Identification of peptides that selectively bind to myoglobin by biopanning of phage displayed-peptide library

Investigation of Peptides for Molecular Recognition of C-Reactive Protein-Theoretical and Experimental Studies

We investigate the interactions between C-reactive protein (CRP) and new CRP-binding peptide materials using experimental (biological and physicochemical) methods with the support of theoretical simulations (computational modeling analysis). Three specific CRP-binding peptides (P2, P3, and P9) derived from an M13 bacteriophage have been identified using phage-display technology. The binding efficiency of the peptides exposed on phages toward the CRP protein was demonstrated via biological methods. Fibers of the selected phages/peptides interact differently due to different compositions of amino acid sequences on the exposed peptides, which was confirmed by transmission electron microscopy. Numerical and experimental studies consistently showed that the P3 peptide is the best CRP binder. A combination of theoretical and experimental methods demonstrates that identifying the best binder can be performed simply, cheaply, and fast. Such an approach has not been reported previously for peptide screening and demonstrates a new trend in science where calculations can replace or support laborious experimental techniques. Finally, the best CRP binder─the P3 peptide─was used for CRP recognition on silicate-modified indium tin oxide-coated glass electrodes. The obtained electrodes exhibit a wide range of operation (1.0-100 μg mL-1) with a detection limit (LOD = 3σ/S) of 0.34 μg mL-1. Moreover, the dissociation constant Kd of 4.2 ± 0.144 μg mL-1 (35 ± 1.2 nM) was evaluated from the change in the current. The selectivity of the obtained electrode was demonstrated in the presence of three interfering proteins. These results prove that the presented P3 peptide is a potential candidate as a receptor for CRP, which can replace specific antibodies.

Determination of the Dissociation Constant for Polyvalent Receptors Using ELISA: A Case of M13 Phages Displaying Troponin T-Specific Peptides

Phage-derived affinity peptides have become widespread thanks to their easy selection via phage display. Interactions between a target protein and its specific peptide are similar to those between antibodies and antigens. The strength of these non-covalent complexes may be described by the dissociation constant (K_d). In this paper, protein-specific peptides are exposed on the pIII protein present in the M13 bacteriophage virion with up to five copies. Therefore, one phage particle can bind from one to five ligands. Here, we discuss the dependences between phage-displayed peptides and their ligands in solution using a model system based on troponin T (TnT) binding phages. Moreover, a method of calculating K_d values from ELISA experiments was developed and is presented. The determined K_d values are in the picomolar range.

Dual synergistic response for the electrochemical detection of H1N1 virus and viral proteins using high affinity peptide receptors

Identifying alternatives to antibodies as bioreceptors to test samples feasibly is crucial for developing next-generation in vitro diagnostic methods. Here, we aimed to devise an analytical method for detecting H1N1 viral proteins (hemagglutinin [HA] and neuraminidase [NA]) as well as the complete H1N1 virus with high sensitivity and selectivity. By applying biopanning of M13 peptide libraries, high affinity peptides specific for HA or NA were successfully identified. After selection, three different synthetic peptides that incorporated gold-binding motifs were designed and chemically synthesized on the basis of the original sequence identified phage display technique with or without two repeat. Their binding interactions were characterized by enzyme-linked immunosorbent assay (ELISA), square wave voltammetry (SWV), Time of flight-secondary ion mass spectroscopy (ToF-SIMS) and X-ray photoelectron spectroscopy (XPS). The binding constants (K_d) of HA BP1, HA BP2 and NA BP1 peptides were found to be 169.72 nM, 70.02 nM and 224.49 nM for HA or NA proteins by electrochemical measurements (SWV). The single use of HA BP2 peptide enabled the detection of either H1N1 viral proteins or the actual H1N1 virus, while NA BP1 peptide exhibited lower binding for real H1N1 virus particles. Moreover, the use of both HA BP1 and BP2 as a divalent capturing reagent improved sensor performance as well as the strength of the electrochemical signal, thereby exhibiting a dual synergistic effect for the electrochemical detection of H1N1 antigens with satisfactory specificity and sensitivity (limit of detection of 1.52 PFU/mL).

The Use of Bacteriophages in Biotechnology and Recent Insights into Proteomics

Phages have certain features, such as their ability to form protein-protein interactions, that make them good candidates for use in a variety of beneficial applications, such as in human or animal health, industry, food science, food safety, and agriculture. It is essential to identify and characterize the proteins produced by particular phages in order to use these viruses in a variety of functional processes, such as bacterial detection, as vehicles for drug delivery, in vaccine development, and to combat multidrug resistant bacterial infections. Furthermore, phages can also play a major role in the design of a variety of cheap and stable sensors as well as in diagnostic assays that can either specifically identify specific compounds or detect bacteria. This article reviews recently developed phage-based techniques, such as the use of recombinant tempered phages, phage display and phage amplification-based detection. It also encompasses the application of phages as capture elements, biosensors and bioreceptors, with a special emphasis on novel bacteriophage-based mass spectrometry (MS) applications.

Phage-Based Sensors in Medicine: A Review

Bacteriophages are interesting entities on the border of biology and chemistry. In nature, they are bacteria parasites, while, after genetic manipulation, they gain new properties, e.g., selectively binding proteins. Owing to this, they may be applied as recognition elements in biosensors. Combining bacteriophages with different transducers can then result in the development of innovative sensor designs that may revolutionize bioanalytics and improve the quality of medical services. Therefore, here, we review the use of bacteriophages, or peptides from bacteriophages, as new sensing elements for the recognition of biomarkers and the construction of the highly effective diagnostics tools.

A Specific Nonenal-Binding Peptide, P4 Screened by Phage Display can Remove Trans-2-Nonenal

Trans-2-nonenal is a fatty aldehyde with a long-chain, containing nine carbons. It was known that trans-2-nonenal is a cause of the odor associated with aging, and mainly found from the ages of 40 years. Phage display was a famous laboratory technique for proteins, peptides, and DNA interaction using bacteriophages to connect proteins with the genetic information. In this study, we have carried out random phage display screening to identify specific binding peptides for trans-2-nonenal. Trans-2-nonenal was directly coated on the plate. To select the phages against trans-2-nonenal, the random phages were attached to trans-2-nonenal and selected by 1-5 panning steps. Individual DNA of phage after 5 panning was analyzed to find the specific peptide sequence against trans-2-nonenal. The affinity of positive and negative binding phages was verified by ELISA assay using M13 phage-specific antibody. Among the phages, the phage with sequence of AHKSKLHQHVMFGGG (called as P4) in the end of tail, has shown the highest response. To explore a role of the peptide selected in sequence analysis and ELISA assay, the peptide was connected to magnetic beads. The peptide-coated beads were treated within trans-2-nonenal: treatment of P4 peptide shows significant decrease of trans-2-nonenal compared to negative peptide. Based on our results, it is suggested that the peptide, which is selected by phage display, could be used for the removal of trans-2-nonenal and odor associated with aging.

High-affinity phage-displayed peptide as a recognition probe for the detection of Cry2Ad2-3

Cry2A is widely used in transgenic crops in combination with Cry1A toxins. The sensitive and robust detection of Cry2A toxin in food and the environment is necessary to monitor the safety of biopesticides. Here, we describe an approach that involves the use of phage-displayed peptide for the detection of Cry2Ad2-3-the main area of Cry2Ad2 insecticidal activity. After four rounds of panning, six positive monoclonal phage particles were obtained. Pep5 with a sequence of ACSYNHNSKCGGG displayed low cross-reactivity with other Cry toxins. The working range of detection for Cry2Ad2-3 toxin standards in the brush border membrane vesicle (BBMV)-peptide sandwich ELISA was 10-50.625 ng mL^-1 and the detection limit (LOD) was 8 ng mL^-1. Molecular insight into the interaction of pep5 with Cry2Ad2-3 was gleaned using homology modeling and docking. Molecular docking results showed that high-affinity peptide tended to dock in the groove between the two domains of Cry2Ad2-3. The interactions within the toxin-pep5 complex were due to hydrogen bond and hydrophobic interaction. Pep5 also lead us to trap the binding region. Therefore, peptides may be a cost-efficient alternative for detecting Cry toxins and studying their mechanisms.

A Phage Display-Identified Peptide Selectively Binds to Kidney Injury Molecule-1 (KIM-1) and Detects KIM-1-Overexpressing Tumors in vivo

PURPOSE

This study was carried out to identify a peptide that selectively binds to kidney injury molecule-1 (KIM-1) by screening a phage-displayed peptide library and to use the peptide for the detection of KIM-1overexpressing tumors in vivo.

MATERIALS AND METHODS

Biopanning of a phage-displayed peptide library was performed on KIM-1-coated plates. The binding of phage clones, peptides, and a peptide multimer to the KIM-1 protein and KIM-1-overexpressing and KIM-1-low expressing cells was examined by enzyme-linked immunosorbent assay, fluorometry, and flow cytometry. A biotin-peptide multimer was generated using NeutrAvidin. In vivo homing of the peptide to KIM-1-overexpressing and KIM1-low expressing tumors in mice was examined by whole-body fluorescence imaging.

RESULTS

A phage clone displaying the CNWMINKEC peptide showed higher binding affinity to KIM-1 and KIM-1-overexpressing 769-P renal tumor cells compared to other phage clones selected after biopanning. The CNWMINKEC peptide and a NeutrAvidin/biotin-CNWMINKEC multimer selectively bound to KIM-1 over albumin and to KIM-1-overexpressing 769-P cells and A549 lung tumor cells compared to KIM-1-low expressing HEK293 normal cells. Co-localization and competition assays using an anti-KIM-1 antibody demonstrated that the binding of the CNWMINKEC peptide to 769-P cells was specifically mediated by KIM-1. The CNWMINKEC peptide was not cytotoxic to cells and was stable for up to 24 hours in the presence of serum. Whole-body fluorescence imaging demonstrated selective homing of the CNWM-INKEC peptide to KIM-1-overexpressing A498 renal tumor compared to KIM1-low expressing HepG2 liver tumor in mice.

CONCLUSION

The CNWMINKEC peptide is a promising probe for in vivo imaging and detection of KIM-1‒overexpressing tumors.

Characterization of In Vivo Selected Bacteriophage for the Development of Novel Tumor-Targeting Agents with Specific Pharmacokinetics and Imaging Applications

Bacteriophage (phage) display technology is a powerful strategy for the identification of peptide-based tumor targeting agents for drug discovery. Phage selections performed in vitro often result in many phage clones/peptides with similar properties and often similar sequence. However, these phage and corresponding peptides are selected, validated, and characterized outside the complicated milieu of a living animal. Thus, there is no guarantee that peptides from in vitro selections will successfully meet the requirements of an in vivo targeting compound. In comparison, in vivo phage display selections have the distinct advantage of identifying phage clones with robust pharmacokinetics and tumor/tissue targeting ability. This capacity has allowed for the identification of peptides with specific in vivo localization and/or clearance profiles. However, in vivo phage display selections also have the potential to result in an array of phage clones with various and unknown targets and little to no sequence similarity. Given these shortcomings, we have developed methods to select phage peptide display libraries in living mice to identify phage (and corresponding synthesized peptides) with specific clearance and/or tumor-targeting propensity. Additionally, we describe the use of labeled phage clones for the efficient screening of selected phage/peptides to aid in the identification and characterization of a phage clone with an optimal and specific pharmacokinetic profile.

Phage Display-Derived Ligand for Mucosal Transcytotic Receptor GP-2 Promotes Antigen Delivery to M Cells and Induces Antigen-Specific Immune Response

Successful oral immunization depends on efficient delivery of antigens (Ags) to the mucosal immune induction site. Glycoprotein-2 (GP-2) is an integral membrane protein that is expressed specifically on M cells within follicle-associated epithelium (FAE) and serves as transcytotic receptor for luminal Ags. In this study, we selected peptide ligands against recombinant human GP-2 by screening a phage display library and evaluated their interaction with GP-2 in vitro and ex vivo. Selected peptides were conjugated to the C-terminal of enhanced green fluorescence protein (EGFP) and evaluated for their ability to induce an immune response in mice. One of our selected peptides, Gb-1, showed high binding affinity to GP-2 and, when fused to EGFP, significantly increased the uptake of EGFP by M cells compared to EGFP alone. After oral administration, the Gb1-EGFP fusion induced efficient mucosal and systemic immune responses in mice measured at the level of antigen-specific serum and fecal antibodies, cytokine secretion, and lymphocyte proliferation. Furthermore, the IgG subclasses and cytokine secretion showed that ligand Gb-1 induced a Th2-type immune response. Collectively, our findings suggest that the ligand we selected through phage library screening is capable of targeting Ags to GP-2 on M cells and can be used as an oral vaccine adjuvant.

Continuous microfluidic assortment of interactive ligands (CMAIL)

Finding an interactive ligand-receptor pair is crucial to many applications, including the development of monoclonal antibodies. Biopanning, a commonly used technique for affinity screening, involves a series of washing steps and is lengthy and tedious. Here we present an approach termed continuous microfluidic assortment of interactive ligands, or CMAIL, for the screening and sorting of antigen-binding single-chain variable antibody fragments (scFv) displayed on bacteriophages (phages). Phages carrying native negative charges on their coat proteins were electrophoresed through a hydrogel matrix functionalized with target antigens under two alternating orthogonal electric fields. During the weak horizontal electric field phase, phages were differentially swept laterally depending on their affinity for the antigen, and all phages were electrophoresed down to be collected during the strong vertical electric field phase. Phages of different affinity were spatially separated, allowing the continuous operation. More than 10⁵ CFU (colony forming unit) antigen-interacting phages were isolated with ~100% specificity from a phage library containing 3 × 10⁹ individual members within 40 minutes of sorting using CMAIL. CMAIL is rapid, sensitive, specific, and does not employ washing, elution or magnetic beads. In conclusion, we have developed an efficient and cost-effective method for isolating and sorting affinity reagents involving phage display.

Bladder tumor-targeted delivery of pro-apoptotic peptide for cancer therapy

The overall prognosis of conventional chemotherapy for the treatment of bladder cancer is poor and reduction of its systemic side effects remains an unsolved issue. Targeted therapy for bladder cancer could improve therapeutic efficacy and reduce side effects. This study investigated a hybrid peptide (named Bld-1-KLA) composed of the CSNRDARRC peptide (Bld-1), which binds to bladder tumor cells, and the d-KLAKLAKKLAKLAK (KLA) peptide, which disrupts mitochondrial membrane and induces apoptotic cell death, as a bladder cancer-targeted therapeutic agent. Bld-1-KLA selectively bound to HT1376 bladder tumor cells and efficiently internalized into the cells but not to other types of tumor and normal cell lines. Bld-1-KLA exerted cytotoxic effects selectively to HT1376 cells (LC50=41.5μM), but not to other types of cells. Pretreatment of cells with Bld-1 inhibited the binding and cytotoxicity by Bld-1-KLA in HT1376 cells. It induced apoptosis of bladder tumor cells, while Bld-1 or KLA alone showed much lesser effect on apoptosis, and was co-localized in mitochondria. Bld-1-KLA was stable up to 24h in serum. In vivo fluorescence imaging showed that homing of Bld-1-KLA in the tumor in HT1376 tumor-bearing nude mice was greater than that of the control peptide-KLA after intravenous injection. Treatment of tumor-bearing mice with Bld-1-KLA, compared to the control peptide-KLA, induced apoptosis of tumor cells and inhibited tumor growth more efficiently. No significant side effects on body weight and the liver and myeloid function were observed in mice treated with Bld-1-KLA. These results suggest that Bld-1-KLA is a promising therapeutic agent for targeted therapy of bladder cancer.

An Electrochemical Biosensor Based on a Myoglobin-specific Binding Peptide for Early Diagnosis of Acute Myocardial Infarction

In this study, a simple, highly sensitive electrochemical biosensor for myoglobin was developed using a myoglobin-specific binding peptide as a sensing probe. A peptide (Myo-3R7, CPSTLGASC, 838 Da) identified by phage display and that specifically binds to myoglobin was covalently immobilized on a gold electrode functionalized via a dithiobis(succinimidyl propionate) (DSP) self-assembled monolayer (SAM). The peptide immobilization was confirmed with fluorescence microarray scanning and cyclic voltammetry (CV). The electrochemical performance of the biosensor with respect to myoglobin was characterized by CV and differential pulse voltammetry (DPV) using Fe(CN)6(3-)/Fe(CN)6(4-) as a redox probe. We successfully detected myoglobin in a broad working range of 17.8 to 1780 ng mL(-1) with a correlation coefficient (R(2)) of 0.998. The estimated limit of detection (LOD) was fairly low, 9.8 ng mL(-1) in 30 min. The electrochemical biosensor based on a myoglobin-specific binding peptide offers sensitivity, selectivity, and rapidity, making it an attractive tool for the early detection of cardiac infarction.