Rational design of peptide affinity ligands for the purification of therapeutic enzymes

Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics

Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.

Aptamer-Based Affinity Chromatography for Protein Extraction and Purification

Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.

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.

Microarrays for the screening and identification of carbohydrate-binding peptides

The development of carbohydrate-binding ligands is crucial for expanding knowledge on the glycocode and for achieving systematic carbohydrate targeting. Amongst such ligands, carbohydrate-binding peptides (CBPs) are attractive for use in bioanalytical and biomedical systems due to their biochemical and physicochemical properties; moreover, given the biological significance of lectin-carbohydrate interactions, these ligands offer an opportunity to study peptide sequence and binding characteristics to inform on natural target/ligand interactions. Here, a high-throughput microarray screening technique is described for the identification and study of CBPs, with a focus on polysialic acid (PSA), a polysaccharide found on neural stem cells. The chemical and biological uniqueness of PSA suggests that an ability to exclusively target this glycan may promote a number of diagnostic and therapeutic applications. PSA-binding peptides from phage display screening and from epitope mapping of an scFv for oligosialic acid were screened in an optimized microarray format with three ligand density conditions. Hypothesis-driven mutations were additionally applied to select peptides to modulate peptide affinity and selectivity to PSA. Peptide compositional and positional analyses revealed the significance of various residues for PSA binding and suggested the importance of basic residue positioning for PSA recognition. Furthermore, selectivity studies performed directly on microarrays with chondroitin sulfate A (CS-A) demonstrated the value of screening for both affinity and selectivity in the development of CBPs. Thus, the integrated approach described, with attention to design strategy, screening, and peptide characterization, successfully identified novel PSA-binding ligands and offers a platform for the identification and study of additional polysaccharide-binding peptides.