provide an effective treatment modality against gastric cancer. Thus, the main objective of this study was to isolate scFvs specific to CCK2R.

METHODS

To isolate scFvs specific to the CCK2R, we capitalized on a semi-synthetic diverse phage antibody library (PAL) and a solution-phase biopanning process. The library was panned against a biotinylated peptide of the second extracellular loop (ECL2) of CCK2R. After four rounds of biopanning, the selected soluble scFv clones were screened by enzyme-linked immunosorbent assay (ELISA) and examined for specific binding to the peptide. The selected scFvs were purified using immobilized metal affinity chromatography (IMAC). The binding affinity and specificity of the scFvs were examined by the surface plasmon resonance (SPR), immunoblotting and flow cytometry assays and molecular docking using ZDOCK v3.0.2.

RESULTS

Ten different scFvs were isolated, which displayed binding affinity ranging from 0.68 to 8.0 (nM). Immunoblotting and molecular docking analysis revealed that eight scFvs were able to detect the denatured form of CCK2R protein. Of the isolated scFvs, two scFvs showed high-binding affinity to the human gastric adenocarcinoma AGS cells.

CONCLUSIONS

Based on our findings, a couple of the selected scFvs showed markedly high-binding affinity to immobilized CCK2R peptide and CCK2R-overexpressing AGS cells. Therefore, these scFvs are proposed to serve as targeting and/or treatment agents in the diagnosis and immunotherapy of CCK2R-positive tumors. Graphical abstract ᅟ.

A gold nanoparticle-single-chain fragment variable antibody as an immunoprobe for rapid detection of morphine by dipstick

Gold nanoparticle (AuNP)-based optical assays are of significant interest since the molecular phenomenon can be examined easily with change in the color of AuNPs. Herein, we report the development of a dipstick using a AuNP-labeled single-chain fragment variable (scFv) antibody for the detection of morphine. The scFv antibodies for morphine were developed using phage display-based antibody library. Immunoglobulin variable regions of heavy (V H)- and light (V L)-chain genes were connected via a glycine-serine linker isolated from murine immune repertoire and cloned into the expression vector pIT2. The scFv was produced in Escherichia coli HB2151, yielding a functional protein with a molecular weight of approximately 32 kDa. The morphine scFv was labeled with gold nanoparticles and used as an optical immunoprobe in a dipstick. The competitive dipstick assay characterized the ability of the scFv antibody to recognize free morphine. The detection range was 1-1000 ng mL-1 with a limit of detection (LOD) of 5 ng mL-1 under optimal conditions, and the IC50 value was 14 ng mL-1 for morphine. The developed optical dipstick kit of scFv antibody was capable of specifically binding to free morphine and its analogs in a solution in less than 5 min and could be useful for on-site screening of a real sample in blood, urine, and saliva.

Pitfalls to avoid when using phage display for snake toxins

Antivenoms against bites and stings from snakes, spiders, and scorpions are associated with immunological side effects and high cost of production, since these therapies are still derived from the serum of hyper-immunized production animals. Biotechnological innovations within envenoming therapies are thus warranted, and phage display technology may be a promising avenue for bringing antivenoms into the modern era of biologics. Although phage display technology represents a robust and high-throughput approach for the discovery of antibody-based antitoxins, several pitfalls may present themselves when animal toxins are used as targets for phage display selection. Here, we report selected critical challenges from our own phage display experiments associated with biotinylation of antigens, clone picking, and the presence of amber codons within antibody fragment structures in some phage display libraries. These challenges may be detrimental to the outcome of phage display experiments, and we aim to help other researchers avoiding these pitfalls by presenting their solutions.

Isolation of soluble scFv antibody fragments specific for small biomarker molecule, L-Carnitine, using phage display

Isolation of single chain antibody fragment (scFv) clones from naïve Tomlinson I+J phage display libraries that specifically bind a small biomarker molecule, L-Carnitine, was performed using iterative affinity selection procedures. L-Carnitine has been described as a conditionally essential nutrient for humans. Abnormally high concentrations of L-Carnitine in urine are related to many health disorders including diabetes mellitus type 2 and lung cancer. ELISA-based affinity characterization results indicate that selectants preferentially bind to L-Carnitine in the presence of key bioselecting component materials and closely related L-Carnitine derivatives. In addition, the affinity results were confirmed using biophysical fluorescence quenching for tyrosine residues in the V segment. Small-scale production of the soluble fragment yielded 1.3mg/L using immunopure-immobilized protein A affinity column. Circular Dichroism data revealed that the antibody fragment (Ab) represents a folded protein that mainly consists of β-sheets. These novel antibody fragments may find utility as molecular affinity interface receptors in various electrochemical biosensor platforms to provide specific L-Carnitine binding capability with potential applications in metabolomic devices for companion diagnostics and personalized medicine applications. It may also be used in any other biomedical application where detection of the L-Carnitine level is important.

Selection of potential therapeutic human single-chain Fv antibodies against cholecystokinin-B/gastrin receptor by phage display technology

BACKGROUND AND OBJECTIVE

Gastric/gastrointestinal cancers are associated with high mortality worldwide. G-protein coupled receptor (GPCR) superfamily members such as gastrin/cholecystokinin-B receptor (CCK-BR) are involved in progression of gastric tumors, thus CCK-BR is considered as a potential target for immunotherapy. However, production of functional monoclonal antibodies (mAbs) against GPCR seems to be very challenging, in part due to its integration in cell membranes and inaccessibility for selection. To tackle this problem, we implemented phage display technology and a solution-phase biopanning (SPB) scheme for production of mAbs specific to the native conformation of CCK-BR.

METHODS

To perform the SPB process, we utilized a synthetic biotinylated peptide corresponding to the second extracellular loop (ECL2) of CCK-BR and a semi-synthetic phage antibody library. After enzyme-linked immunosorbent assay (ELISA) screening, the CCK-BR specificity of the selected single-chain variable fragments (scFvs) were further examined using immunoblotting, whole-cell ELISA, and flow cytometry assays.

RESULTS

After performing four rounds of selection, we identified nine antibody clones which showed positive reactivity with the CCK-BR peptide in an ELISA assay. Of these, eight clones were unique scFv antibodies and one was a V(L) single domain antibody. Specificity analysis of the selected scFvs revealed that five of the selected scFvs recognized a denatured form of CCK-BR, while the majority of the selected scFvs were able to recognize the native conformation of CCK-BR on the surface of human gastric adenocarcinoma cells and cervical carcinoma HeLa cells.

CONCLUSION

For the first time, we report on the establishment of a diverse panel of scFv antibody fragments that are specific to the native conformation of CCK-BR. Based on these results, we suggest the selected scFv antibody fragments as potential agents for diagnosis, imaging, targeting, and/or immunotherapy of cancers that overexpress CCK-BR.

Latex agglutination test based on single-chain Fv recombinant antibody fragment

Recombinant antibodies have been proposed as invaluable tools for various therapeutic and diagnostic purposes. Here, we describe the development of a novel latex agglutination test (LAT) using single-chain Fv recombinant antibody fragment for the detection of K99(+) enterotoxigenic Escherichia coli strains. For the production of a single-chain Fv antibody fragment (scFv) against the major colonization factor (FanC) of K99 antigen, the scFv gene was integrated into a bacterial expression vector under the control of T7 promoter. After high-level expression of soluble scFv (approximately 50 mg/l) in flask cultivation of E. coli DE3 and purification, scFv was immobilized on different latex particles, and then, these sensitized beads were used in LAT. Results obtained with our latex reagents revealed that the recombinant antibody-coated particles were able to give a good agglutination signal with purified antigen, intact cells displaying this protein and clinical specimens. The strength of agglutination of scFv-coated beads for antigen was comparable to that of polyclonal anti-K99-coated particles. However, the assay proved to be simple and rapid, similar to conventional LATs, and owing to more convenient and economical production of recombinant antibodies, they can be considered as a useful reagent for replacing monoclonal antibodies in LATs.

Molecular considerations for development of phage antibody libraries

Nowadays, phage display libraries are used as robust tools for discovery and evolution of peptide/protein based drugs as well as targeting molecules, in particular monoclonal antibodies (mAbs) and its fragments (i.e., scFvs, Fabs, or bivalent F(ab')₂). Phage display technology, as a molecular diversity approach, enables selection of antibody fragments (e.g., scFv/Fab) with high affinity, specificity and effector functions against various targets. However, such selection process itself is largely dependent upon various molecular factors such as methods for construction of phage library, phage/phagemid vectors, helper phage, host cells and biopanning processes. The current review article provides important molecular considerations for successful development of phage antibody libraries that may be used as a platform for translation of antibody fragments into viable diagnostic/therapeutic reagents.

Improvement of the crystallizability and expression of an RNA crystallization chaperone

Crystallizing RNA has been an imperative and challenging task in the world of RNA research. Assistive methods such as chaperone-assisted RNA crystallography (CARC), employing monoclonal antibody fragments (Fabs) as crystallization chaperones have enabled us to obtain RNA crystal structures by forming crystal contacts and providing initial phasing information. Despite the early successes, the crystallization of large RNA-Fab complex remains a challenge in practice. The possible reason for this difficulty is that the Fab scaffold has not been optimized for crystallization in complex with RNA. Here, we have used the surface entropy reduction (SER) technique for the optimization of ΔC209 P4-P6/Fab2 model system. Protruding lysine and glutamate residues were mutated to a set of alanines or serines to construct Fab2SMA or Fab2SMS. Expression with the shake flask approach was optimized to allow large scale production for crystallization. Crystal screening shows that significantly higher crystal-forming ratio was observed for the mutant complexes. As the chosen SER residues are far away from the CDR regions of the Fab, the same set of mutations can now be directly applied to other Fabs binding to a variety of ribozymes and riboswitches to improve the crystallizability of Fab-RNA complex.

Isolation of scFv fragments specific for monokine induced by interferon-gamma (MIG) using phage display

Iterative affinity selection procedures were used to isolate a number of single chain Fv (scFv) antibody fragment clones from naïve Tomlinson I+J phage display libraries that specifically recognize and bind a chemokine, monokine induced by interferon-gamma (MIG/CXCL9). MIG is an important transplant rejection/biology chemokine protein. ELISA-based affinity characterization results indicate that selectants preferentially bind to MIG in the presence of key biopanning component materials and closely related chemokine proteins. These novel antibody fragments may find utility as molecular affinity interface receptors in various electrochemical biosensor platforms to provide specific MIG binding capability with potential applications in transplant rejection monitoring, and other biomedical applications where detection of MIG level is important.

The selection of single-chain Fv antibody fragments specific to Bhlp 29.7 protein of Brachyspira hyodysenteriae

Single-chain antibodies (scFv) specific to Brachyspira hyodysenteriae were isolated from a phagemid library. Recombinant Bhlp 29.7 protein was used for scFv selection and individual clones were tested by ELISA and immunofluorescent test; four unique clones were isolated. One of selected clones was able to bind specifically B. hyodysenteriae in ELISA and immunofluorescence test. This is the first report of species-specific recombinant antibodies against B. hyodysenteriae.

SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting

The signal recognition particle (SRP) cotranslationally targets proteins to cell membranes by coordinated binding and release of ribosome-associated nascent polypeptides and a membrane-associated SRP receptor. GTP uptake and hydrolysis by the SRP-receptor complex govern this targeting cycle. Because no GTPase-activating proteins (GAPs) are known for the SRP and SRP receptor GTPases, however, it has been unclear whether and how GTP hydrolysis is stimulated during protein trafficking in vivo. Using both biochemical and genetic experiments, we show here that SRP RNA enhances GTPase activity of the SRP-receptor complex above a critical threshold required for cell viability. Furthermore, this stimulation is a property of the SRP RNA tetraloop. SRP RNA tetraloop mutants that confer defective growth phenotypes can assemble into SRP-receptor complexes, but fail to stimulate GTP hydrolysis in these complexes in vitro. Tethered hydroxyl radical probing data reveal that specific positioning of the RNA tetraloop within the SRP-receptor complex is required to stimulate GTPase activity to a level sufficient to support cell growth. These results explain why no external GAP is needed and why the phylogenetically conserved SRP RNA tetraloop is required in vivo.