Multi-dimensional fractionation and characterization of crude protein mixtures: toward establishment of a database of protein purification process development parameters.

A multi-dimensional fractionation and characterization scheme was developed for fast acquisition of the relevant molecular properties for protein separation from crude biological feedstocks by ion-exchange chromatography (IEX), hydrophobic interaction chromatography (HIC), and size-exclusion chromatography. In this approach, the linear IEX isotherm parameters were estimated from multiple linear salt-gradient IEX data, while the nonlinear IEX parameters as well as the HIC isotherm parameters were obtained by the inverse method under column overloading conditions. Collected chromatographic fractions were analyzed by gel electrophoresis for estimation of molecular mass, followed by mass spectrometry for protein identification. The usefulness of the generated molecular properties data for rational decision-making during downstream process development was equally demonstrated. Monoclonal antibody purification from crude hybridoma cell culture supernatant was used as case study. The obtained chromatographic parameters only apply to the employed stationary phases and operating conditions, hence prior high throughput screening of different chromatographic resins and mobile phase conditions is still a prerequisite. Nevertheless, it provides a quick, knowledge-based approach for rationally synthesizing purification cascades prior to more detailed process optimization and evaluation.

Selection of pH-related parameters in ion-exchange chromatography using pH-gradient operations.

This work demonstrates that the type of ion-exchanger (anion or cation), the mode of operation (bind-and-elute or flow-through), and the operational pH of ion-exchange chromatography (IEX) can be selected in a fast and rational way by analytical pH-gradient IEX operations, thereby eliminating the need for pH scouting or high-throughput screening. The developed approach was applied for the selection of an IEX process for the capture of a monoclonal antibody (MAb) from hybridoma cell culture supernatant (CCS). It was found within a day that MAb can optimally be captured by bind-and-elute mode cation-exchange chromatography (CEX) at pH 4.5 or anion-exchange chromatography (AEX) at pH 7.2 without lowering the salt concentration in the CCS. The performance of both CEX and AEX was predicted to be equal for this particular MAb capture.

pH-gradient ion-exchange chromatography: an analytical tool for design and optimization of protein separations.

This work demonstrates that a highly linear, controllable and wide-ranged pH-gradient can be generated through an ion-exchange chromatography (IEC) column. Such a pH-gradient anion-exchange chromatography was evaluated with 17 model proteins and found that acidic (pI<6) and basic (pI>8) proteins elute roughly at their pI, whereas neutral proteins (pI 6-8) elute at pH 8-9 regardless their pI values. Because of the flat nature of protein titration curves from pH approximately 6 to approximately 9, neutral proteins indeed exhibit nearly zero net charge at pH approximately 9. The elution-pH in pH-gradient IEC or the titration curve, but not the pI, was identified as the key parameter for pH optimization of preparative IEC in a fast and rational way. The pH-gradient IEC was also applied and found to be an excellent analytical tool for the fractionation of crude protein mixtures.

Analytical characterization of complex, biotechnological feedstocks by pH gradient ion exchange chromatography for purification process development.

The accelerating growth of the market for proteins and the growing interest in new, more complex molecules are bringing new challenges to the downstream process development of these proteins. This results in a demand for faster, more cost efficient, and highly understood downstream processes. Screening procedures based on high-throughput methods are widely applied nowadays to develop purification processes for proteins. However, screening highly complex biotechnological feedstocks, such as complete cell lysates containing target proteins often expressed with a low titre, is still very challenging. In this work we demonstrate a multidimensional, analytical screening approach based on pH gradient ion exchange chromatography (IEC), gel electrophoresis and protein identification via mass spectrometry to rationally characterize a biotechnological feedstock for the purpose of purification process development. With this very simple characterization strategy a two-step purification based on consecutive IEC operations was rapidly laid out for the purification of a diagnostic protein from a cell lysate reaching a purity of ∼80%. The target protein was recombinantly produced using an insect cell expression system.

Model-based high-throughput process development for chromatographic whey proteins separation.

In this study, an integrated approach involving the combined use of high-throughput screening (HTS) and column modeling during process development was applied to an industrial case involving the evaluation of four anion-exchange chromatography (AEX) resins and four hydrophobic interaction chromatography (HIC) resins for the separation of whey proteins having close pIs. From the HTS data, one resin of each type was selected (Capto Q and Octyl Sepharose 4 FF). Next, batch uptake experiments were performed to determine the adsorption isotherms of the major whey proteins on the selected resins, followed by isotherm parameters regression. Using the obtained isotherm parameters, the candidate chromatographic operations were modeled and experimentally validated. Finally, these were model-optimized and evaluated based on their optimized performances. In this example, Capto Q performed much better than Octyl Sepharose 4 FF in terms of column capacity, loading, throughput and productivity; hence, Capto Q was selected as the resin of choice for whey proteins separation. This operation was further scaled up from the lab scale (1 mL) to a preparative scale (35 L), with reproducible column elution profile. By this approach, a much wider space of operating variables could be investigated, thereby increasing the chances of finding the ideal operating conditions while keeping experimentation to the minimum.

High-throughput protein precipitation and hydrophobic interaction chromatography: salt effects and thermodynamic interrelation.

Salt-induced protein precipitation and hydrophobic interaction chromatography (HIC) are two widely used methods for protein purification. In this study, salt effects in protein precipitation and HIC were investigated for a broad combination of proteins, salts and HIC resins. Interrelation between the critical thermodynamic salting out parameters in both techniques was equally investigated. Protein precipitation data were obtained by a high-throughput technique employing 96-well microtitre plates and robotic liquid handling technology. For the same protein-salt combinations, isocratic HIC experiments were performed using two or three different commercially available stationary phases-Phenyl Sepharose low sub, Butyl Sepharose and Resource Phenyl. In general, similar salt effects and deviations from the lyotropic series were observed in both separation methods, for example, the reverse Hofmeister effect reported for lysozyme below its isoelectric point and at low salt concentrations. The salting out constant could be expressed in terms of the preferential interaction parameter in protein precipitation, showing that the former is, in effect, the net result of preferential interaction of a protein with water molecules and salt ions in its vicinity. However, no general quantitative interrelation was found between salting out parameters or the number of released water molecules in protein precipitation and HIC. In other words, protein solubility and HIC retention factor could not be quantitatively interrelated, although for some proteins, regular trends were observed across the different resins and salt types.

Model-based rational strategy for chromatographic resin selection.

A model-based rational strategy for the selection of chromatographic resins is presented. The main question being addressed is that of selecting the most optimal chromatographic resin from a few promising alternatives. The methodology starts with chromatographic modeling,parameters acquisition, and model validation, followed by model-based optimization of the chromatographic separation for the resins of interest. Finally, the resins are rationally evaluated based on their optimized operating conditions and performance metrics such as product purity, yield, concentration, throughput, productivity, and cost. Resin evaluation proceeds by two main approaches. In the first approach, Pareto frontiers from multi-objective optimization of conflicting objectives are overlaid for different resins, enabling direct visualization and comparison of resin performances based on the feasible solution space. The second approach involves the transformation of the resin performances into weighted resin scores, enabling the simultaneous consideration of multiple performance metrics and the setting of priorities. The proposed model-based resin selection strategy was illustrated by evaluating three mixed mode adsorbents (ADH, PPA, and HEA) for the separation of a ternary mixture of bovine serum albumin, ovalbumin, and amyloglucosidase. In order of decreasing weighted resin score or performance, the top three resins for this separation were ADH [PPA[HEA. The proposed model-based approach could be a suitable alternative to column scouting during process development, the main strengths being that minimal experimentation is required and resins are evaluated under their ideal working conditions, enabling a fair comparison. This work also demonstrates the application of column modeling and optimization to mixed mode chromatography.

High-throughput isotherm determination and thermodynamic modeling of protein adsorption on mixed mode adsorbents.

The thermodynamic modeling of protein adsorption on mixed-mode adsorbents functionalized with ligands carrying both hydrophobic and electrostatic groups was undertaken. The developed mixed mode isotherm was fitted with protein adsorption data obtained for five different proteins on four different mixed mode adsorbents by 96-well microtitre plate high throughput batch experiments on a robotic workstation. The developed mixed mode isotherm was capable of describing the adsorption isotherms of all five proteins (having widely different molecular masses and iso-electric points) on the four mixed mode adsorbents and over a wide range of salt concentrations and solution pH, and provided a unique set of physically meaningful parameters for each resin-protein-pH combination. The model could capture the typically observed minimum in mixed mode protein adsorption and predict the precise salt concentration at which this minimum occurs. The possibility of predicting the salt concentration at which minimum protein binding occurs presents new opportunities for designing better elution strategies in mixed mode protein chromatography. Salt-protein interactions were shown to have important consequences on mixed mode protein adsorption when they occur. Finally, the mixed mode isotherm also gave very good fit with literature data of BSA adsorption on a different mixed mode adsorbent not examined in this study. Hence, the mixed mode isotherm formalism presented in this study can be used with any mixed mode adsorbent having the hydrophobic and electrostatic functional groups. It also provides the basis for detailed modeling and optimization of mixed mode chromatographic separation of proteins.

Rational and systematic protein purification process development: the next generation.

Current biopharmaceutical manufacturing strongly relies on using purification platform processes, offering harmonization of practices and speed-to-market. However, the ability of such processes to respond quickly to anticipated higher quality and capacity demands is under question. Here, we describe novel approaches for purification process development that incorporate biothermodynamics, modern high throughput experimentation and simulation tools. Such development leads to production platform-specific databases containing thermodynamic protein descriptors of major host cell proteins over a range of experimental conditions. This will pave the way for in silico purification process development, providing better process understanding and the potential to respond quickly to product quality and market demands. Future efforts will focus on improving this field further and enabling more rationale in process development.

Metabolic flux analysis of a glycerol-overproducing Saccharomyces cerevisiae strain based on GC-MS, LC-MS and NMR-derived C-labelling data.

This study focuses on unravelling the carbon and redox metabolism of a previously developed glycerol-overproducing Saccharomyces cerevisiae strain with deletions in the structural genes encoding triosephosphate isomerase (TPI1), the external mitochondrial NADH dehydrogenases (NDE1 and NDE2) and the respiratory chain-linked glycerol-3-phosphate dehydrogenase (GUT2). Two methods were used for analysis of metabolic fluxes: metabolite balancing and (13)C-labelling-based metabolic flux analysis. The isotopic enrichment of intracellular primary metabolites was measured both directly (liquid chromatography-MS) and indirectly through proteinogenic amino acids (nuclear magnetic resonance and gas chromatography-MS). Because flux sensitivity around several important metabolic nodes proved to be dependent on the applied technique, the combination of the three (13)C quantification techniques generated the most accurate overall flux pattern. When combined, the measured conversion rates and (13)C-labelling data provided evidence that a combination of assimilatory metabolism and pentose phosphate pathway activity diverted some of the carbon away from glycerol formation. Metabolite balancing indicated that this results in excess cytosolic NADH, suggesting the presence of a cytosolic NADH sink in addition to those that were deleted. The exchange flux of four-carbon dicarboxylic acids across the mitochondrial membrane, as measured by the (13)C-labelling data, supports a possible role of a malate/aspartate or malate/oxaloacetate redox shuttle in the transfer of these redox equivalents from the cytosol to the mitochondrial matrix.