Construction of Nonnatural Cysteine-Cross-Linked Phage Libraries

Phage display is a powerful technique for rapid construction and screening of peptide libraries with over 109 sequence diversity. The M13 bacteriophage genome can be edited to incorporate randomized amino acids, which will be displayed on its minor coat protein (pIII). To enable screening of nonnatural cyclic peptides on phage, the minor coat protein can be modified with a chemical cross-linker. By taking advantage of the nucleophilicity and low abundance of free cysteines on phage, a variety of cysteine cross-linkers can be installed on the pIII protein. Here, we describe the construction of a chemically modified cyclic phage library through a cysteine cross-linking reagent, 1,3-dichloroacetone (DCA).

A Simple Whole-Plasmid PCR Method to Construct High-Diversity Synthetic Phage Display Libraries

Phage display technology utilises peptide and antibody libraries with very high diversities to select ligands with specific binding properties. The production of such libraries can be labour intensive and technically challenging and whilst there are commercial sources of libraries, the exploitation of the resulting binders is constrained by ownership of the libraries. Here, a peptide library of ~ 1 × 10⁹ variants for display on gene VIII was produced alongside three VHH antibody libraries with similar diversity, where 12mer, 16mer or 21mer CDR3s were introduced into the highly stable cAbBCII10 scaffold displayed on gene III. The cloning strategy used a simple whole-plasmid PCR method and type IIS restriction enzyme assembly that facilitate the seamless insertion of diversity into any suitable phage coat protein or antibody scaffold. This method reproducibly produced 1 × 10⁹ variants from just 10 transformations and the four libraries had relatively low bias with 82 to 86% of all sequences present as single copies. The functionality of both peptide and antibody libraries were demonstrated by selection of ligands with specific binding properties by biopanning. The peptide library was used to epitope map a monoclonal antibody. The VHH libraries were pooled and used to select an antibody to recombinant human collagen type 1.

Identification of novel paraben-binding peptides using phage display

Parabens are alkyl esters of 4-hydroxybenzoic acid, which is derived from a family of synthetic esters of p-hydroxybenzoic acid. Among all the kinds of paraben, two parabens (methyl paraben, MP; and n-propyl paraben, PP) are the most generally used as preservatives in personal care products, such as cosmetics, pharmaceuticals, and food also, and are often presented together. However, a number of studies have reported that the toxicity of parabens affects the water environment, and human as well. This study utilized M13 phage display technology to provide easy, efficient, and relatively inexpensive methods to identify peptides that bind to MP and PP, respectively, to remove in wastewater. At first, biopanning was performed, to sort MP and PP specific binding phages, and three cases of experiment, including negative control (NC), which could sort unspecific binding phage, were conducted at the same time. Phage binding affinity tests were substituted by concentration reduction using antibody conjugated magnetic beads, and paraben concentration was measured by HPLC. Analysis showed that the MP concentration reduction of 38% was the highest in M4 phage, while the PP concentration reduction of 44% was the highest in P3 phage. We successfully screened two peptides specific to MP and PP, namely, MP4 and PP3, respectively; the results showed that the MP concentration reduction in MP4 was the highest at 44%, and the PP concentration reduction in PP3 was the highest at 39%, and their specificity was measured by the capture rate between target and control. In conclusion, the phage display technique shows applicability to the removal of parabens in water; furthermore, it also shows the possibility of the detection or removal of other chemicals.

Anti-tumor effect of single-chain antibody to Reg3a in colorectal cancer

BACKGROUND

Regenerating protein 3a (Reg3a) is a trophic factor that functions as a stimulus in cell proliferation and neogenesis. Previous studies showed that Reg3a is ectopically upregulated in a majority of colorectal cancers (CRC) and detectable in the serum.

METHODS

Single-chain variable fragment targeting Reg3a (scFv-Reg3a) was screened from a phage library. The bioactivity of recombinant Reg3a (rReg3a) and scFv-Reg3a were tested in LoVo and RKO cell lines using MTT, flow cytometry, wound healing and transwell analyses. Whether scFv-Reg3a inhibits tumor growth and enhances 5-fluorouracil (5-FU)-caused cell death were further examined in LoVo cell-transplanted nude BALB/c mice.

RESULTS

A scFv-Reg3a from clone C2 was obtained and its binding affinity (KD) to rReg3a was determined to be 4.44 × 10^-10. In cultured LoVo and RKO cells, rReg3a promoted but scFv-Reg3a inhibited cell proliferation, survival, migration and invasion. In LoVo cell-xenografted nude mice, administration of rReg3a accelerated tumor growth while scFv-Reg3a suppressed cell proliferation and reinforced 5-FU-induced cell death.

CONCLUSION

The newly developed scFv-Reg3a is an anti-cancer agent which is potent to suppress CRC cell proliferation and survival. The use of scFv-Reg3a could enhance the effectiveness of 5-FU-based chemotherapy in the cancerous treatment.

A novel CNS-homing peptide for targeting neuroinflammatory lesions in experimental autoimmune encephalomyelitis

Using phage peptide library screening, we identified peptide-encoding phages that selectively home to the inflamed central nervous system (CNS) of mice with experimental autoimmune encephalomyelitis (EAE), a model of human multiple sclerosis (MS). A phage peptide display library encoding cyclic 9-amino-acid random peptides was first screened ex-vivo for binding to the CNS tissue of EAE mice, followed by in vivo screening in the diseased mice. Phage insert sequences that were present at a higher frequency in the CNS of EAE mice than in the normal (control) mice were identified by DNA sequencing. One of the phages selected in this manner, denoted as MS-1, was shown to selectively recognize CNS tissue in EAE mice. Individually cloned phages with this insert preferentially homed to EAE CNS after an intravenous injection. Similarly, systemically-administered fluorescence-labeled synthetic MS-1 peptide showed selective accumulation in the spinal cord of EAE mice. We suggest that peptide MS-1 might be useful for targeted drug delivery to CNS in EAE/MS.

Magnetic bead-based semi-automated phage display panning strategy for the directed evolution of antibodies

Directed evolution is a proven approach to fine tune or modify biomolecules for various applications ranging from research to industry. The process of evolution requires methods that are capable of not only generating genetic diversity but also to distinguish the variants of desired characteristics. One method that is synonymous with directed evolution of proteins is phage display. Here, we present a protocol describing the application of magnetic nanoparticles coupled with a processor to carry out the identification of monoclonal antibodies (mAbs) from a diverse antibody library via phage display. Target antigens are coupled to magnetic nanoparticles as the solid phase for the isolation of the binding mAbs via affinity. A gradual enrichment in clones would result in increasing ELISA readouts with increasing rounds of panning. During monoclonal level analysis, positivity can be deduced with comparison to background and controls. The biopanning process can also be adopted for the directed evolution of enzymes, scaffold proteins or even peptides.

Specific determination of influenza H7N2 virus based on biotinylated single-domain antibody from a phage-displayed library

The unpredicted spread of avian influenza virus subtype H7N2 in the world is threatening animals and humans. Specific and effective diagnosis and supervision are required to control the influenza. However, the existing detecting methods are laborious, are time-consuming, and require appropriate laboratory facilities. To tackle this problem, we isolated VHH antibodies against the H7N2 avian influenza virus (AIV) and performed an enzyme-linked immunosorbent assay (ELISA) to detect the H7N2 virus. To obtain VHH antibodies with high affinity and specificity, a camel was immunized. A VHH antibody library was constructed in a phage display vector pMECS with diversity of 2.8 × 10(9). Based on phage display technology and periplasmic extraction ELISA, H7N2-specific VHH antibodies were successfully isolated. According to a pairing test, two VHH antibodies (Nb79 and Nb95) with good thermal stability and specificity can recognize different epitopes of H7N2 virus. The capture antibody (Nb79) was biotinylated in vivo, and the detection antibody (Nb95) was coupled with horseradish peroxidase (HRP). Based on biotin-streptavidin interaction, a novel sandwich immune ELISA was performed to detect H7N2. The immunoassay exhibited a linear range from 5 to 100 ng/ml. Given the above, the newly developed VHH antibody-based double sandwich ELISA (DAS-ELISA) offers an attractive alternative to other diagnostic approaches for the specific detection of H7N2 virus.

Selection of specific interactors from phage display library based on sea lamprey variable lymphocyte receptor sequences

Variable lymphocyte receptors (VLRs) are non-immunoglobulin components of adaptive immunity in jawless vertebrates. These proteins composed of leucine-rich repeat modules offer some advantages over antibodies in target binding and therefore are attractive candidates for biotechnological applications. In this paper we report the design and characterization of a phage display library based on a previously proposed dVLR scaffold containing six LRR modules [Wezner-Ptasinska et al., 2011]. Our library was designed based on a consensus approach in which the randomization scheme reflects the frequencies of amino acids naturally occurring in respective positions responsible for antigen recognition. We demonstrate general applicability of the scaffold by selecting dVLRs specific for lysozyme and S100A7 protein with KD values in the micromolar range. The dVLR library could be used as a convenient alternative to antibodies for effective isolation of high affinity binders.

Bacteriophages and their applications in the diagnosis and treatment of hepatitis B virus infection

Hepatitis B virus (HBV) infection is a major global health challenge leading to serious disorders such as cirrhosis and hepatocellular carcinoma. Currently, there exist various diagnostic and therapeutic approaches for HBV infection. However, prevalence and hazardous effects of chronic viral infection heighten the need to develop novel methodologies for the detection and treatment of this infection. Bacteriophages, viruses that specifically infect bacterial cells, with a long-established tradition in molecular biology and biotechnology have recently been introduced as novel tools for the prevention, diagnosis and treatment of HBV infection. Bacteriophages, due to tremendous genetic flexibility, represent potential to undergo a huge variety of surface modifications. This property has been the rationale behind introduction of phage display concept. This powerful approach, together with combinatorial chemistry, has shaped the concept of phage display libraries with diverse applications for the detection and therapy of HBV infection. This review aims to offer an insightful overview of the potential of bacteriophages in the development of helpful prophylactic (vaccine design), diagnostic and therapeutic strategies for HBV infection thereby providing new perspectives to the growing field of bacteriophage researches directing towards HBV infection.

In vivo phage display--a discovery tool in molecular biomedicine

In vivo phage display is a high-throughput method for identifying target ligands specific for different vascular beds. Targeting is possible due to the heterogeneous expression of receptors and other antigens in a particular vascular bed. Such expression is additionally influenced by the physiological or pathological status of the vasculature. In vivo phage display represents a technique that is usable in both, vascular mapping and targeted drug development. In this review, several important methodological aspects of in vivo phage display experiments are discussed. These include choosing an appropriate phage library, an appropriate animal model and the route of phage library administration. In addition, peptides or antibodies identified by in vivo phage display homing to specific types of vascular beds, including the altered vasculature present in several types of diseases are summarized. Still, confirmation in independent experiments and reproduction of identified sequences are needed for enhancing the clinical applicability of in vivo phage display research.

Affinity peptide developed by phage display selection for targeting gastric cancer

AIM: To develop an affinity peptide that binds to gastric cancer used for the detection of early gastric cancer.

METHODS: A peptide screen was performed by biopanning the PhD-12 phage display library, clearing non-specific binders against tumor-adjacent normal appearing gastric mucosa and obtaining selective binding against freshly harvested gastric cancer tissues. Tumor-targeted binding of selected peptides was confirmed by bound phage counts, enzyme-linked immunosorbent assay, competitive inhibition, fluorescence microscopy and semi-quantitative analysis on immunohistochemistry using different types of cancer tissues.

RESULTS: Approximately 92.8% of the non-specific phage clones were subtracted from the original phage library after two rounds of biopanning against normal- appearing gastric mucosa. After the third round of positive screening, the peptide sequence AADNAKTKSFPV (AAD) appeared in 25% (12/48) of the analyzed phages. For the control peptide, these values were 6.8 ± 2.3, 5.1 ± 1.7, 3.5 ± 2.1, 4.6 ± 1.9 and 1.1 ± 0.5, respectively. The values for AAD peptide were statistically significant (P < 0.01) for gastric cancer as compared with other histological classifications and control peptide.

CONCLUSION: A novel peptide is discovered to have a specific binding activity to gastric cancer, and can be used to distinguish neoplastic from normal gastric mucosa, demonstrating the potential for early cancer detection on endoscopy.