Mobile phase modifier effects in multimodal cation exchange chromatography

Modeling Chromatography Binding through Molecular Dynamics Simulations with Resin Fragments

Accurate atomistic modeling of the interactions of a chromatography resin with a solute can inform the selection of purification conditions for a product, an important problem in the biotech and pharmaceutical industries. We present a molecular dynamics simulation-based approach for the qualitative prediction of interaction sites (specificity) and retention times (affinity) of a protein for a given chromatography resin. We mimicked the resin with an unrestrained ligand composed of the resin headgroup coupled with successively larger fragments of the agarose backbone. The interactions of the ligand with the protein are simulated in an explicit solvent using the Replica Exchange Molecular Dynamics enhanced sampling approach in conjunction with Hydrogen Mass Repartitioning (REMD-HMR). We computed the ligand interaction surface from the simulation trajectories and correlated the features of the interaction surface with experimentally determined retention times. The simulation and analysis protocol were first applied to a series of ubiquitin mutants for which retention times on Capto MMC resin are available. The ubiquitin simulations helped identify the optimal ligand that was used in subsequent simulations on six proteins for which Capto MMC elution times are available. For each of the six proteins, we computed the interaction surface and characterized it in terms of a range of simulation-averaged residue-level physicochemical descriptors. Modeling of the salt concentrations required for elution with respect to the descriptors resulted in a linear fit in terms of aromaphilicity and Kyte-Doolittle hydrophobicity that was robust to outliers, showed high correlation, and correctly ranked the protein elution order. The physics-based model building approach described here does not require a large experimental data set and can be readily applied to different resins and diverse biomolecules.

Evaluation of preferred binding regions on ubiquitin and IgG1 FC for interacting with multimodal cation exchange resins using DEPC labeling/mass spectrometry

There is significant interest in identifying the preferred binding domains of biological products to various chromatographic materials. In this work, we develop a biophysical technique that uses diethyl pyrocarbonate (DEPC) based covalent labeling in concert with enzymatic digestion and mass spectrometry to identify the binding patches for proteins bound to commercially available multimodal (MM) cation exchange chromatography resins. The technique compares the changes in covalent labeling of the protein in solution and in the bound state and uses the differences in this labeling to identify residues that are sterically shielded upon resin binding and, therefore, potentially involved in the resin binding process. Importantly, this approach enables the labeling of many amino acids and can be carried out over a pH range of 5.5-7.5, thus enabling the protein surface mapping at conditions of interest in MM cation exchange systems. The protocol is first developed using the model protein ubiquitin and the results indicate that lysine residues located on the front face of the protein show dramatic changes in DEPC labeling while residues present on other regions have minimal or no reductions. This indicates that the front face of ubiquitin is likely involved in resin binding. In addition, surface property maps indicate that the hypothesized front face binding region consists of overlapping positively charged and hydrophobic patches. The technique is then employed with an IgG1 F_C and the results indicate that residues on the C_H 2-C_H 3 interface and the hinge are significantly sterically shielded upon binding to the resin. Further, these regions are again associated with significant overlap of positively charged and hydrophobic patches. On the other hand, while, residues on the C_H 2 and the front face of the IgG1 F_C also exhibited some changes in DEPC labeling upon binding, these regions have less distinct charged and hydrophobic patches. Importantly, the hypothesized binding patches identified for both ubiquitin and F_C using this approach are shown to be consistent with previously reported NMR studies. In contrast to NMR, this new approach enables the identification of preferred binding regions without the need for isotopically labeled proteins or chemical shift assignments. The technique developed in this work sets the stage for the evaluation of the binding domains of a wide range of biological products to chromatographic surfaces, with important implications for designing biomolecules with improved biomanufacturability properties.

Protein association on multimodal chromatography media

The phenomenon of protein-protein association on multimodal chromatography resins was described for two different case study examples. The adsorption pattern of single-component solutions of calcium-rich alpha-lactalbumin (aLaCa) and calcium-depleted alpha-lactalbumin (aLa) and their mixtures with bovine serum albumin was determined on a multimodal anion-exchange chromatography medium. In single-component solutions, both aLaCa and aLa exhibited identical adsorption behavior at low resin loadings, whereas at high loadings the adsorption strength of aLa markedly exceeded that of alaCa. In binary mixtures, the adsorption of BSA enhanced at high concentrations of aLa or aLaCa in the adsorbed phase. The unusual adsorption patterns observed were attributed to the tendency of the proteins for molecular association in the adsorbed phase in single and binary solutions. The phenomena was examined for different pH of the solution: pH 6, 7, 8, and different solvent environments: phosphate buffer (PB), bis tris buffer (BT), 100 mM NaCl in BT and bis tris propane buffer (BTP). The strongest effect was observed for PB and for 100 mM NaCl in BT. Its occurrence was also evidenced for other case study example, i.e., adsorption of single-component solutions and binary mixtures of a monoclonal antibody (mAb) and lysozyme (LYZ) on a multimodal cation-exchange chromatography medium. The enhancement of adsorption of mAb was observed at high concentrations of LYZ in the adsorbed phase. To quantify the underlying effects, a mechanistic model was used, which accounted for both protein association and exclusion resulting from attractive and repulsive protein-protein iterations in the adsorbed phase.

Systematic workflow for studying domain contributions of bispecific antibodies to selectivity in multimodal chromatography

In this article, a systematic workflow was formulated and implemented to understand selectivity differences and preferred binding patches for bispecific monoclonal antibodies (mAbs) and their parental mAbs on three multimodal cation exchange resin systems. This workflow incorporates chromatographic screening of the parent mAbs and their fragments at various pH followed by surface property mapping and protein footprinting using covalent labeling followed by liquid chromatography-mass spectrometry analysis. The chromatography screens on multimodal resins with the intact mAbs indicated enhanced selectivity as compared to single-mode interaction systems. While the bispecific antibody (bsAb) eluted between the two parental mAbs on most of the resins, the retention of the bispecific transitioned from co-eluting with one parental mAb to the other parental mAb on Capto MMC. To investigate the contribution of different domains, mAb fragments were evaluated and the results indicated that the interactions were likely dominated by the Fab domain at higher pH. Protein surface property maps were then employed to hypothesize the potential preferred binding patches in the solvent-exposed regions of the parental Fabs. Finally, protein footprinting was carried out with the parental mAbs and the bsAb in the bound and unbound states at pH 7.5 to identify the preferred binding patches. Results with the intact mAb analysis supported the hypothesis that interactions with the resins were primarily driven by the residues in the Fab fragments and not the Fc. Furthermore, peptide mapping data indicated that the light chain may be playing a more important role in the higher binding of Parent A as compared with Parent B in these resin systems. Finally, results with the bsAb indicated that both halves of the molecule contributed to binding with the resins, albeit with subtle differences as compared to the parental mAbs. The workflow presented in this paper lays the foundation to systematically study the chromatographic selectivity of large multidomain molecules which can provide insights into improved biomanufacturability and expedited downstream bioprocess development.

Probing IgG1 FC-Multimodal Nanoparticle Interactions: A Combined Nuclear Magnetic Resonance and Molecular Dynamics Simulations Approach

In this study, NMR and molecular dynamics simulations were employed to study IgG1 F_C binding to multimodal surfaces. Gold nanoparticles functionalized with two multimodal cation-exchange ligands (Capto and Nuvia) were synthesized and employed to carry out solution-phase NMR experiments with the F_C. Experiments with perdeuterated ¹⁵N-labeled F_C and the multimodal surfaces revealed micromolar residue-level binding affinities as compared to millimolar binding affinities with these ligands in free solution, likely due to cooperativity and avidity effects. The binding of F_C with the Capto ligand nanoparticles was concentrated near an aliphatic cluster in the C_H2/C_H3 interface, which corresponded to a focused hydrophobic region. In contrast, binding with the Nuvia ligand nanoparticles was more diffuse and corresponded to a large contiguous positive electrostatic potential region on the side face of the F_C. Results with lower-ligand-density nanoparticles indicated a decrease in binding affinity for both systems. For the Capto ligand system, several aliphatic residues on the F_C that were important for binding to the higher-density surface did not interact with the lower-density nanoparticles. In contrast, no significant difference was observed in the interacting residues on the F_C to the high- and low-ligand density Nuvia surfaces. The binding affinities of F_C to both multimodal-functionalized nanoparticles decreased in the presence of salt due to the screening of multiple weak interactions of polar and positively charged residues. For the Capto ligand nanoparticle system, this resulted in an even more focused hydrophobic binding region in the interface of the C_H2 and C_H3 domains. Interestingly, for the Nuvia ligand nanoparticles, the presence of salt resulted in a large transition from a diffuse binding region to the same focused binding region determined for Capto nanoparticles at 150 mM salt. Molecular dynamics simulations corroborated the NMR results and provided important insights into the molecular basis of F_C binding to these different multimodal systems containing clustered (observed at high-ligand densities) and nonclustered ligand surfaces. This combined biophysical and simulation approach provided significant insights into the interactions of F_C with multimodal surfaces and sets the stage for future analyses with even more complex biotherapeutics.

Influence of excipients in Protein A chromatography and virus inactivation

The purification of monoclonal antibodies and Fc fusion proteins consist of several unit operations operated commonly as a platform approach, starting with Protein A chromatography. The first capture step, the following low pH virus inactivation, and subsequent ion exchange chromatography steps are mostly able to remove any impurities, like host cell proteins, aggregates, and viruses. The changes in pH and conductivity during these steps can lead to additional unwanted product species like aggregates. In this study, excipients with stabilizing abilities, like polyols, were used as buffer system additives to study their impact on several aspects during Protein A chromatography, low pH virus inactivation, and cation exchange chromatography. The results show that excipients, like PEG4000, influence antibody elution behavior, as well as host-cell protein elution behavior in a pH-gradient setup. Sugar excipients, like Sucrose, stabilize the antibody during low pH virus inactivation. All excipients tested show no negative impact on virus inactivation and dynamic binding capacity in a subsequent cation exchange chromatography step. This study indicates that excipients and, possibly excipient combinations, can have a beneficial effect on purification without harming subsequent downstream processing steps.

Using multimodal chromatography for post-conjugation antibody-drug conjugate purification: A methodology from high throughput screening to in-silico process development

In this paper, a methodology for the development of a multimodal chromatography process is presented that is aimed at removal of under-conjugated antibody-drug conjugate (ADC) species. Two ADCs are used as case studies: One ADC results from site-directed conjugation to inserted cysteine residues and has a drug-to-antibody ratio (DAR) of two, the other is the product of conjugation to interchain disulfide bonds with a DAR of eight. First, filter plate screening studies are designed for the unconjugated antibody and the ADCs. Different metrics for the analysis of these data sets are presented and discussed. From this analysis, the selected process conditions are then carried out using a benchtop chromatography system to confirm the separations observed in the filter plate studies while simultaneously generating data to estimate steric mass-action isotherm and mass transport parameters for process simulation. This column model is then employed to develop separation processes in-silico for the removal of the unconjugated parent antibody and under-conjugated product variants. The optimized process conditions identified using the model are then verified experimentally. The methodology presented in this work utilizes multimodal chromatography for ADC purification and provides the framework for a streamlined systematic approach to process development.

Identification of preferred multimodal ligand-binding regions on IgG1 FC using nuclear magnetic resonance and molecular dynamics simulations

In this study, the binding of multimodal chromatographic ligands to the IgG1 F_C domain were studied using nuclear magnetic resonance and molecular dynamics simulations. Nuclear magnetic resonance experiments carried out with chromatographic ligands and a perdeuterated ¹⁵ N-labeled F_C domain indicated that while single-mode ion exchange ligands interacted very weakly throughout the F_C surface, multimodal ligands containing negatively charged and aromatic moieties interacted with specific clusters of residues with relatively high affinity, forming distinct binding regions on the F_C . The multimodal ligand-binding sites on the F_C were concentrated in the hinge region and near the interface of the C_H 2 and C_H 3 domains. Furthermore, the multimodal binding sites were primarily composed of positively charged, polar, and aliphatic residues in these regions, with histidine residues exhibiting some of the strongest binding affinities with the multimodal ligand. Interestingly, comparison of protein surface property data with ligand interaction sites indicated that the patch analysis on F_C corroborated molecular-level binding information obtained from the nuclear magnetic resonance experiments. Finally, molecular dynamics simulation results were shown to be qualitatively consistent with the nuclear magnetic resonance results and to provide further insights into the binding mechanisms. An important contribution to multimodal ligand-F_C binding in these preferred regions was shown to be electrostatic interactions and π-π stacking of surface-exposed histidines with the ligands. This combined biophysical and simulation approach has provided a deeper molecular-level understanding of multimodal ligand-F_C interactions and sets the stage for future analyses of even more complex biotherapeutics.

Single-step purification of a small non-mAb biologic by peptide-ELP-based affinity precipitation

Affinity precipitation using stimulus-responsive biopolymers such as elastin-like polypeptides (ELPs) have been successfully employed for the purification of monoclonal antibodies. In the current work, we extend these studies to the development of an ELP-peptide fusion for the affinity precipitation of the therapeutically relevant small non-mAb biologic, AdP. A 12-mer affinity peptide ligand (P10) was identified by a primary phage biopanning followed by a secondary in-solution fluorescence polarization screen. Peptide P10 and AdP interacted with a K_D of 19.5 µM. A fusion of P10 with ELP was then shown to be successful in selectively capturing the biologic from a crude mixture. While pH shifts alone were not sufficient for product elution, the use of pH in concert with fluid-phase modifiers such as NaCl, arginine, or ethylene glycol was effective. In particular, the use of pH 8.5 and an arginine concentration of 500 mM enabled >80% product recovery. The overall process performance evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and reversed-phase ultra-performance liquid chromatography analyses indicated successful single-step purification of the biologic from an Escherichia coli lysate resulting in ∼90% purity and >80% recovery. These results demonstrate that phage display can be readily employed to identify a peptide ligand capable of successfully carrying out the purification of a non-antibody biological product using ELP-based affinity precipitation.

Recombinant human erythropoietin separation using a cation-exchange multimodal adsorbent

This work deals with the capture of human recombinant erythropoietin (rhEPO) from a mixture of proteins in a concentrated postcultivation supernatant. Cation-exchange multimodal adsorbent Capto MMC ImpRes was selected as potential chromatographic separation material. Its equilibrium properties were investigated in batch adsorption experiments. The effect of pH in the range of 5.5—7.5 and NaCl concentration in the range of 0—300 mM on the adsorption of rhEPO and contaminant proteins was examined. Optimal conditions found in these equilibrium experiments were applied to rhEPO adsorption in a chromatographic column. Several experiments were carried out at different elution conditions to optimize the rhEPO yield and selectivity.

Downstream Processing Technologies/Capturing and Final Purification : Opportunities for Innovation, Change, and Improvement. A Review of Downstream Processing Developments in Protein Purification

Increased pressure on upstream processes to maximize productivity has been crowned with great success, although at the cost of shifting the bottleneck to purification. As drivers were economical, focus is on now on debottlenecking downstream processes as the main drivers of high manufacturing cost. Devising a holistically efficient and economical process remains a key challenge. Traditional and emerging protein purification strategies with particular emphasis on methodologies implemented for the production of recombinant proteins of biopharmaceutical importance are reviewed. The breadth of innovation is addressed, as well as the challenges the industry faces today, with an eye to remaining impartial, fair, and balanced. In addition, the scope encompasses both chromatographic and non-chromatographic separations directed at the purification of proteins, with a strong emphasis on antibodies. Complete solutions such as integrated USP/DSP strategies (i.e., continuous processing) are discussed as well as gains in data quantity and quality arising from automation and high-throughput screening (HTS). Best practices and advantages through design of experiments (DOE) to access a complex design space such as multi-modal chromatography are reviewed with an outlook on potential future trends. A discussion of single-use technology, its impact and opportunities for further growth, and the exciting developments in modeling and simulation of DSP rounds out the overview. Lastly, emerging trends such as 3D printing and nanotechnology are covered. Graphical Abstract Workflow of high-throughput screening, design of experiments, and high-throughput analytics to understand design space and design space boundaries quickly. (Reproduced with permission from Gregory Barker, Process Development, Bristol-Myers Squibb).

Protein Solvent Interaction: Transition of Protein-solvent Interaction Concept from Basic Research into Solvent Manipulation of Chromatography

Previously, we have reviewed in this journal (Arakawa, T., Kita, Y., Curr. Protein Pept. Sci., 15, 608-620, 2014) the interaction of arginine with proteins and various applications of this solvent additive in the area of protein formulations and downstream processes. In this special issue, we expand the concept of protein-solvent interaction into the analysis of the effects of solvent additives on various column chromatography, including mixed-mode chromatography. Earlier in our research, we have studied the interactions of such a variety of solvent additives as sugars, salts, amino acids, polymers and organic solvents with a variety of proteins, which resulted in mechanistic understanding on their protein stabilization and precipitation effects, the latter known as Hofmeister series. While such a study was then a pure academic research, rapid development of genetic engineering technologies and resultant biotechnologies made it a valuable knowledge in fully utilizing solvent additives in manipulation of protein solution, including column chromatography.

Use of mobile phase additives for the elution of bispecific and monoclonal antibodies from phenyl based hydrophobic interaction chromatography resins

Hydrophobic interaction chromatography (HIC) is routinely used in the purification of biopharmaceuticals such as antibodies. However, hydrophobic proteins can be difficult to elute resulting in low recovery of product thereby complicating early phase process development and potentially excluding the use of HIC resins for their manufacture. Mobile phase additives such as hexylene glycol and arginine facilitate protein elution from resins including HIC; therefore, these additives were evaluated toward the recovery and purification of bispecific and monoclonal antibodies from Phenyl Sepharose HP and Capto Phenyl ImpRes resins. The influences of gradient versus step elution as well as superficial linear velocity on product quality were evaluated. Improved protein recovery and reduction of both soluble product aggregate and host cell protein were observed for the tested antibodies with both hexylene glycol and arginine. Furthermore, the impact of salt removal from the HIC load on protein-resin binding was examined providing opportunities to minimize processing time. This method was successfully scaled using a Phenyl Sepharose HP (5 cm i.d. × 20.0 cm) and Capto Phenyl ImpRes (3.2 cm i.d. × 21.4 cm) column demonstrating potential for manufacturing purposes.

Interactions of Multimodal Ligands with Proteins: Insights into Selectivity Using Molecular Dynamics Simulations

Fundamental understanding of protein-ligand interactions is important to the development of efficient bioseparations in multimodal chromatography. Here we employ molecular dynamics (MD) simulations to investigate the interactions of three different proteins--ubiquitin, cytochrome C, and α-chymotrypsinogen A, sampling a range of charge from +1e to +9e--with two multimodal chromatographic ligands containing similar chemical moieties--aromatic, carboxyl, and amide--in different structural arrangements. We use a spherical harmonic expansion to analyze ligand and individual moiety density profiles around the proteins. We find that the Capto MMC ligand, which contains an additional aliphatic group, displays stronger interactions than Nuvia CPrime ligand with all three proteins. Studying the ligand densities at the moiety level suggests that hydrophobic interactions play a major role in determining the locations of high ligand densities. Finally, the greater structural flexibility of the Capto MMC ligand compared to that of the Nuvia cPrime ligand allows for stronger structural complementarity and enables stronger hydrophobic interactions. These subtle and not-so-subtle differences in binding affinities and modalities for multimodal ligands can result in significantly different binding behavior towards proteins with important implications for bioprocessing.

Generic chromatography-based purification strategies accelerate the development of downstream processes for biopharmaceutical proteins produced in plants

Plants offer a valuable alternative to cultured mammalian cells for the production of recombinant biopharmaceutical proteins. However, the target protein typically represents only a minor fraction of the total protein in the initial plant extract, which means that the development of product-specific chromatography-based purification strategies is often laborious and expensive. To address this challenge, we designed a generic downstream process that is suitable for the purification of recombinant proteins with diverse properties from plant production platforms. This was achieved by focusing on the binding behavior of tobacco host cell proteins (HCPs) to a broad set of chromatography resins under different pH and conductivity conditions. Strong cation exchanger and salt-tolerant anion exchanger resins exhibited the best resolution of tobacco HCPs among the 13 tested resins, and their selectivity was easy to manipulate through the adjustment of pH and conductivity. The advantages, such as direct capture of a target protein from leaf extract, and limitations, such as low binding capacity, of various chromatography ligands and resins are discussed. We also address the most useful applications of the chromatography ligands, namely recovery of proteins with a certain pI, in a downstream process that aims to purify diverse plant-derived biopharmaceutical proteins. Based on these results, we describe generic purification schemes that are suitable for acidic, neutral, and basic target proteins, as a first step toward the development of industrial platform processes.

The use of quantitative structure-activity relationship models to develop optimized processes for the removal of tobacco host cell proteins during biopharmaceutical production

The production of recombinant pharmaceutical proteins in plants benefits from the low cost of upstream production and the greater scalability of plants compared to fermenter-based systems. Now that manufacturing processes that comply with current good manufacturing practices have been developed, plants can compete with established platforms on equal terms. However, the costs of downstream processing remain high, in part because of the dedicated process steps required to remove plant-specific process-related impurities. We therefore investigated whether the ideal strategy for the chromatographic removal of tobacco host cell proteins can be predicted by quantitative structure-activity relationship (QSAR) modeling to reduce the process development time and overall costs. We identified more than 100 tobacco proteins by mass spectrometry and their structures were reconstructed from X-ray crystallography, nuclear magnetic resonance spectroscopy and/or homology modeling data. The resulting three-dimensional models were used to calculate protein descriptors, and significant descriptors were selected based on recently-published retention data for model proteins to develop QSAR models for protein retention on anion, cation and mixed-mode resins. The predicted protein retention profiles were compared with experimental results using crude tobacco protein extracts. Because of the generic nature of the method, it can easily be transferred to other expression systems such as mammalian cells. The quality of the models and potential improvements are discussed.