Identification of a peptide ligand for antibody immobilization on biosensor surfaces

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.

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.

From nanoaggregates to mesoscale ribbons: the multistep self-organization of amphiphilic peptides

This paper reports atomic force microscopy results and molecular dynamics simulations of the striking differences of long-term self-organization structures of negatively charged (AcA₄)₂KD (double tail) and AcA₄D (single tail) peptides, respectively, forming micrometer-long, linearly ordered ribbon-like structures and nanometer-sized, unstructured, round-shaped aggregates. The subsequent formation steps of the long-range nanoribbons, experimentally observed only for the "double tail" (AcA₄)₂KD peptide, are analyzed in detail, showing that the initial "primary" unstructured round-shaped aggregates progressively evolve into longer nanofilaments and into micrometer-long, network-forming nanoribbon moieties. In particular, the long-range self-organization of the "double tail" peptides appears to be closely related to electrostatically driven diffusional motions of the primary aggregates and nanofilaments. The diffusional freedom degrees are prompted by the formation of a dynamic ternary air/liquid/substrate interface, due to the water evaporation process from the ultrathin films of the peptide solution cast onto a solid mica substrate. Overall, the initial aggregation of unstructured round-shaped moieties, for both the peptides, can be seen as an entropy-driven process, involving the intra- and intermolecular interactions of hydrophobic parts of the peptides, while the further formation of long nanoribbons, only for "double tail" peptides, can be viewed in terms of an enthalpy-driven process, mainly due to the predominant electrostatic interactions between the charged heads of the interacting peptides. The role of the solid-liquid interface, as the locus of the enthalpy-driven linear organization, is also highlighted.

Biomaterials-Based Delivery of Therapeutic Antibodies for Cancer Therapy

Considerable breakthroughs in the treatment of malignant tumors using antibody drugs, especially immunomodulating monoclonal antibodies (mAbs), have been made in the past decade. Despite technological advancements in antibody design and manufacture, multiple challenges face antibody-mediated cancer therapy, such as instability in vivo, poor tumor penetration, limited response rate, and undesirable off-target cytotoxicity. In recent years, an increasing number of biomaterials-based delivery systems have been reported to enhance the antitumor efficacy of antibody drugs. This review summarizes the advances and breakthroughs in integrating biomaterials with therapeutic antibodies for enhanced cancer therapy. A brief introduction to the principal mechanism of antibody-based cancer therapy is first established, and then various antibody immobilization strategies are provided. Finally, the current state-of-the-art in biomaterials-based antibody delivery systems and their applications in cancer treatment are summarized, highlighting how the delivery systems augment the therapeutic efficacy of antibody drugs. The outlook and perspective on biomaterials-based delivery of antitumor antibodies are also discussed.

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.

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.