A hexamer peptide ligand that binds selectively to staphylococcal enterotoxin B: isolation from a solid phase combinatorial library

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.

Emerging biomaterials for downstream manufacturing of therapeutic proteins

Downstream processing is considered one of the most challenging phases of industrial manufacturing of therapeutic proteins, accounting for a large portion of the total production costs. The growing demand for therapeutic proteins in the biopharmaceutical market in addition to a significant rise in upstream titers have placed an increasing burden on the downstream purification process, which is often limited by high cost and insufficient capacities. To achieve efficient production and reduced costs, a variety of biomaterials have been exploited to improve the current techniques and also to develop superior alternatives. In this work, we discuss the significance of utilizing traditional biomaterials in downstream processing and review the recent progress in the development of new biomaterials for use in protein separation and purification. Several representative methods will be highlighted and discussed in detail, including affinity chromatography, non-affinity chromatography, membrane separations, magnetic separations, and precipitation/phase separations. STATEMENT OF SIGNIFICANCE: Nowadays, downstream processing of therapeutic proteins is facing great challenges created by the rapid increase of the market size and upstream titers, starving for significant improvements or innovations in current downstream unit operations. Biomaterials have been widely used in downstream manufacturing of proteins and efforts have been continuously devoted to developing more advanced biomaterials for the implementation of more efficient and economical purification methods. This review covers recent advances in the development and application of biomaterials specifically exploited for various chromatographic and non-chromatographic techniques, highlighting several promising alternative strategies.

Screening and characterization of anti-SEB peptides using a bacterial display library and microfluidic magnetic sorting

Bacterial peptide display libraries enable the rapid and efficient selection of peptides that have high affinity and selectivity toward their targets. Using a 15-mer random library on the outer surface of Escherichia coli (E.coli), high-affinity peptides were selected against a staphylococcal enterotoxin B (SEB) protein after four rounds of biopanning. On-cell screening analysis of affinity and specificity were measured by flow cytometry and directly compared to the synthetic peptide, off-cell, using peptide-ELISA. DNA sequencing of the positive clones after four rounds of microfluidic magnetic sorting (MMS) revealed a common consensus sequence of (S/T)CH(Y/F)W for the SEB-binding peptides R338, R418, and R445. The consensus sequence in these bacterial display peptides has similar amino acid characteristics with SEB peptide sequences isolated from phage display. The K_d measured by peptide-ELISA off-cell was 2.4 nM for R418 and 3.0 nM for R445. The bacterial peptide display methodology using the semiautomated MMS resulted in the discovery of selective peptides with affinity for a food safety and defense threat. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. Journal of Molecular Recognition published by John Wiley & Sons, Ltd.

Depletion and fractionation technologies in plasma proteomic analysis

This review intends to survey the traditional and current technologies in the depletion and subfractionation of plasma proteins for further analyses. The value of depletion aims to enrich low-abundant proteins by removing highly abundant proteins, such as albumin or immunoglobulin G, from plasma. With this approach, one can examine both the resulting high- and low-abundant protein fractions. The depleted protein population can be further subfractionated based on their isoelectric point ranges, creating a more discrete pool of proteins for detailed post-translational modification studies by methods such as 2D gel electrophoresis and mass spectrometry. The concept of divide to conquer will greatly enhance our ability to identify and characterize low-abundant proteins and cleaved peptides from plasma as important diagnostic markers or potential drug targets. This can potentially reverse the decline in the development of new plasma diagnostic tests.

Reversible cyclic peptide libraries for the discovery of affinity ligands

A novel strategy is presented for the identification of cyclic peptide ligands from combinatorial libraries of reversible cyclic depsipeptides. A method for the solid-phase synthesis of individual cyclic depsipeptides and combinatorial libraries of these compounds is proposed, which employs lactic acid (Lact) and the dipeptide ester (Nα-Ac)-Ser(Ala)- as linkers for dilactonization. Upon alkaline treatment of the beads selected by screening a model library, the cyclic depsipeptides are linearized and released from the solid support to the liquid phase, to be sequenced via single-step tandem mass spectrometry (MS/MS). The protocol presented for library synthesis provides for wide structural diversity. Two model sequences, VVWVVK and AAWAAR, were chosen to present different structural examples for depsipeptide libraries and demonstrate the process of sequence determination by mass spectrometry. Further, a case study using the IgG binding cyclic depsipeptide cyclo[(Nα-Ac)-S(A)-RWHYFK-Lact-E] is presented to demonstrate the process of library screening and sequence determination on the selected beads. Finally, a method is shown for synthesis of the irreversible cyclic peptide corresponding to the proposed depsipeptide structure, to make the ligand stable to the aqueous acid and alkaline conditions encountered in affinity chromatographic applications. The cyclic peptide ligand was synthesized on a poly(methacrylate) resin and used for chromatographic binding of the target IgG.

Thermodynamic and structural analysis of interactions between peptide ligands and SEB

Staphylococcal enterotoxin B (SEB) is an exotoxin produced by Staphylococcus aureus and commonly associated with food poisoning. In this study, SEB-binding peptides were identified by screening a phage displayed peptide library. The binding of peptides to SEB was tested with isothermal titration calorimetry (ITC) and of the five selected peptides, three showed affinity to SEB, with one measured to have the highest affinity constant (10(5) M(-1)). ITC revealed that the interaction of peptide ligands with SEB was driven entropically and the binding was dominated by hydrophobic interactions. Circular dichroism (CD) measurements and molecular dynamics (MD) simulations, together, give a structural insight into the interaction of peptides with SEB. While SEB binding peptides showed random coil structure before binding, after complex formation they had more ordered structures. The peptide with highest affinity to SEB showed stable conformation during MD simulation. Taken together, our approach about thermodynamic and structural characterization of peptide ligands can be used to develop aptamers, with high affinity and selectivity, for biosensor applications.

Generation of Fab fragment-like molecular recognition proteins against staphylococcal enterotoxin B by phage display technology

Antigen-binding fragments (Fab fragments) and single-chain variable fragments (scFv) against staphylococcal enterotoxin B (SEB) were produced by phage display technology. SEB epitopes were first identified by phage display approach using the commercial anti-SEB monoclonal antibody ab53981 as the target. Heptamer and dodecamer mimotope peptides recognized by ab53981 were screened from Ph.D-7 or Ph.D-12 random peptide phage libraries expressed in Escherichia coli. The isolated 7-mer and 12-mer mimotopes were shown to share a sequence homologous to ⁸PDELHK¹⁴S in the amino acid sequence of SEB. The N-terminal 15-mer peptide of SEB was determined to be an epitope of ab53981. After immunization of mice with maltose-binding protein-tagged N-terminal 15-mer peptide, a phage display Fab library was constructed using cDNA prepared from the mRNAs of spleen cells. Three phage clones displaying the Fab molecule which recognized SEB were isolated through three rounds of panning. Only one of them produced a soluble Fab fragment from the transformed cells, and the fragment fused with a histidine tag sequence was produced in E. coli cells and converted into scFv. Surface plasmon resonance analysis showed that the dissociation constants of these proteins with SEB were (4.1 ± 1.1) × 10⁻⁹ M and (8.4 ± 2.3) × 10⁻¹⁰ M, respectively. The produced molecule was applied to the determination of SEB by enzyme-linked immunosorbent assay and Western blot analysis.

Screening of one-bead-one-peptide combinatorial library using red fluorescent dyes. Presence of positive and false positive beads

To screen one-bead-one-compound (OBOC) combinatorial libraries, tens of thousands to millions of compound beads are first mixed with a target molecule. The beads that interact with this molecule are then identified and isolated for compound structure determination. Here we describe an OBOC peptide library screening using streptavidin (SA) as probe protein, labeled with a red fluorescent dye and using the COPAS BIO-BEAD flow sorting equipment to separate fluorescent from nonfluorescent beads. The red dyes used were ATTO 590 and Texas Red. After incubating the library with the SA-red fluorescent dye conjugate, we isolated positive beads caused by peptide-SA interaction and false positive beads produced by peptide fluorescent dye interaction. These false positives were a drawback when sorting beads by COPAS. However,an in depth analysis of both kinds of beads allowed the differentiation of positives from false positives. The false positive beads showed bright homogeneous fluorescence, while positive beads had a heterogeneous fluorescence, exhibiting a characteristic halo appearance, with fluorescence intensity greatest at the bead surface and lowest in the core. The difference was more evident when using Texas Red instead of ATTO 590. Thus, positive beads could be manually separated from false positive ones. The beads were analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Most of the sequences obtained from positive beads had the His-Pro-Gln motif. Peptides from false positive beads were rich in Leu/Ileu, His, Phe, and Tyr.

Design of Adsorptive Columns for Specific Pathogen Removal: Application to Staphylococcal Enterotoxin B

The removal of pathogens such as toxins, viruses, bacteria, and prions in human blood, mammalian cell culture media, fermentation broths, food items, and water streams has gained increasing importance in ensuring product safety and in combatting acts of terrorism. Adsorption processes can play an important role in removing such pathogens from solution without affecting other desirable components. Adsorptive columns that can remove specific families of pathogens would need to achieve a reduction of several logs in pathogen concentration. This requirement is much more stringent than the normal yield requirements associated with adsorptive separations aimed at product recovery and purification in a process stream. This paper considers the design of an adsorptive column aimed at reducing the concentration of infectious agents from a known volume of solution by several logs in a fixed amount of time. The general rate (GR) model of chromatography is used in the analysis, including all major transport and kinetic steps in the adsorption process. The theory, with no adjustable parameters, is shown to predict with great accuracy the effect of residence time on the log removal of staphylococcal enterotoxin B (SEB) from solution using an affinity resin with a small peptide (YYWLHH) that has been found to bind specifically to this toxin.

Identification of trimeric peptides that bind porcine parvovirus from mixtures containing human blood plasma

Virus contamination in human therapeutics is of growing concern as more therapeutic products from animal or human sources come into the market. All biopharmaceutical processes are required to have at least two distinct viral clearance steps to remove viruses. Most of these steps work well for enveloped viruses and large viruses, whether enveloped or not. That leaves a class of small non-enveloped viruses, like parvoviruses and hepatitis A, which are not easily removed by these typical steps. In this study, we report the identification of trimeric peptides that bind specifically to porcine parvovirus (PPV) and their potential use to remove this virus from process solutions. All of the trimeric peptides isolated completely removed all detectable PPV from buffer in the first nine column volumes, corresponding to a clearance of 4.5-5.5 log of infectious virus. When the virus was spiked into a more complex matrix consisting of 7.5% human blood plasma, one of the trimers, WRW, was able to remove all detectable PPV in the first three column volumes, after which human blood plasma began to interfere with the binding of the virus to the peptide resin. These trimer resins removed considerably more virus than weak ion exchange resins. The results of this work indicate that small peptide ligand resins have the potential to be used in virus removal processes where removal of contaminating virus is necessary to ensure product safety.

Functional identification of novel activities: Activity-based selection of proteins from complete proteomes

The identification of proteins with desired activities, especially from complex samples such as plasma and whole blood, is a continual challenge. We have developed a technology platform called Functional Identification of Novel Activities (FIoNA) to discover desired protein activities from complex biological samples. FIoNA uses immobilized libraries of combinatorial peptide ligands to purify and concentrate essentially all of the components of a complex mixture on ligands synthesized on individual beads. No depletion or prefractionation of the starting material is performed before it is incubated with the library, and no a priori knowledge of the active protein or of the ligand to which it binds is required. Instead, the protein-loaded beads are individually evaluated en masse in disease- relevant assays to identify proteins possessing a desired function. Beads associated with the activity are selected, and the ligand is sequenced and resynthesized in bulk on the original backbone for purification and characterization of the active component. Here we illustrate the use of FIoNA in a cell proliferation assay to detect a growth factor present in conditioned cell medium at nanogram/milliliter concentrations. We also have selected beads associated with hydrolysis of nerve agent analogs in assays performed in 100,000-well microtiter plates.

One-step affinity purification of recombinant urokinase-type plasminogen activator receptor using a synthetic peptide developed by combinatorial chemistry

Several lines of evidence have pointed to a role of urokinase-type plasminogen activator receptor (uPAR) as a modulator of certain biochemical processes that are active during tumor invasion and metastasis. Consequently, the structure and function of this receptor have been studied extensively, using recombinantly produced uPAR that has been purified by either affinity chromatography using its cognate ligand, the urokinase-type plasminogen activator (uPA), or a monoclonal anti-uPAR antibody (R2), or by hydroxyapatite. Here, we present a new method for the efficient one-step affinity purification of recombinant uPAR exploiting a high-affinity synthetic peptide antagonist (AE152). The corresponding parent peptide was originally identified in a random phage-display library and subsequently subjected to affinity maturation by combinatorial chemistry. This study compares the affinity purification of a soluble, recombinant uPAR using the monoclonal antibody R2 or the peptide AE152 immobilized on Sepharose. The two affinity ligands perform equally well in purifying uPAR from Drosophila melanogaster Schneider 2 cell culture medium and yield products of comparable purity, activity, and stability as judged by SDS-PAGE, size exclusion chromatography and surface plasmon resonance analysis. The general availability of peptide synthesis renders the present AE152-based affinity purification of uPAR more accessible than the traditional protein-based affinity purification strategies. In this way, large amounts of recombinant uPAR can conveniently be purified for further structural and functional studies.

The Bead blot: A method for identifying ligand–protein and protein–protein interactions using combinatorial libraries of peptide ligands

Small molecules that bind proteins can be used as ligands for protein purification and for investigating protein-protein and protein-drug interactions. Unfortunately, many methods used to identify new ligands to desired proteins suffer from common shortcomings, including the requirement that the target protein be purified and/or the requirement that the ligands be selected under conditions different from those under which it will be used. We have developed a new method called the Bead blot that can (i) select ligands to unpurified proteins, including trace proteins, present in complex materials (e.g., unfractionated plasma); (ii) select ligands to multiple proteins under a variety of conditions in a single experiment; and (iii) be used with libraries of different types of ligands. In the Bead blot, a library of ligands, synthesized on chromatography resin beads, is incubated with a starting material containing a target protein for which a ligand is sought. The proteins in the material bind to their complementary ligands according to specific affinity interactions. Then the protein-loaded beads are immobilized in a porous matrix, and the proteins are directionally eluted from the beads and captured on a membrane superimposed on the beads. The location of the target protein on the membrane is determined, and because the position of the protein(s) on the membrane reflects the position of the bead(s) in the matrix, the bead that originally bound the protein is identified, with subsequent elucidation of the ligand sequence. Ligands to several targets can be identified in one experiment. Here we demonstrate the broad utility of this method by the selection of ligands that purify plasma protein complexes or that remove pathogens from whole blood with very high affinity constants. We also select ligands to a protein based on competitive elution.

Affinity chromatography matures as bioinformatic and combinatorial tools develop

Affinity chromatography has the reputation of a more expensive and less robust than other types of liquid chromatography. Furthermore, the technique is considered to stand a modest chance of large-scale purification of proteinaceous pharmaceuticals. This perception is changing because of the pressure for quality protein therapeutics, and the realization that higher returns can be expected when ensuring fewer purification steps and increased product recovery. These developments necessitated a rethinking of the protein purification processes and restored the interest for affinity chromatography. This liquid chromatography technique is designed to offer high specificity, being able to safely guide protein manufactures to successfully cope with the aforementioned challenges. Affinity ligands are distinguished into synthetic and biological. These can be generated by rational design or selected from ligand libraries. Synthetic ligands are generated by three methods. The rational method features the functional approach and the structural template approach. The combinatorial method relies on the selection of ligands from a library of synthetic ligands synthesized randomly. The combined method employs both methods, that is, the ligand is selected from an intentionally biased library based on a rationally designed ligand. Biological ligands are selected by employing high-throughput biological techniques, e.g. phage- and ribosome-display for peptide and microprotein ligands, in addition to SELEX for oligonucleotide ligands. Synthetic mimodyes and chimaeric dye-ligands are usually designed by rational approaches and comprise a chloro-triazinlyl scaffold. The latter substituted with various amino acids, carbocyclic, and heterocyclic groups, generates libraries from which synthetic ligands can be selected. A 'lead' compound may help to generating a 'focused' or 'biased' library. This can be designed by various approaches, e.g.: (i) using a natural ligand-protein complex as a template; (ii) applying the principle of complementarity to exposed residues of the protein structure; and (iii) mimicking directly a natural biological recognition interaction. Affinity ligands, based on the peptide structure, can be peptides, peptide-mimetic derivatives (<30 monomers) and microproteins (e.g. 25-200 monomers). Microprotein ligands are selected from biological libraries constructed of variegated protein domains, e.g. minibody, Kunitz, tendamist, cellulose-binding domain, scFv, Cytb562, zinc-finger, SpA-analogue (Z-domain).

Characterization of a peptide affinity support that binds selectively to staphylococcal enterotoxin B

The influences of mass transfer and adsorption-desorption kinetics on the binding of staphylococcal enterotoxin B (SEB) to an affinity resin with the peptide ligand, Tyr-Tyr-Trp-Leu-His-His (YYWLHH) have been studied. The bed and particle porosities, the axial dispersion coefficient and the pore diffusivity were measured using pulse experiments under unretained conditions. Adsorption isotherms for SEB on YYWLHH resins with peptide densities in the range from 6 to 220 micromol/g were measured and fitted to a bi-Langmuir equation. At peptide densities below 9 micromol/g and above 50 micromol/g, dissociation constants were lower (2 x 10(-3) to 7 x 10(-3) mol/m3), and binding capacities were larger (43-47 mg SEB/g). In the range from 9 to 50 micromol/g dissociation constants were larger (13 x 10(-3) to 24 x 10(-3) mol/m3) and capacities were lower (33-37 mg SEB/g). These observations are consistent with a transition from single point attachment of the protein to the ligand at low peptide densities to multipoint attachment at high peptide densities. The general rate (GR) model of chromatography was used to fit experimental breakthrough curves under retained conditions to determine the intrinsic rate constants for adsorption, which varied from 0.13 to 0.50 m3 mol(-1) s(-1), and exhibited no clear trend with increasing peptide density. An analysis of the number of transfer units for the various mass transfer steps in the column indicated that film mass transfer, pore diffusion (POR) and the kinetics of adsorption can all play an important role in the overall rate of adsorption, with the intrinsic adsorption step apparently being the rate determining step at peptide densities below 50 micromol/g.

Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin

MOTIVATION

Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting.

RESULTS

We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set of ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A, we identified a conserved/unique pocket in close proximity (but not overlapping) the active site that is suitable for bi-dentate ligand development. These methods are generally applicable to identification of surface epitopes and binding pockets for development of diagnostic reagents, therapeutics and vaccines.