Screening of peptide ligands that bind to the Fc region of IgG using peptide array and its application to affinity purification of antibody

Zirconium dioxide as electrochemiluminescence emitter for D-dimer determination based on dual-quenching sensing strategy

The ECL emission of simple and stable zirconium dioxide nanomaterials has always been a blank slate in the ECL sensors field. In this work, zirconium dioxide (ZrO₂)-titanium dioxide (TiO₂)-gold nanoparticle (AuNPs) composite (ZT-Au), a novel self-enhanced ECL emitter, was introduced the system of dual-quenching ECL immunosensor. The anodic luminescence of ZrO₂ in the system of tripropylamine (TPrA) as a co-reagent was first reported and explored. Meanwhile, TiO₂ was designed into the ECL scheme as a co-reaction accelerator to form the ZrO₂/TPrA/TiO₂ ternary system, which can efficiently amplify the ECL signal of the emitter. In addition, cuprous oxide-triaminophenol (Cu₂O-APF) as the quencher was devoted to the dual-quenching sensing strategy. The dual-quenching mechanism that effectively boosted the immunosensor sensitivity was adequately investigated and conjectured in this paper. The sensing model based on the luminophor ZT-Au and the quencher Cu₂O-APF was utilized for the detection of D-dimer, a reliable marker for the diagnosis and evaluation of thrombotic diseases. The short peptide ligands NARKFYKGC (NFC) with efficient biological affinity were used to site-directionally capture antibodies for adequately protecting the activity of antigen binding sites during the construction of the immunosensor. The implemented immunosensor was equipped with a broad linear range of 0.01-500 ng/mL and a low detection limit of 3.6 pg/mL. The original methodology opens up the field of vision for the detection of additional biomarkers.

IgG Fc Affinity Ligands and Their Applications in Antibody-Involved Drug Delivery: A Brief Review

Antibodies are not only an important class of biotherapeutic drugs, but also are targeting moieties for achieving active targeting drug delivery. Meanwhile, the rapidly increasing application of antibodies and Fc-fusion proteins has inspired the emerging development of downstream processing technologies. Thus, IgG Fc affinity ligands have come into being and have been widely exploited in antibody purification strategies. Given the high binding affinity and specificity to IgGs, binding stability in physiological medium conditions, and favorable toxicity and immunogenicity profiles, Fc affinity ligands are gradually applied to antibody delivery, non-covalent antibody-drug conjugates or antibody-mediated active-targeted drug delivery systems. In this review, we will briefly introduce IgG affinity ligands that are widely used at present and summarize their diverse applications in the field of antibody-involved drug delivery. The challenges and outlook of these systems are also discussed.

Machine Learning Model for Biomimetic Chromatography Peptide Ligands

Purification is an essential part of antibody production, which are important therapeutic biomolecules. Common methods of antibody purification rely on affinity chromatography (AC), wherein whole proteins are oftentimes used as ligands to catch the antibodies to be purified. While AC has been successful in purifying antibodies, it is associated with multiple challenges such as high cost and low stability, among others. A promising alternative is using short peptide sequences in place of whole proteins as the stationary phase for the chromatographic separation of the antibodies. In an effort to accelerate the discovery and development of short peptides for biomimetic chromatography, this study reports the creation of a machine learning classification which was trained and tested on 480 tetrapeptides. The optimized logistic regression model uses Cruciani properties as the input variables and can categorize peptides into one of two classes based on their binding affinity with immunoglobulin G (IgG). The externally validated model demonstrates satisfactory predictive performance and excellent discrimination as demonstrated by performance metrics such as AUC = 0.874, Balanced Accuracy = 0.874, F1 = 0.871, Precision = 0.884, and Recall = 0.859. Apart from this, the classifier has also provided valuable insights into important variables that influence the classification, such as electrostatic and hydrophobic interactions. Overall, the classifier can be regarded as a welcome development for biomimetic chromatography and is the first study that aims to integrate machine learning in the biomimetic chromatography peptide development process.

Highly Efficient PTCA/Co3O4/CuO/S2O82- Ternary Electrochemiluminescence System Combined with a Portable Chip for Bioanalysis

Herein, we reported an efficient electrochemiluminescence (ECL) biosensor chip for sensitive detection of neuron-specific enolase (NSE). First, 3,4,9,10-perylenetetracarboxylic acid with good luminescence characteristics was used as a luminophore to obtain a stable ECL signal. Subsequently, hollow porous Co₃O₄/CuO concave polyhedron nanocages (CPNCs) were designed as co-reaction promoters to amplify the luminescence signals for highly sensitive trace detection of NSE. In brief, the rapid cyclic conversion of Co³⁺/Co²⁺ and Cu²⁺/Cu⁺ redox pairs could continuously catalyze the reduction of persulfate (S₂O₈^2-), thus providing a large number of essential active intermediates (SO₄^•-) for ECL emission. Meanwhile, the unique structure of Co₃O₄/CuO CPNCs possessed a large specific surface area, which greatly improved its catalytic efficiency. Third, NKFRGKYKC was developed as an affinity ligand for specific antibody fixation, which improved incubation efficiency and protected bioactivity of antibodies. Finally, we independently designed a microchip and applied it for ECL detection to improve the practical application ability of the sensor. The developed biosensor exhibited good sensitivity with a wide linear range (10 fg/mL to 100 ng/mL) and a low detection limit (3.42 fg/mL), which played an active role in the clinical application of sensing analysis.

Peptide-Modified Surfaces for Binding Carbamylated Proteins from Plasma

Carbamylation of blood proteins is a common post-translational modification that occurs upon kidney dysfunction that is strongly associated with deleterious outcomes for patients treated using hemodialysis. In this study, we focused on the removal of two representative carbamylated plasma proteins, carbamylated albumin (cHSA) and fibrinogen (cFgn), through adsorption onto a surface functionalized with a specific peptide (cH2p1). Surfaces modified with poly(hydroxyethyl methacrylate) (p(HEMA)) were prepared using surface-initiated atom transfer radical polymerization (SI-ATRP) techniques and functionalized with cH2p1. cH2p1-functionalized surfaces showed selective binding toward cHSA and cFgn, compared to their native protein form, with NH-cH2p1 of superior selectivity than CO-cH2p1. The adsorption capacity of carbamylated protein on NH-cH2p1 was maintained in diluted plasma, and ultralow adsorption of native Fgn was observed. Similar to unmodified p(HEMA) surfaces, NH-cH2p1 showed a low platelet adhesion and activation, suggesting that the designed surface does not adversely affect platelets.

Peptide Affinity Chromatography Applied to Therapeutic Antibodies Purification

The interest in therapeutic monoclonal antibodies (mAbs) has significantly grown in the pharmaceutical industry, exceeding 100 FDA mAbs approved. Although the upstream processing of their industrial production has been significantly improved in the last years, the downstream processing still depends on immobilized protein A affinity chromatography. The high cost, low capacity and short half-life of immobilized protein A chromatography matrices, encouraged the design of alternative short-peptide ligands for mAb purification. Most of these peptides have been obtained by screening combinatorial peptide libraries. These low-cost ligands can be easily produced by solid-phase peptide synthesis and can be immobilized on chromatographic supports, thus obtaining matrices with high capacity and selectivity. Furthermore, matrices with immobilized peptide ligands have longer half-life than those with protein A due to the higher stability of the peptides. In this review the design and synthesis of peptide ligands, their immobilization on chromatographic supports and the evaluation of the affinity supports for their application in mAb purification is described.

Peptide-Based Electrochemiluminescence Biosensors Using Silver Nanoclusters as Signal Probes and Pd-Cu2O Hybrid Nanoconcaves as Coreactant Promoters for Immunoassays

Metal nanoclusters (NCs) possess high light stability and biocompatibility because of their unique quantum size effect, which has gradually become a new type of electrochemiluminescence (ECL) nanomaterial for immunoassays. However, the luminescence efficiency of metal NCs is too low to meet the needs of trace analysis, which limits its application. Herein, Ag NCs served as signal probes and Pd-Cu₂O hybrid nanoconcaves served as coreaction promoters, developing a highly efficient peptide-based biosensor for neuron-specific enolase (NSE) detection. Utilizing the reversible cycle of Cu⁺/Cu²⁺ and the reduction characteristics of Pd NPs, Pd-Cu₂O greatly accelerates the reduction of S₂O₈^2-. Meanwhile, Pd-Cu₂O has good hydrogen evolution activity, which promotes the generation of oxygen by improving the redox efficiency of the overall reaction, thus increasing the yield of active intermediates (OH^•) to promote the reduction of S₂O₈^2-. Specially, this is an effective attempt to use the hydrogen evolution reaction (HER) to accelerate the ECL emission of the S₂O₈^2- system. In addition, a short peptide ligand (NARKFYKGC, NFC) was developed to implement the targeted immobilization of antibodies, which can specifically bind to the Fc fragment of antibodies, thereby avoiding the occupation of the antigen binding site (Fab fragment). The introduction of NFC not only improves the binding efficiency of antibodies but also protects its bioactivity, thus significantly improving the sensitivity of the biosensor. Based on these strategies, the proposed biosensor provides a new perspective for the applications of metal NCs in ECL systems.

Development of histidine-tagged cyclic peptide functionalized monolithic material for the affinity purification of antibodies in biological matrices

The rapidly increasing applications of monoclonal antibodies (mAbs) in therapy have necessitated the development of mAb production and purification technologies for both academic and industrial usage. Herein, a histidine-tagged cyclic peptide (HHHHHHGSGSGSDC*AWHLGELVWC*T, the disulfide-bonded cysteines of which are indicated by asterisks, named HT25-cyclopeptide) functionalized monolithic material was developed by the metal ion chelation-based approach. The resulting material possessed suitable affinity and peptide ligand density (13.8 mg peptide ligand per mL of material), good porosity (67.1 %), acceptable specific surface area (52.95 m²/g), and lots of macropores (4.13 μm). Moreover, excellent antibody-specific selectivity, comparable or even better binding capacity (for dried material, maximum static binding capacity and dynamic binding capacity are about 119.3 mg/g and 17.05 mg/g, respectively) for antibody compared to previously developed affinity materials, acceptable resistance to trypsin digestion, and negligible nonspecific protein adsorption, were also achieved on this novel monolithic material. Compared with the corresponding cyclic peptide-based sepharose material, milder elution conditions were employed for the HT25-cyclopeptide-based monolithic material, which could effectively prevent the aggregation and denaturation of the enriched antibodies. This novel material was then successfully applied to the affinity enrichment and purification of mAbs (including infliximab and rituximab) in different cell culture media or IgG in human serum.

Surface grafting of Fc-binding peptides as a simple platform to immobilize and identify antibodies that selectively capture circulating endothelial progenitor cells

Antibody surface immobilization is a promising strategy to capture cells of interest from circulating fluids in vitro and in vivo. An application of particular interest in vascular interventions is to capture endothelial progenitor cells (EPCs) on the surface of stents to accelerate endothelialization. The clinical impact of EPC capture stents has been limited by the lack of efficient selective cell capture. Here, we describe a simple method to immobilize a variety of immunoglobulin G antibodies through their fragment crystallizable (Fc) regions via surface-conjugated RRGW peptides for cell capture applications. As an EPC capture model, peripheral blood endothelial colony-forming cells suspended in cell culture medium with up to 70% serum were captured by immobilized anti-CD144, anti-CD34 or anti-CD309 antibodies under laminar flow. The endothelial colony-forming cells were successfully enriched from a mixture with peripheral blood mononuclear cells using surfaces with anti-CD309 but not anti-CD45. This antibody immobilization approach holds great promise to engineer vascular biomaterials with improved EPC capture potential. The ease of immobilizing different antibodies using the same Fc-binding peptide surface grafting chemistry renders this platform suitable to screen antibodies that maximize cell capture efficiency and selectivity.

Screening and characterisation of CdTe/CdS quantum dot-binding peptides for material surface functionalisation

Quantum dots (QDs) are promising nanomaterials due to their unique photophysical properties. For them to be useful in biological applications, the particle surface generally needs to be conjugated to biological molecules, such as antibodies. In this study, we screened CdTe/CdS QD-binding peptides from a phage display library as linkers for simple and bio-friendly QD modification. Among five QD-binding peptide candidates, a series of truncated peptides designed from two high-affinity peptides were subjected to an array-based binding assay with QDs to assess their functional core sequences and characteristics. Linking these isolated, shortened peptides (PWSLNR and SGVYK) with an antibody-binding peptide (NKFRGKYK) created dual-functional peptides that are capable of QD surface functionalisation by antibodies. Consequently, the dual-functional peptides could mediate anti-CD9 antibody functionalisation onto CdTe/CdS QD surface; CD9 protein imaging of cancer cells was also demonstrated. Our proposed peptides offer an effective vehicle for QD surface functionalisation in biological applications.

Rational design of affinity ligands for bioseparation

Affinity adsorbents have been the cornerstone in protein purification. The selective nature of the molecular recognition interactions established between an affinity ligands and its target provide the basis for efficient capture and isolation of proteins. The plethora of affinity adsorbents available in the market reflects the importance of affinity chromatography in the bioseparation industry. Ligand discovery relies on the implementation of rational design techniques, which provides the foundation for the engineering of novel affinity ligands. The main goal for the design of affinity ligands is to discover or improve functionality, such as increased stability or selectivity. However, the methodologies must adapt to the current needs, namely to the number and diversity of biologicals being developed, and the availability of new tools for big data analysis and artificial intelligence. In this review, we offer an overview on the development of affinity ligands for bioseparation, including the evolution of rational design techniques, dating back to the years of early discovery up to the current and future trends in the field.

Thermodynamic and conformational analysis of the interaction between antibody binding proteins and IgG

Studying interaction of IgG with bacterial proteins such as proA (Protein A) and proG is essential for development in the areas of drug discovery and biotechnology. Some solution studies in the past have hinted at the possibility of variable binding ratios for IgG with proA and proG. Since earlier crystallographic studies focussed mostly on monomeric complexes, the knowledge about the binding interfaces and protein conformational changes involved in multimeric complexes is scarce. In this paper, we observed that single proA molecule was able to bind to three IgG molecules (1:3, proA:IgG) in ITC accentuating the presence of conformational flexibility in proA, corroborated also by CD results. By contrast, proG binds with 1:1 stoichiometry to IgG, which also involves key structural rearrangement within the binding interface of IgG-proG complex, confirmed by fluorescence KI quenching study. It is implicit from CD and fluorescence results that IgG does not undergo any significant conformational changes, which further suggests that proA and proG dictate the phenomenon of recognition in antibody complexes. ANS as a hydrophobic probe helped in revealing the distinctive antibody binding mechanism of proA and proG. Additionally, the binding competition experiments using ITC established that proA and proG cannot bind IgG concurrently.

Screening of bacteria-binding peptides and one-pot ZnO surface modification for bacterial cell entrapment

Short functional peptides are promising materials for use as targeting recognition probes. Toll-like receptor 4 (TLR4) plays an essential role in pathogen recognition and in activation of innate immunity. Here, the TLR4 amino acid sequence was used to screen for bacterial cell binding peptides using a peptide array. Several octamer peptides, including GRHIFWRR, demonstrated binding to Escherichia coli as well as lipopolysaccharides. Linking this peptide with the ZnO-binding peptide HKVAPR, creates a bi-functional peptide capable of one-step ZnO surface modification for bacterial cell entrapment. Ten-fold increase in entrapment of E. coli was observed using the bi-functional peptide. The screened peptides and the simple strategy for nanomaterial surface functionalization can be employed for various biotechnological applications including bacterial cell entrapment onto ZnO surfaces.

Linking the screened bacteria-binding peptide with the ZnO-binding peptide HKVAPR, created a bifunctional peptide capable of one-step simple ZnO surface modification and of bacterial cell entrapment.

Alginate dialdehyde meets nylon membrane: a versatile platform for facile and green fabrication of membrane adsorbers

Alginate dialdehyde, a biocompatible polymer, is used as an intermediate layer on a nylon membrane to readily fabricate different membrane adsorbers.

Array-based functional peptide screening and characterization of gold nanoparticle synthesis

Based on inorganic material production through biomineralization in organisms, the use of biological molecules in nanomaterial production has received increasing attention as a vehicle to synthesize inorganic materials with selected properties in ambient conditions. Among various biological molecules that interact with metallic surfaces, short peptides are putative ligand molecules as they exhibit potential to control the synthesis of nanoscale materials with tailored functions. Herein, using a spot synthesis-based peptide array, the gold nanoparticle (AuNP) binding activities of approximately 1800 peptides were evaluated and revealed various activities ranging from positive (high-affinity binding peptides) to negative (weak- or null-affinity binding peptides). Among 50 peptides showing the highest AuNP binding activity, 46 sequences showed the presence of tryptophan-based motifs including W[X_n]W, H[X_n]W, and W[X_n]H (W: tryptophan, X: any amino acid, n: 1-8 amino acid residues), whereas none of these motifs was found in the WORST50 peptides. Notably, three peptides showing the highest binding affinities possessed bi-functionality in AuNP binding and Au(III) reduction in solution and on solid surfaces. In addition, the characterization of truncated peptide derivatives revealed unique peptide motifs for their function expressions that also supported the importance of tryptophan-based motifs for peptide-AuNP binding. These findings open the door for peptide-mediated precise regulation of AuNP synthesis in ambient condition and for site dependent controlled AuNP integration onto nanotechnological devices.

STATEMENT OF SIGNIFICANCE

The development of a technique for functionally regulated nanosized material production in ambient condition is broadly required according to the expansion of nanomaterial based applications. Short peptides, which bind to metallic surfaces, have great potential for the technique development, but the realization remains a difficult challenge due to the lack of metal binding peptide varieties. Herein, approximately 1800 peptides with the gold nanoparticle (AuNP) binding activity are reported and characterized. Furthermore, by three highest binding peptides, the expression of bi-functionality in AuNP binding and Au(III) reduction was serendipitously discovered in solution and on solid surfaces. These findings will be attributed to new technique development of functional nanoparticle synthesis in mild condition, and for site-dependent AuNP integration in various nanotechnological devices.

Affinity chromatography: A versatile technique for antibody purification

Antibodies continue to be extremely utilized entities in myriad applications including basic research, imaging, targeted delivery, chromatography, diagnostics, and therapeutics. At production stage, antibodies are generally present in complex matrices and most of their intended applications necessitate purification. Antibody purification has always been a major bottleneck in downstream processing of antibodies, due to the need of high quality products and associated high costs. Over the years, extensive research has focused on finding better purification methodologies to overcome this holdup. Among a plethora of different techniques, affinity chromatography is one of the most selective, rapid and easy method for antibody purification. This review aims to provide a detailed overview on affinity chromatography and the components involved in purification. An array of support matrices along with various classes of affinity ligands detailing their underlying working principles, together with the advantages and limitations of each system in purifying different types of antibodies, accompanying recent developments and important practical methodological considerations to optimize purification procedure are discussed.

Fc-Binding Ligands of Immunoglobulin G: An Overview of High Affinity Proteins and Peptides

The rapidly increasing application of antibodies has inspired the development of several novel methods to isolate and target antibodies using smart biomaterials that mimic the binding of Fc-receptors to antibodies. The Fc-binding domain of antibodies is the primary binding site for e.g., effector proteins and secondary antibodies, whereas antigens bind to the Fab region. Protein A, G, and L, surface proteins expressed by pathogenic bacteria, are well known to bind immunoglobulin and have been widely exploited in antibody purification strategies. Several difficulties are encountered when bacterial proteins are used in antibody research and application. One of the major obstacles hampering the use of bacterial proteins is sample contamination with trace amounts of these proteins, which can invoke an immune response in the host. Many research groups actively develop synthetic ligands that are able to selectively and strongly bind to antibodies. Among the reported ligands, peptides that bind to the Fc-domain of antibodies are attractive tools in antibody research. Besides their use as high affinity ligands in antibody purification chromatography, Fc-binding peptides are applied e.g., to localize antibodies on nanomaterials and to increase the half-life of proteins in serum. In this review, recent developments of Fc-binding peptides are presented and their binding characteristics and diverse applications are discussed.

Effects of the properties of short peptides conjugated with cell-penetrating peptides on their internalization into cells

Peptides, especially intracellular functional peptides that can play a particular role inside a cell, have attracted attention as promising materials to control cell fate. However, hydrophilic materials like peptides are difficult for cells to internalize. Therefore, the screening and design of intracellular functional peptides are more difficult than that of extracellular ones. An effective high-throughput screening system for intracellular functional peptides has not been reported. Here, we demonstrate a novel peptide array system for screening intracellular functional peptides, in which both cell-penetrating peptide (CPP) domain and photo-cleavable linkers are used. By using this screening system, we determined how the cellular uptake properties of CPP-conjugated peptides varied depending on the properties of the conjugated peptides. We found that the internalization ability of CPP-conjugated peptides varied greatly depending on the property of the conjugated peptides, and anionic peptides drastically decreased the uptake ability. We summarized our data in a scatter diagram that plots hydrophobicity versus isoelectric point (pI) of conjugated peptides. These results define a peptide library suitable for screening of intracellular functional peptides. Thus, our system, including the diagram, is a promising tool for searching biological active molecules such as peptide-based drugs.

Design of a dual-function peptide probe as a binder of angiotensin II and an inducer of silver nanoparticle aggregation for use in label-free colorimetric assays

Label-free colorimetric assays using metallic nanoparticles have received much recent attention, for their application in simple and sensitive methods for detection of biomolecules. Short peptide probes that can bind to analyte biomolecules are attractive ligands in molecular nanotechnology; however, identification of biological recognition motifs is usually based on trial-and-error experiments. Herein, a peptide probe was screened for colorimetric detection of angiotensin II (Ang II) using a mechanism for non-crosslinking aggregation of silver nanoparticles (AgNPs). The dual-function peptides, which bind to the analyte and induce AgNP aggregation, were identified using a two-step strategy: (1) screening of an Ang II-binding peptide from an Ang II receptor sequence library, using SPOT technology, which enable peptides synthesis on cellulose membranes via an Fmoc method and (2) selection of peptide probes that effectively induce aggregation of AgNPs using a photolinker modified peptide array. Using the identified peptide probe, KGKNKRRR, aggregation of AgNPs was detected by observation of a pink color in the absence of Ang II, whereas AgNPs remained dispersed in the presence of Ang II (yellow). The color changes were not observed in the presence of other hormone molecules. Ang II could be detected within 15 min, with a detection limit of 10 µM, by measuring the ratio of absorbance at 400 nm and 568 nm; the signal could also be observed with the naked eye. These data suggest that the peptide identified here could be used as a probe for simple and rapid colorimetric detection of Ang II. This strategy for the identification of functional peptides shows promise for the development of colorimetric detection of various diagnostically important biomolecules.

FcUni-RLuc: an engineered Renilla luciferase with Fc binding ability and light emission activity

Schematic representation of the labelling of IgG using FcUni-RLuc.

A molecular peptide beacon for IgG detection

A molecular peptide beacon was designed for fluorescence detection of IgG in a homogeneous assay.