Synthesis and Characterization of High-Affinity, Low Molecular Weight Displacers for Cation-Exchange Chromatography

The use of predictive models to develop chromatography-based purification processes

Chromatography is the workhorse of biopharmaceutical downstream processing because it can selectively enrich a target product while removing impurities from complex feed streams. This is achieved by exploiting differences in molecular properties, such as size, charge and hydrophobicity (alone or in different combinations). Accordingly, many parameters must be tested during process development in order to maximize product purity and recovery, including resin and ligand types, conductivity, pH, gradient profiles, and the sequence of separation operations. The number of possible experimental conditions quickly becomes unmanageable. Although the range of suitable conditions can be narrowed based on experience, the time and cost of the work remain high even when using high-throughput laboratory automation. In contrast, chromatography modeling using inexpensive, parallelized computer hardware can provide expert knowledge, predicting conditions that achieve high purity and efficient recovery. The prediction of suitable conditions in silico reduces the number of empirical tests required and provides in-depth process understanding, which is recommended by regulatory authorities. In this article, we discuss the benefits and specific challenges of chromatography modeling. We describe the experimental characterization of chromatography devices and settings prior to modeling, such as the determination of column porosity. We also consider the challenges that must be overcome when models are set up and calibrated, including the cross-validation and verification of data-driven and hybrid (combined data-driven and mechanistic) models. This review will therefore support researchers intending to establish a chromatography modeling workflow in their laboratory.

Surface plasmon resonance spectroscopy-based high-throughput screening of ligands for use in affinity and displacement chromatography

We describe an approach that uses surface plasmon resonance (SPR) spectroscopy and self-assembled monolayers (SAMs) for the high-throughput screening of ligands for use in displacement and affinity chromatographic processes. We identified a set of commercially available organic amines and allowed them to react with SAMs presenting interchain carboxylic anhydride groups; the resulting surfaces presented ligands of interest in a background of carboxylic acid groups. We used SPR spectroscopy to determine the extent of adsorption of two model proteinslysozyme and cytochrome conto these "multimodal" surfaces and to select promising "affinity" ligands for further characterization. The attachment of selected ligands to UltraLink Biosupport resulted in beads with a significantly greater affinity for lysozyme than for cytochrome c that would be suitable for use in affinity chromatographic processes. Furthermore, we also used the screens to design "affinity displacers"small molecules that selectively retain lysozyme on chromatographic resins, while displacing cytochrome c. The combination of SPR spectroscopy and SAMs represents a powerful technique for identifying novel ligands that enable the purification of complex protein mixtures.

An affinity-based strategy for the design of selective displacers for the chromatographic separation of proteins

We describe an affinity-based strategy for designing selective protein displacers for the chromatographic purification of proteins. To design a displacer that is selective for a target protein, we attached a component with affinity for the target protein to a resin-binding component; we then tested the ability of such displacers to selectively retain the target protein on a resin relative to another protein having a similar retention time. In particular, we synthesized displacers based on biotin, which selectively retained avidin as compared to aprotinin on SP Sepharose high performance resin. In addition, we have extended this approach to develop an affinity-peptide-based displacer that discriminates between lysozyme and cytochrome c. Here, a selective displacer was designed from a lysozyme-binding peptide that had been identified and optimized previously using phage-display technology. Our results suggest a general strategy for designing highly selective affinity-based displacers by identifying molecules (e.g., peptides) that bind to a protein of interest and using an appropriate linker to attach these molecules to a moiety that binds to the stationary phase.

Purification of proteins using displacement chromatography

Displacement chromatography has several advantages over the nonlinear elution technique, as well as the linear elution mode, such as the recovery of purified components at high concentrations, less tailing during elution, high throughput and high resolution. Displacer affinity and its utilization are the critical components of displacement chromatography. Particularly, the nonspecific interactions between the displacer and the stationary phase can be exploited to generate high affinity displacers. This chapter will discuss the design and execution of displacer selection and implementation in a separation specifically focusing on its utilization in ion exchange chromatography.

Mannosylated G(0) Dendrimers with Nanomolar Affinities toEscherichia coli FimH

Pentaerythritol and bis-pentaerythritol scaffolds were used for the preparation of first generation glycodendrimers bearing aryl alpha-D-mannopyranoside residues assembled using single-step Sonogashira and click chemistry. The carbohydrate precursors were built with either para-iodophenyl, propargyl, or 2-azidoethyl aglycones whereas the pentaerythritol moieties were built with terminal azide or propargyl groups, respectively. Cross-linking abilities of this series of glycodendrimers were first evaluated with the lectin from Canavalia ensiformis (Concanavalin A). Surface plasmon resonance measurements showed these two families of mannosylated clusters as the best ligands known to date toward Escherichia coli K12 FimH with subnanomolar affinities. Tetramer 4 had a K(d) of 0.45 nM. These clusters were 1000 times more potent than mannose for their capacity to inhibit the binding of E. coli to erythrocytes in vitro.

Tri- and hexavalent mannoside clusters as potential inhibitors of type 1 fimbriated bacteria using pentaerythritol and triazole linkages

Several oligomannoside clusters having a hundred-fold increase in affinities toward E. coli were synthesized by Cu(I)-catalyzed [1,3]-dipolar cycloadditions using pentaerythritol scaffolds bearing either alkyne or azide functionalities.

A priori prediction of adsorption isotherm parameters and chromatographic behavior in ion-exchange systems

The a priori prediction of protein adsorption behavior has been a long-standing goal in several fields. In the present work, property-modeling techniques have been used for the prediction of protein adsorption thermodynamics in ion-exchange systems directly from crystal structure. Quantitative structure-property relationship models of protein isotherm parameters and Gibbs free energy changes in ion-exchange systems were generated by using a support vector machine regression technique. The predictive ability of the models was demonstrated for two test-set proteins not included in the model training set. Molecular descriptors selected during model generation were examined to gain insights into the important physicochemical factors influencing stoichiometry, equilibrium, steric effects, and binding affinity in protein ion-exchange systems. The a priori prediction of protein isotherm parameters can have direct implications for various ion-exchange processes. As proof of concept, a multiscale modeling approach was used for predicting the chromatographic separation of a test set of proteins using the isotherm parameters obtained from the quantitative structure-property relationship models. The simulated column separation showed good agreement with the experimental data. The ability to predict chromatographic behavior of proteins directly from their crystal structures may have significant implications for a range of biotechnology processes.

The effect of multi-component adsorption on selectivity in ion exchange displacement systems

This paper examines chemically selective displacement chromatography using affinity ranking plots, batch displacer screening experiments, column displacements, multi-component adsorption isotherms and spectroscopy. The affinity ranking plot indicated that the displacers, sucrose octasulfate (SOS) and tatrazine, should possess sufficient affinity to displace the proteins amyloglucosidase and apoferritin over a wide range of operating conditions. In addition, the plots indicated that the separation of these proteins by displacement chromatography would be extremely difficult. Further, the two proteins were shown to have very similar retention times under shallow linear gradient conditions. When batch displacement experiments were carried out, both tartrazine and SOS exhibited significant selectivity differences with respect to their ability to displace these two proteins, in contrast to the affinity ranking plot results. Column displacement experiments carried out with sucrose octasulfate agreed with the predictions of the affinity ranking plots, with both proteins being displaced but poorly resolved under several column displacement conditions. On the other hand, column displacement with tartrazine as the displacer resulted in the selective displacement and partial purification of apoferritin. Single- and multi-component isotherms of the proteins with or without the presence of displacers were determined and were used to help explain the selectivity reversals observed in the column and batch displacement experiments. In addition, fluorescence and CD spectra suggested that the displacers did not induce any structural changes to either of the proteins. The results in this paper indicate that multi-component adsorption behavior can be exploited for creating chemically selective displacement separations.

Parallel screening of selective and high-affinity displacers for proteins in ion-exchange systems

This paper employs a parallel batch screening technique for the identification of both selective and high-affinity displacers for a model binary mixture of proteins in a cation-exchange system. A variety of molecules were screened as possible displacers for the proteins ribonuclease A (RNAseA) and alpha-chymotrypsinogen A (alpha-chyA) on high performance Sepharose SP. The batch screening data for each protein was used to select leads for selective and high-affinity displacers and column experiments were carried out to evaluate the performance of the selected leads. The data from the batch displacements was also employed to generate quantitative structure-efficacy relationship (QSER) models based on a support vector machine regression approach. The resulting models had high correlation coefficients and were able to predict the behaviour of molecules not included in the training set. The descriptors selected in the QSER models for both proteins were examined to provide insights into factors influencing displacer selectivity in ion-exchange systems. The results presented in this paper demonstrate that this parallel batch screening-QSER approach can be employed for the identification of selective and high-affinity displacers for protein mixtures.

Molecular Tectonics. Dendritic Construction of Porous Hydrogen-Bonded Networks

Molecules that associate to form porous networks can be made by attaching multiple hydrogen-bonding sites to suitable cores. Pentaerythrityl tetraphenyl ether, a four-armed core, is the progenitor of dendritic derivatives with more arms, including dipentaerythrityl hexaphenyl ether 7. An advantage of such dendritic derivatives is that the resulting networks are held together by larger numbers of intermolecular hydrogen bonds. [structure: see text]

Investigation of particle-based and monolithic columns for cation exchange protein displacement chromatography using poly(diallyl-dimethylammonium chloride) as displacer

The overall topic of the investigation was the separation of basic proteins by cation exchange displacement chromatography. For this purpose two principal column morphologies were compared for the separation of ribonuclease A and alpha-chymotrypsinogen, two proteins found in the bovine pancreas. These were a column packed with porous particles (Macro-Prep S, 10 microm, 1000 A) and a monolithic column (UNO S1). Both columns are strong cation exchangers, carrying -SO3(-)-groups linked to a hydrophilic polymer support. Poly(diallyl-dimethylammonium chloride) (PDADMAC), a linear cationic polyelectrolyte composed of 100-200 quaternary pyrrolidinium rings, was used as displacer. The steric mass action (SMA) model and, in particular, the operating regime and dynamic affinity plots were used to aid method development. To date the SMA model has been applied primarily to simulate non-linear displacement chromatography of proteins using low molar mass displacers. Here, the model is applied to polyelectrolytes with a molar mass below 20000 g mol(-1), which corresponds to a degree of polymerization below 125 and an average contour length of less than 60 nm. The columns were characterized in terms of the adsorption isotherms (affinity, capacity) of the investigated proteins and the displacer.

Identification of Chemically Selective Displacers Using Parallel Batch Screening Experiments and Quantitative Structure Efficacy Relationship Models

Parallel batch screening experiments were carried out to examine how displacer chemistry and salt counterions affect the selectivity of batch protein displacements in anion exchange chromatographic systems. The results indicate that both salt type and displacer chemistry can have a significant impact on the amount of protein displaced. Importantly, the results indicate that, by changing the displacer, salt counterion, or both, one can induce significant selectivity changes in the relative displacement of two model proteins. This indicates that highly selective separations can be developed in ion exchange systems by the appropriate selection of displacer chemistry and salt counterion. The experimental batch screening data were also used in conjunction with various molecular descriptors to generate quantitative structure efficacy relationship (QSER) models based on a support vector machine feature selection and regression tool. The models resulted in good correlations and successful predictions for an external test set of displacers. A star plot approach was shown to be a powerful tool to aid in the interpretation of the QSER models. These results indicate that this modeling approach can be employed for the a priori prediction of displacer efficacy as well as for providing insight into displacer design and the selection of proper mobile-phase conditions for highly selective separations.

Stationary phase effects on the dynamic affinity of low-molecular-mass displacers

In this paper, the selectivity of a variety of cation-exchange stationary phases was investigated using a homologous series of displacer molecules based on pentaerythritol. These displacers were derived from pentaerythritol and contained either four trimethyl ammonium groups [pentaerythrityl-(trimethylammonium chloride)4, PE(TMA)4], benzene rings [pentaerythrityl-(benzyl dimethylammonium chloride)4, PE(DMABzCl)4], heptyl groups [pentaerythrityl-(heptyl dimethylammonium iodide)4, PE(DMAHepI)4] or cyclohexyl groups [pentaerythrityl-(cyclohexyl dimethylammonium iodide)4, PE(DMACyI)4]. This series enabled us to probe the secondary interactions that can play a role in the affinity of low-molecular-mass displacers for different stationary phases. The relative affinities of these displacers were examined using a displacer ranking plot based on the steric mass action (SMA) isotherm model. While hydrophobicity and aromaticity played important roles in generating the affinity to the hydrophilized polystyrene-divinylbenzene (Source 15S) and polymethacrylate-based (Toyopearl 650M) resins, these secondary interactions had a minimal impact on the selectivity in agarose resins coated with dextran (SP Sepharose XL), "gel in a shell" (S Ceramic HyperD F), and monolithic (Bio-Rad Uno S6) cation-exchange materials. Further, the results with a tentacular stationary phase (Fractogel EMD) suggest that the alkyl chains on PE(DMAHepI)4 play an important role in increasing the affinity, possibly because of strong interactions between the alkyl moiety and the polymer matrix as well as between the charged groups and the polyelectrolyte tentacles. The results of this study provide insight into the design of high affinity, low-molecular-mass displacers for different cation-exchange stationary phase materials.

Purification of an oligonucleotide at high column loading by high affinity, low-molecular-mass displacers

The development of efficient techniques for large-scale oligonucleotide purification is of great interest due to the increased demand for antisense oligonucleotides as therapeutics as well as their use for target validation and gene functionalization. This paper describes the use of anion-exchange displacement chromatography for the purification of 20-mer phosphorothioate oligonucleotide from its closely related impurities using low-molecular-mass amaranth as the displacer. Experiments were carried out to examine the effect of the feed load on the performance of the displacement chromatography. In contrast to prior work, displacement chromatography was successfully scaled-up to high column loadings while maintaining high purity and yields. Experiments carried out on a Source 15Q column indicated that crude oligonucleotide loading as high as 39.2 mg/ml of column were readily processed, resulting in product recovery of 86% and purity of 92%. These results demonstrate that anion-exchange displacement chromatography can indeed be employed for large-scale oligonucleotide separations at high column loading.

Hydrophobic displacement chromatography of proteins

Displacement chromatography of proteins was successfully carried out in both hydrophobic interaction and reversed-phase chromatographic systems using low-molecular weight displacers. The displacers employed for hydrophobic displacement chromatography were water soluble, charged molecules containing several short alkyl and/or aryl groups. Spectroscopy was employed to verify the absence of structural changes to the proteins displaced on these hydrophobic supports. Displacement chromatography on a reversed-phase material was employed to purify a growth factor protein from its closely related variants, demonstrating the high resolutions that can be achieved by hydrophobic displacement chromatography. This process combines the high-resolution/high-throughput characteristics of displacement chromatography with the unique selectivity of these hydrophobic supports and offers the chromatographic engineer a powerful tool for the preparative purification of proteins.

Structural characteristics of low-molecular-mass displacers for cation-exchange chromatography. II. Role of the stationary phase

The relative efficacy of a variety of low-molecular-mass displacers was examined on three different stationary phase materials. Several homologous series of displacer molecules were evaluated on these ion-exchange resins using a displacer ranking plot based on the steric mass action model. The results demonstrate that while aromaticity and hydrophobicity can play a significant role in the affinity of displacer molecules on polymethacrylate based and hydrophilized polystyrene-divinylbenzene based materials, this effect is much less pronounced on an agarose based resin. The work presented in this paper demonstrates that different structural features of low-molecular-mass displacers can dominate their affinity on various stationary phase materials employed and provides rules of thumb for the design of high affinity, low-molecular-mass displacers for a variety of commercial cation-exchange materials.