Development of temperature-controlled batch and 3-column counter-current protein A system for improved therapeutic purification

Maximizing product quality attributes by optimizing process parameters and performance attributes is a crucial aspect of bioprocess chromatography process design. Process parameters include but are not limited to bed height, eluate cut points, and elution pH. An under-characterized chromatography process parameter for protein A chromatography is process temperature. Here, we present a mechanistic understanding of the effects of temperature on the protein A purification of a monoclonal antibody (mAb) using a commercial chromatography resin for batch and continuous counter-current systems. A self-designed 3D-printed heating jacket controlled the 1 mL chromatography process temperature during the loading, wash, elution, and cleaning-in-place (CIP) steps. Batch loading experiments at 10, 20, and 30 °C demonstrated increased dynamic binding capacity (DBC) with temperature. The experimental data were fit to mechanistic and correlation-based models that predicted the optimal operating conditions over a range of temperatures. These model-based predictions optimized the development of a 3-column temperature-controlled periodic counter-current chromatography (TCPCC) and were validated experimentally. Operating a 3-column TCPCC at 30 °C led to a 47% increase in DBC relative to 20 °C batch chromatography. The DBC increase resulted in a two-fold increase in productivity relative to 20 °C batch. Increasing the number of columns to the TCPCC to optimize for increasing feed concentration resulted in further improvements to productivity. The feed-optimized TCPCC showed a respective two, three, and four-fold increase in productivity at feed concentrations of 1, 5, and 15 mg/mL mAb, respectively. The derived and experimentally validated temperature-dependent models offer a valuable tool for optimizing both batch and continuous chromatography systems under various operating conditions.

Advanced score system and automated search strategies for parameter estimation in mechanistic chromatography modeling

Least squares estimation of unknown parameters from measurement data is a well-established standard method in chromatography modeling but can suffer from critical disadvantages. The description of real-world systems is generally prone to unaccounted mechanisms, such as dispersion in external holdup volumes, and systematic measurement errors, such as caused by pump delays. In this scenario, matching the shape between simulated and measured chromatograms has been found to be more important than the exact peak positions. We have therefore developed a new score system that separately accounts for the shape, position and height of individual peaks. A genetic algorithm is used for optimizing these multiple objectives. Even for non-conflicting objectives, this approach shows superior convergence in comparison to single-objective gradient search, while conflicting objectives indicate incomplete models or inconsistent data. In the latter case, Pareto optima provide important information for understanding the system and improving experiments. The proposed method is demonstrated with synthetic and experimental case studies of increasing complexity. All software is freely available as open source code (https://github.com/modsim/CADET-Match).

Role of configurational flexibility on the adsorption kinetics of bivalent bispecific antibodies on porous cation exchange resins

The adsorption kinetics of a monoclonal antibody (mAb) used as a reference and of bivalent bispecific antibodies (BiSAb) on a macroporous cation exchanger is studied experimentally by examining the transient patterns of bound protein within the particles using confocal microscopy for a range of protein concentrations, buffer concentrations and pH, and temperatures. The mAb adsorption kinetics is controlled by pore diffusion and conforms to the classical shrinking core model. While the mAb adsorption rate increases with temperature, the ratio of effective and free solution diffusivity, D_e /D₀, remains constant and has a value of 0.20. The BiSAb's structure is comprised of scFv domains that are genetically fused to a framework IgG through flexible peptide linkers which results in conformational flexibility leading to multiple binding forms with varying affinity for the adsorbent surface. As a result, adsorption of the BiSAbs shows complex patterns of total bound protein within the particles. These BiSAb adsorption patterns are influenced by buffer ionic strength, pH, and temperature in unique ways. Sharper intraparticle profiles are observed for conditions where the binding strength is greater (lower buffer concentration and/or pH) or when the protein is chemically crosslinked to restrict configurational flexibility. Temperature affects the BiSAb pore diffusivity as well as the interconversion kinetics. While the effects of temperature on BiSAb transport are also described by a constant D_e /D₀ = 0.15, the temperature also affects the rate of interconversion between binding forms leading to faster equilibration at higher temperatures. A phenomenological model indicates that the interplay of pore diffusion and adsorption with the kinetically limited interconversion between binding forms is responsible for the experimental trends.

Purification of Modified Therapeutic Proteins Available on the Market: An Analysis of Chromatography-Based Strategies

Proteins, which have inherent biorecognition properties, have long been used as therapeutic agents for the treatment of a wide variety of clinical indications. Protein modification through covalent attachment to different moieties improves the therapeutic's pharmacokinetic properties, affinity, stability, confers protection against proteolytic degradation, and increases circulation half-life. Nowadays, several modified therapeutic proteins, including PEGylated, Fc-fused, lipidated, albumin-fused, and glycosylated proteins have obtained regulatory approval for commercialization. During its manufacturing, the purification steps of the therapeutic agent are decisive to ensure the quality, effectiveness, potency, and safety of the final product. Due to the robustness, selectivity, and high resolution of chromatographic methods, these are recognized as the gold standard in the downstream processing of therapeutic proteins. Moreover, depending on the modification strategy, the protein will suffer different physicochemical changes, which must be considered to define a purification approach. This review aims to deeply analyze the purification methods employed for modified therapeutic proteins that are currently available on the market, to understand why the selected strategies were successful. Emphasis is placed on chromatographic methods since they govern the purification processes within the pharmaceutical industry. Furthermore, to discuss how the modification type strongly influences the purification strategy, the purification processes of three different modified versions of coagulation factor IX are contrasted.

Patterns of protein adsorption in ion-exchange particles and columns: Evolution of protein concentration profiles during load, hold, and wash steps predicted for pore and solid diffusion mechanisms

Elucidation of protein transport mechanism in ion exchanges is essential to model separation performance. In this work we simulate intraparticle adsorption profiles during batch adsorption assuming typical process conditions for pore, solid and parallel diffusion. Artificial confocal laser scanning microscopy images are created to identify apparent differences between the different transport mechanisms. Typical sharp fronts for pore diffusion are characteristic for Langmuir equilibrium constants of K_L ≥1. Only at K_L = 0.1 and lower, the profiles are smooth and practically indistinguishable from a solid diffusion mechanism. During hold and wash steps, at which the interstitial buffer is removed or exchanged, continuation of diffusion of protein molecules is significant for solid diffusion due to the adsorbed phase concentration driving force. For pore diffusion, protein mobility is considerable at low and moderate binding strength. Only when pore diffusion if completely dominant, and the binding strength is very high, protein mobility is low enough to restrict diffusion out of the particles. Simulation of column operation reveals substantial protein loss when operating conditions are not adjusted appropriately.

Chromatographic and adsorptive behavior of a bivalent bispecific antibody and associated fragments

The elution and adsorptive behavior of a bivalent bispecific antibody (BiSAb), comprising an IgG1 framework with a scFv domain genetically fused to each heavy chain C-terminus via flexible linkers, and of two associated fragments were studied on two cation exchange chromatography media - ProPac WCX-10, which is pellicular and suitable for analytical use, and Nuvia HR-S, which is macroporous and suitable for preparative and process scale uses. Both fragments were identified by MS as missing one of the two scFv domains and its flexible linker, but one of them also contains an additional C-terminal lysine. The separation of these fragments on both resins occurs as a result of differences in non-specific ligand-protein interactions that are modulated by the salt concentration. For the ProPac WCX-10 column, complex, multipeak elution behaviors are observed, since, as a result of the linker flexibility, both the intact molecule and the fragments appear to exist in multiple binding configurations with each scFv domains either collapsed onto the IgG framework or extended away from it. With a residence time of 2.5 min and at 21 °C, two peak elution is observed for the fragments which contain a single linked scFv and three peak elution for the intact molecule which contains two linked scFvs. This behavior is affected by residence time, temperature, and hold time. Increasing the residence time to 25 min or increasing temperature to 40°C results in elution of a single, merged peak for each of the protein species. For Nuvia HR-S, the broader peaks, obtained as a result of mass transfer limitations, tend to obscure the multipeak elution behavior. Nevertheless, even for this resin, the effects of configurational flexibility are still manifested at the single-particle scale and affect the evolution of the patterns of protein binding within individual resin particles as evident from confocal microscopy observations.

Experimental investigation and mass transfer modelling of 3D printed monolithic cation exchangers

3D printing has recently found application in chromatography as a means to create ordered stationary phases with improved separation efficiency. Currently, 3D printed stationary phases are limited by the lack of 3D printing materials suitable for chromatographic applications, and require a strict compromise in terms of desired resolution, model size and the associated print time. Modelling of mass transfer in 3D printed monoliths is also fundamental to understand and further optimise separation performance of 3D printed stationary phases. In this work, a novel 3D printing material was formulated and employed to fabricate monolithic cation exchangers (CEXs) with carboxyl functionalities. CEXs were printed with ligand densities of 0.7, 1.4, 2.1 and 2.8 mmol/g and used in batch adsorption experiments with lysozyme as model protein. All CEXs demonstrated high binding strength towards lysozyme, with maximum binding capacities of up to 108 mg/mL. The experimental results were described using mass transfer models based on lumped pore diffusion and lumped solid diffusion mechanisms adapted to reflect the complex geometry of the 3D printed monoliths. An exact 3D model as well as less computationally demanding 1D and 2D approximations were evaluated in terms of their quality to capture the experimental trend of batch adsorption kinetic data. Overall, the model results indicate that mass transfer in the fabricated CEXs is mostly controlled by pore diffusion at high protein concentrations in the mobile phase, with solid diffusion becoming important at low protein concentrations. Also, the kinetic data were approximated equally well by both the full 3D model as well as the 2D approximation, indicating leaner mathematical models of lower dimensionality can be employed to describe mass transfer in complex three dimensional geometries. We believe this work will help spur the development of 3D printable materials for separations and aid in the development of quantitative platforms to evaluate and optimise the performance of 3D printed monoliths.

Separation of monoclonal antibody monomer-dimer mixtures by gradient elution with ceramic hydroxyapatite

Modeling the chromatographic separations of proteins at manufacturing scale is important since downstream processing costs are often dominant. At such scales, the columns are highly overloaded heightening the challenge of predicting performance. In this work, the separation of a monoclonal antibody monomer-dimer mixture is conducted by gradient elution chromatography with ceramic hydroxyapatite (CHT) columns Type I and Type II under overloaded conditions. Phosphate gradients are shown to be preferable over sodium chloride gradients since the latter result in undesirable pH transitions generated within the column itself. Using sodium phosphate gradients separation is obtained with both CHT types, achieving approximately 90% recovery at 99% monomer purity starting with a mixture containing 30% dimer at total protein loads up to 30 mg/mL. Because of its higher binding capacity, even higher loadings can be obtained with CHT Type I without monomer breakthrough. A hybrid model is developed to describe the separation. The model, based on an empirical description of two-component, competitive isotherms at low sodium phosphate concentration coupled with the stoichiometric displacement model at higher sodium phosphate concentrations, is in good agreement with the experiments using the linear driving force (LDF) approximation to describe adsorption/desorption kinetics. The same LDF rate coefficient predicts the separation at loadings between 0.8 and 30 mg/mL. The model developed in this work can be used as a general tool to optimize operating conditions, understand what factors limit performance, and compare different operating modes.

Retention and diffusion characteristics of oligonucleotides in a solid phase with polymer grafted anion-exchanger

In the chromatographic separation process of oligonucleotides (ONs), mechanistic understanding of their binding and diffusion processes is of significant importance to determine operating conditions in a fast and robust way. In this work, we determined the number of binding sites and the diffusivities of ONs in a polymer grafted anion exchange chromatography through linear gradient experiments (LGE) being carried out at selected four to five gradient slopes. Synthetic poly (T)s with length ranging from 3 to 90-mer were employed as a model of an antisense oligonucleotide with typical lengths of 10 - 30 bases. Comparison of the retention was also conducted between the grafted anion exchanger with a conventional ligand and an anion monolith disk. For the ONs up to 50 bases, the number of binding sites determined can be correlated with the length of ONs, and the grafted resin showed a better diffusion and narrower peak width compared to the nongrafted one. The retention behavior became similar for porous media when the longer ONs (> 50mer) were applied. The results obtained suggest that antisense ONs can be separated with grafted ligands without sacrificing mass transfer properties.

Volume Transition and Phase Coexistence in Polyelectrolyte Gels Interacting with Amphiphiles and Proteins

Polyelectrolyte gels have the capacity to absorb large amounts of multivalent species of opposite charge from aqueous solutions of low ionic strength, and release them at elevated ionic strengths. The reversibility offers the possibility to switch between “storage” and “release” modes, useful in applications such as drug delivery. The review focuses on systems where so-called volume phase transitions (VPT) of the gel network take place upon the absorption and release of proteins and self-assembling amphiphiles. We discuss the background in terms of thermodynamic driving forces behind complex formation in oppositely charged mixtures, the role played by cross-links in covalent gels, and general aspects of phase coexistence in networks in relation to Gibbs’ phase rule. We also briefly discuss a gel model frequently used in papers covered by the review. After that, we review papers dealing with collapse and swelling transitions of gels in contact with solution reservoirs of macroions and surfactants. Here we describe recent progress in our understanding of the conditions required for VPT, competing mechanisms, and hysteresis effects. We then review papers addressing equilibrium aspects of core–shell phase coexistence in gels in equilibrium. Here we first discuss early observations of phase separated gels and results showing how the phases affect each other. Then follows a review of recent theoretical and experimental studies providing evidence of thermodynamically stable core–shell phase separated states, and detailed analyses of the conditions under which they exist. Finally, we describe the results from investigations of mechanisms and kinetics of the collapse/swelling transitions induced by the loading/release of proteins, surfactants, and amphiphilic drug molecules.

Mechanistic modeling based process analytical technology implementation for pooling in hydrophobic interaction chromatography

A major challenge in chromatography purification of therapeutic proteins is batch-to-batch variability with respect to impurity levels and product concentration in the feed. Mechanistic model can enable process analytical technology (PAT) implementation by predicting impact of such variations and thereby improving the robustness of the resulting process and controls. This article presents one such application of mechanistic model of hydrophobic interaction chromatography (HIC) as a PAT tool for making robust pooling decisions to enable clearance of aggregates for a monoclonal antibody (mAb) therapeutic. Model predictions were performed before the actual chromatography experiments to facilitate feedforward control. The approach has been successfully demonstrated for four different feeds with varying aggregate levels (3.84%-5.54%) and feed concentration (0.6 mg/mL-1 mg/mL). The resulting pool consistently yielded a product with 1.32 ± 0.03% aggregate vs. a target of 1.5%. A comparison of the traditional approach involving column fractionation with the proposed approach indicates that the proposed approach results in achievement of satisfactory product purity (98.68 ± 0.03% for mechanistic model based PAT controlled pooling vs. 98.64 ± 0.16% for offline column fractionation based pooling). © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2758, 2019.

Systematic interpolation method predicts protein chromatographic elution from batch isotherm data without a detailed mechanistic isotherm model

Predicting protein elution for overloaded ion exchange columns requires models capable of describing protein binding over broad ranges of protein and salt concentrations. Although approximate mechanistic models are available, they do not always have the accuracy needed for precise predictions. The aim of this work is to develop a method to predict protein chromatographic behavior from batch isotherm data without relying on a mechanistic model. The method uses a systematic empirical interpolation (EI) scheme coupled with a lumped kinetic model with rate parameters determined from HETP measurements for non-binding conditions, to numerically predict the column behavior. For two experimental systems considered in this work, predictions based on the EI scheme are in excellent agreement with experimental elution profiles under highly overloaded conditions without using any adjustable parameters. A qualitative study of the sensitivity of predicting protein elution profiles to the precision, granularity, and extent of the batch adsorption data shows that the EI scheme is relatively insensitive to the properties of the dataset used, requiring only that the experimental ranges of protein and salt concentrations overlap those under which the protein actually elutes from the column and possess a ± 10% measurement precision.

Evaluation of a novel methacrylate-based Protein A resin for the purification of immunoglobulins and Fc-fusion proteins

Protein A affinity chromatography is a central part of most commercial monoclonal antibody and Fc-fusion protein purification processes. In the last couple years an increasing number of new Protein A technologies have emerged. One of these new Protein A technologies consists of a novel, alkaline-tolerant, Protein A ligand coupled to a macroporous polymethacrylate base matrix that has been optimized for immunoglobulin (Ig) G capture. The resin is interesting from a technology perspective because the particle size and pore distribution of the base beads are reported to have been optimized for high IgG binding and fast mass transfer, while the Protein A ligand has been engineered for enhanced alkaline tolerance. This resin was subjected to a number of technical studies including evaluating dynamic and static binding capacities, alkaline stability, Protein A leachate propensity, impurity clearance, and pressure–flow behavior. The results demonstrated similar static binding capacities as those achieved with industry standard agarose Protein A resins, but marginally lower dynamic binding capacities. Removal of impurities from the process stream, particularly host cell proteins, was molecule dependent, but in most instances matched the performance of the agarose resins. This resin was stable in 0.1 M NaOH for at least 100 h with little loss in binding capacity, with Protein A ligand leakage levels comparable to values for the agarose resins. Pressure–flow experiments in lab-scale chromatography columns demonstrated minimal resin compression at typical manufacturing flow rates. Prediction of resin compression in manufacturing scale columns did not suggest any pressure limitations upon scale up. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1125–1136, 2014

Fluorescence recovery after photobleaching investigation of protein transport and exchange in chromatographic media

A fully-mechanistic understanding of protein transport and sorption in chromatographic materials has remained elusive despite the application of modern continuum and molecular observation techniques. While measuring overall uptake rates in proteins in chromatographic media is relatively straightforward, quantifying mechanistic contributions is much more challenging. Further, at equilibrium in fully-loaded particles, measuring rates of kinetic exchange and diffusion can be very challenging. As models of multicomponent separations rely on accurate depictions of protein displacement and elution, a straightforward method is desired to measure the mobility of bound protein in chromatographic media. We have adapted fluorescence recovery after photobleaching (FRAP) methods to study transport and exchange of protein at equilibrium in a single particle. Further, we have developed a mathematical model to capture diffusion and desorption rates governing fluorescence recovery and investigate how these rates vary as a function of protein size, binding strength and media type. An emphasis is placed on explaining differences between polymer-modified and traditional media, which in the former case is characterized by rapid uptake, slow displacement and large elution pools, differences that have been postulated to result from steric and kinetic limitations. Finally, good qualitative agreement is achieved predicting flow confocal displacement profiles in polymer-modified materials, based solely on estimates of kinetic and diffusion parameters from FRAP observations.

Measurement of uptake curves and adsorption isotherms by automated microscale chromatography pipette tips

Automated microscale chromatography using pipette tips packed with microliters of resin is seen as an increasingly attractive option for high-throughput screening of purification conditions during early phase biopharmaceutical development. Two types of data that can be produced by these studies are uptake curves and isotherms, providing valuable fundamental separation data to assist with the prediction of larger-scale performance. This chapter will describe an operating protocol for this type of experiment using the example of ovine polyclonal antibodies binding to a multimodal weak cation exchange resin.

Experimental characterization of next-generation expanded-bed adsorbents for capture of a recombinant protein expressed in high-cell-density yeast fermentation

Expanded-bed adsorption (EBA) can be particularly useful in protein recovery from high-cell-density fermentation broth where conventional methods for harvest and clarification, such as continuous centrifugation and depth filtration, demand long processing times and are associated with high costs. In this work, the use of next-generation high-particle-density EBA adsorbents, including two mixed-mode resins, for the direct capture of a recombinant protein expressed in yeast at high cell densities is evaluated. Using classical experimental approaches and under different conditions (pH, salt, etc.), Langmuir isotherm parameters for these resins are obtained along with pore diffusivity values. Additional batch adsorption studies with Fastline® MabDirect, the resin that demonstrated the highest static binding capacity for the recombinant protein of interest under the conditions evaluated in this study, indicate competitive binding of nontarget proteins and approximately a 30% reduction in equilibrium binding capacity to 50 mg/mL settled bed in the presence of a 5%-10% cell concentration. Packed-bed (PB) dynamic binding capacities for the MabDirect resin (25-40 mg/mL PB) were significantly higher than for the Fastline® HSA resin and for the MabDirect MM resin in expanded-bed mode (5-10 mg/mL settled bed). Bed expansion behavior for the mMabDirect MM resin along with process yield and eluate purity are identified as a function of linear velocity and cell density, demonstrating process feasibility for pilot scale use.

Purification of β-lactoglobulin with a high-capacity anion exchanger: high-throughput process development and scale-up considerations

BACKGROUND

β-Lactoglobulin is the most abundant protein in bovine whey. It is a valuable nutriceutical with multiple physiological functions. There are many ongoing efforts to improve approaches by which this whey protein can be conveniently and economically purified in significant quantities. High-capacity resins for protein fractionation are currently available in the biotech industry. One such resin is evaluated in the present investigation.

RESULTS

This work describes a high-capacity ion exchange chromatography method for one-column fractionation of β-lactoglobulin from whey. It was obtained with a >90% purity. The dynamic binding capacity was measured in packed columns. Comparable value predicted on the basis of Langmuir isotherm analysis from batch adsorption data in a high-throughput 96-well format is shown. Scale-up considerations are discussed with respect to feed concentration and binding capacity.

CONCLUSIONS

The feasibility of preparing purified β-lactoglobulin with a single high-capacity anion exchanger step was demonstrated. A capacity of >200 mg mL(-1) was obtained. A significant improvement in productivity can be realized by a simultaneous increase of binding capacity and feed concentration.