Isoelectric point separation of proteins by capillary pH-gradient ion-exchange chromatography

Protein concentration and analyzing charge variants in a co-formulation comprising three monoclonal antibodies: A cation-exchange chromatography approach

In the realm of therapeutic antibodies, co-formulations comprising two or more monoclonal antibodies (mAbs) have emerged as a promising strategy, offering enhanced treatment efficacy, improved efficiency, and prolonged intellectual property protection. These advantages have sparked significant interest among both patients and pharmaceutical companies. However, the quantification and analysis of individual mAbs within such co-formulations pose a substantial challenge due to their similar physicochemical properties. To address this challenge, we introduce a pH gradient cation exchange chromatography (CEX) method designed to effectively separate three mAbs that share significant similarities in molecular weight, structure, and isoelectric points (pIs) etc. This versatile approach not only facilitates the accurate quantification of each mAb's concentration and their respective ratios within the co-formulation, but also allows for the comprehensive characterization of all charge variants present. In the case of a co-formulation containing three antibodies, the developed CEX method demonstrated superior performance compared to other techniques. The method's robustness was further underscored by its qualification parameters, including acceptable precision (RSD ≤ 3 %), accuracy (95 %-115 % recovery), and linearity (R2 > 0.99) across a range of 10 to 30 μg load for each mAb. Moreover, the method has been successfully applied in stability studies to quantitatively analyze individual mAb concentrations within co-formulations, marking a significant advancement in the field. Through this work, we contribute a crucial analytical insight into mAb co-formulations, especially those comprising three or more molecules, underscoring its considerable potential to propel the field of biotherapeutic co-formulations forward.

Multiple, simultaneous, independent gradients for a versatile multidimensional liquid chromatography. Part II: Application 3 - Scouting optimization strategies for separation of monoclonal antibodies by dual simultaneous independent gradients of pH & salt on a weak cation exchange stationary phase

In previous publications we have described the pISep dual simultaneous, independent gradients (DSIGs) liquid chromatography (LC) for uncoupling gradients of non-buffering solute (NaCl, urea or acetonitrile) from externally generated pH gradients. In DSIGs the shape and slope of the [salute] gradient does not depend on the shape and slope of the pH gradient. The technique allows in a single run true simultaneous two dimensional LC separation of complex protein mixtures on various stationary phases including anion, cation exchangers (AEX, CEX), reversed phase (RP), mixed mode and mixed bed. Using a humanized IgG1 (HIgG1) monoclonal antibody (MAb) and a variety of pH & [NaCl] DSIGs, we show that most of MAb isoforms can be successfully separated from each other. These experimental observations are supported by an initial theoretical argument presented here predicting an overall improvement of all MAb isoforms separation by DSIGs of pH & [NaCl]. Theoretical calculations predict that, in general, there exists an optimal non-zero isocratic salt concentration in a pH gradient separation that will resolve isoforms close in binding energy, but a wide range of salt concentrations will be required for acceptable resolution of all isoforms. Theory also predicts better separation of weaker rather than stronger binding isoforms. Experimentally, we have found that no one set of DSIGs LC conditions could optimally baseline resolve all identifiable MAb isoforms in a single run of reasonable duration. The versatility and simplicity of the pH & [NaCl] pISep DSIGs LC allows fast, automated scouting of protein separations over any range of pH from 2.4 to 10.8 and [NaCl] from 0 to 1 M without changing the chemistry of the buffering system. Due to the universal applicability of the pISep buffering system in IEX LC, the researcher is given a powerful tool to easily develop pH & [NaCl] DSIGs protocols that vary mobile phase compositions to achieve high resolution separations of targeted proteins.

Theoretical Analysis of a Nonequilibrium Transport Model of Two-Dimensional Nonisothermal Reactive Chromatography Accounting for Bi-Langmuir Isotherm

The current study investigates a nonequilibrium and nonlinear two-dimensional lumped kinetic transport model of nonisothermal reactive liquid chromatography, considering the Bi-Langmuir adsorption isotherm, heterogeneous reaction rates, radial and axial concentration variations, and the adsorption and reaction enthalpies. The mathematical models of packed bed chromatographic processes are expressed by a highly nonlinear system of coupled partial differential algebraic equations connecting the phenomena of convection, diffusion, and reaction, for mass and energy balance, the differential algebraic equations for mass balance in the solid phase, and the algebraical expressions for the adsorption isotherms and for the reaction rates. The nonlinearity of the reaction term and the adsorption isotherm preclude the derivation of an analytical solution for the model equations. For this reason, a semidiscrete, high-resolution, finite-volume technique is extended and employed in this study to obtain the numerical solution. Several consistency checks are performed to evaluate the model predictions and analyze the precision of the proposed numerical scheme. A number of heterogeneously catalyzed stoichiometric reactions are numerically simulated to examine reactor performance under the influence of temperature and Bi-Langmuir adsorption dynamics, the level of coupling between mass and energy fronts, and to study the effects of various critical parameters. The numerical results obtained are beneficial for optimal predictive control and process optimization during production and the development of methods for systematic design and fault detection of nonisothermal liquid chromatographic reactors, and hence constitute the first step to provide deeper insight into the overall evaluation of integrated reaction and separation processes.

Sensitive identification of milk protein allergens using on-line combination of transient isotachophoresis/micellar electrokinetic chromatography and capillary isoelectric focusing in fused silica capillary with roughened part

A method for on-line concentration of milk proteins from large sample volumes using combination of transient isotachophoresis (tITP) and micellar electrokinetic chromatography (MEKC) in fused silica capillary with an inner roughened part has been developed. The method utilizes reversible dynamic adsorption of proteins onto a thin layer of PEG 4000 on the roughened surface of the capillary. In addition, the tITP/MEKC method was combined with capillary isoelectric focusing (CIEF) for on-line concentration, separation, identification and sensitive determination of proteins in skimmed milk. The method allows analysis of up to 50 μL of sample. This study has focused on the four important whey proteins, bovine serum albumin (BSA), α-lactalbumin (α-LA), and two genetic variants of β-lactoglobulin (β-LG A and β-LG B). The proteins were identified on the basis of their migration times and characteristic pI values. The pI values of BSA, α-LA, β-LG A, and β-LG B were determined as 4.7, 4.4, 5.1, and 5.2, respectively. Limits of detection for BSA, α-LA and both β-LG variants were found as 1.2, 1.0 and 1.0 pg mL^-1, respectively. The linearity of calibration curves was characterized by the R² = 0.9982. The method provided highly reproducible results as the relative standard deviations of the migration times and peak areas of the examined proteins did not exceed 1.6%.

In Vitro Biochemical Analysis of Recombinant Plant Proteins Under Oxidation

Biochemical analysis is crucial for determining protein functionality changes during various conditions, including oxidative stress conditions. In this chapter, after giving brief guidelines for experimental design, we provide step-by-step instructions to purify recombinant plant proteins from E. coli, to prepare reduced and oxidized proteins for activity assay, and to characterize the protein under reducing and oxidizing conditions, with a focus on thiol-based oxidative modifications, like S-sulfenylation and disulfide formations.

Adsorptive filtration: A case study for early impurity reduction in an Escherichia coli production process

Primary recovery of intracellular products from Escherichia coli requires cell disruption which leads to a massive release of process-related impurities burdening subsequent downstream process (DSP) unit operations. Especially, DNA and endotoxins challenge purification operations due to their size and concentrations. Consequently, an early reduction in impurities will not only simplify the production process but also increase robustness while alleviating the workload afterward. In the present work, we studied the proof of concept whether a nonwoven anion exchange filter material decreases soluble impurities immediately at the clarification step of E. coli DSP. In a first attempt, endotoxin burden was reduced by 4.6-fold and the DNA concentration by 3.6-fold compared to conventional depth filtration. A design of experiment for the adsorptive filtration approach was carried out to analyze the influence of different critical process parameters (CPPs) on impurity reduction. We showed that depending on the CPPs chosen, a DNA lowering of more than 3 log values, an endotoxin decrease of approximately 7 logs, and a minor HCP clearance of at least 0.3 logs could be achieved. Thus, we further revealed a chromatography column protecting effect when using adsorptive filtration beforehand.

Charge variants characterization and release assay development for co-formulated antibodies as a combination therapy

Combination therapy is a fast-growing strategy to maximize therapeutic benefits to patients. Co-formulation of two or more therapeutic proteins has advantages over the administration of multiple medications, including reduced medication errors and convenience for patients. Characterization of co-formulated biologics can be challenging due to the high degree of similarity in the physicochemical properties of co-formulated proteins, especially at different concentrations of individual components. We present the results of a deamidation study of one monoclonal antibody component (mAb-B) in co-formulated combination antibodies (referred to as COMBO) that contain various ratios of mAb-A and mAb-B. A single deamidation site in the complementarity-determining region of mAb-B was identified as a critical quality attribute (CQA) due to its impact on biological activity. A conventional charge-based method of monitoring mAb-B deamidation presented specificity and robustness challenges, especially when mAb-B was a minor component in the COMBO, making it unsuitable for lot release and stability testing. We developed and qualified a new, quality-control-friendly, single quadrupole Dalton mass detector (QDa)-based method to monitor site-specific deamidation. Our approach can be also used as a multi-attribute method for monitoring other quality attributes in COMBO. This analytical paradigm is applicable to the identification of CQAs in combination therapeutic molecules, and to the subsequent development of a highly specific, highly sensitive, and sufficiently robust method for routine monitoring CQAs for lot release test and during stability studies.

Sodium hypochlorite assisted membrane cleaning: Alterations in the characteristics of organic foulants and membrane permeability

Chemical cleaning is an important approach for alleviating severe fouling in membrane separation processes. In this study, lysozyme (LYS) was exposed to sodium hypochlorite (NaClO) with varied concentrations (0-2000 ppm) to understand the changes in the physicochemical properties and functional groups as well as the variations in membrane permeabilities. The results showed that membrane filterability exhibited an obvious 'U-shaped' trend, and the valley existed when the ratio of Cl/C (the ratio of NaClO and TOC concentrations in feed water) is among 1.35-3.09. Upon exposure to low dose NaClO, three-dimensional fluorescence excitation-emission matrix (3D-EEM) spectra showed that tryptophan protein substances were transformed to more hydrophobic humic-like substances. Fourier transform infrared (FTIR) analysis further confirmed that exposure to low dose NaClO promoted the breakage of aromatic substituents, leading to the formation of hydrophobic condensed aromatic substances. On the contrary, at high NaClO loads, protein structures were destroyed completely and almost no obvious fluorescent intensities could be detected, which promoted the recovery of membrane filterabilities. Notably, the chemical cleaning mechanisms of fouled membranes with NaClO were understood in depth in this study. These results provide new information about the oxidation products of LYS and the cleaning efficiency upon exposure to NaClO.

Capillary ion-exchange chromatography with nanogram sensitivity for the analysis of monoclonal antibodies

Ion-exchange chromatography (IEC) is widely used for profiling the charge heterogeneity of proteins, including monoclonal antibodies (mAbs). Despite good resolving power and robustness, ionic strength-based ion-exchange separations are generally product specific and can be time consuming to develop. In addition, conventional analytical scale ion-exchange separations require tens of micrograms of mAbs for each injection, amounts that are often unavailable in sample-limited applications. We report the development of a capillary IEC (c-IEC) methodology for the analysis of nanogram amounts of mAb charge variants. Several key modifications were made to a commercially available liquid chromatography system to perform c-IEC for charge variant analysis of mAbs with nanogram sensitivity. We demonstrate the method for multiple monoclonal antibodies, including antibody fragments, on different columns from different manufacturers. Relative standard deviations of <10% were achieved for relative peak areas of main peak, acidic and basic regions, which are common regions of interest for quantifying monoclonal antibody charge variants using IEC. The results herein demonstrate the excellent sensitivity of this c-IEC characterization method, which can be used for analyzing charge variants in sample-limited applications, such as early-stage candidate screening and in vivo studies.

Comparison of chromatographic ion-exchange resins

A comparative study on weak anion exchangers was performed to investigate the pH dependence, binding strength, particle size distribution, and static and dynamic capacity of the chromatographic resins. The resins tested included: DEAE Sepharose FF, Poros 50 D, Fractogel EMD DEAE (M), MacroPrep DEAE Support, DEAE Ceramic HyperD 20, and Toyopearl DEAE 650 M. Testing was performed with five different model proteins: Anti-FVII mAb (immunoglobulin G), aprotinin, bovine serum albumin (BSA), Lipolase (Novozymes), and myoglobin. Retention showed an expected increasing trend as a function of pH for proteins with low pI. A decrease in retention was observed for some resins at pH 9 likely due to initiation of deprotonation of the weak anion-exchange ligands. Expected particle size distribution was obtained for all resins compared to previous studies. Binding strength to weak anion-exchange resins as a function of ionic strength depends on the specific protein. Binding and elution at low salt concentration may be performed with Toyopearl DEAE 650 M, while binding and elution at high salt concentration may be performed with MacroPrep DEAE Support. Highest binding capacities were generally obtained with Poros 50 D followed by DEAE Ceramic HyperD 20. A general good agreement was obtained between this study and data obtained by the suppliers. Verification of binding strength trends with model proteins was achieved with human growth hormone (hGH) and a hGH variant on the same resins with different elution salts, sodium chloride, sodium hydrogenphosphate, sodium sulphate, and sodium acetate. Static capacity measurements obtained in the traditional experimental set-up were compared with high-throughput screening (HTS) technique experiments with reasonable agreement. Isotherm data obtained from HTS techniques and pulse experiments were successfully combined with mathematical modelling to simulate, develop and optimise the separation process of two model proteins, Lipolase and BSA. The data presented in this paper may be used for selection of resins for testing in process development.

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.

HPLC analysis and purification of peptides

High-performance liquid chromatography (HPLC) has proved extremely versatile over the past 25 yr for the isolation and purification of peptides varying widely in their sources, quantity and complexity. This article covers the major modes of HPLC utilized for peptides (size-exclusion, ion-exchange, and reversed-phase), as well as demonstrating the potential of a novel mixed-mode hydrophilic interaction/cation-exchange approach developed in this laboratory. In addition to the value of these HPLC modes for peptide separations, the value of various HPLC techniques for structural characterization of peptides and proteins will be addressed, e.g., assessment of oligomerization state of peptides/proteins by size-exclusion chromatography and monitoring the hydrophilicity/hydrophobicity of amphipathic alpha-helical peptides, a vital precursor for the development of novel antimicrobial peptides. The value of capillary electrophoresis for peptide separations is also demonstrated. Preparative reversed-phase chromatography purification protocols for sample loads of up to 200 mg on analytical columns and instrumentation are introduced for both peptides and recombinant proteins.

Visualizing Ion Electromigration during Isotachophoretic Separations with Capillary Isotachophoresis-NMR

Sample stacking techniques in electrophoresis are gaining popularity due to their ability to provide improved sensitivity and separation efficiency. The principles behind sample stacking and electrophoretic migration have been studied extensively. Nevertheless, there are still a number of observations and descriptions of ionic boundaries and migration modes for which the underlying principles are not yet fully understood. For example, the behavior of capillary isotachophoresis (cITP) systems that exhibit self-sharpening effects can be complex, especially when the buffer systems contain many ionic components. In this work, cITP coupled with 1H NMR detection is used to study electrophoretic migration of ions in both anionic and cationic cITP. A significant advantage of 1H NMR over other detection methods is the high specificity of this method, allowing detection of individual buffer and analyte constituents within the migration zones.

Chromatographic and electrophoretic characterization of protein variants

Almost all proteins are expressed in several variants, also known as isoforms. Individual protein variants differ by modifications of the individual amino acid side chains, or the N- or C-terminus. Typical modifications are glycosylation, phosphorylation, acetylation, methylation, deamidation or oxidation. It is of utmost interest to either get a quantitative picture of the variants of a particular protein or to separate the variants in order to be able to identify their molecular structure. Protein variants are present in native as well as in recombinant proteins. In the case of protein production it is interesting, how variants are generated during fermentation, purification processes, storage, and how present individual variants influence the biological activity. This review provides a comparison of chromatographic and electrophoretic separation methods to analyze and to prepare protein variants.

Can the theory of gradient liquid chromatography be useful in solving practical problems?

Advances in the theory of gradient liquid chromatography and their practical impacts are reviewed. Theoretical models describing retention in reversed-phase, normal-phase and ion-exchange modes are compared. Main attention is focused on practically useful models described by two- or three-parameter equations fitting the experimental data in the range of mobile phase composition utilized for sample migration during gradient elution. The applications of theory for gradient method development, optimization and transfer are addressed. The origins and possibilities for overcoming possible pitfalls are discussed, including the effects of the instrumental dwell volume, uptake of mobile phase components on the column and size of the sample molecules. Special attention is focused on gradient separations of large molecules.

Column selectivity for two-dimensional liquid chromatography

Selectivity of phase system is of primary concern when designing a 2-D separation, as it affects the 2-D system orthogonality and consequently the peak capacity controlling the number of peaks that can be separated in the available 2-D retention space limited by the time of analysis. Possibilities for characterization of LC phase system selectivity with respect to different polar and nonpolar structural units are compared, with special attention to multidimensional samples with various types of repeat groups, such as homopolymers, (co)polymers, fatty acid esters with various acyl lengths and number and position of double bonds, etc. Possibilities of the 2-D LC separations of these and other sample types, including pharmaceuticals, natural phenolic compounds, biopolymers, etc., using various combinations of separation modes are reviewed. Rules for design of comprehensive 2-D LC x LC systems are discussed, with respect to mobile phase compatibility in the two systems and modulation techniques suppressing band broadening connected with the sample fraction transfer from the first to the second dimension. Pitfalls connected with online connection of normal-phase and RP LC systems and their possible practical solutions are addressed and illustrated by practical examples.

Two-dimensional capillary liquid chromatography: pH Gradient ion exchange and reversed phase chromatography for rapid separation of proteins

In the present work, an orthogonal two-dimensional (2D) capillary liquid chromatography (LC) method for fractionation and separation of proteins using wide range pH gradient ion exchange chromatography (IEC) in the first dimension and reversed phase (RP) in the second dimension, is demonstrated. In the first dimension a strong anion exchange (SAX) column subjected to a wide range (10.5-3.5) descending pH gradient was employed, while in the second dimension, a large pore (4,000 A) polystyrene-divinylbenzene (PS-DVB) RP analytical column was used for separation of the protein pH-fractions from the first dimension. The separation power of the off-line 2D method was demonstrated by fractionation and separation of human plasma proteins. Seventeen pH-fractions were manually collected and immediately separated in the second dimension using a column switching capillary RP-LC system. Totally, more than 200 protein peaks were observed in the RP chromatograms of the pH-fractions. On-line 2D analysis was performed for fractionation and separation of ten standard proteins. Two pH-fractions (basic and acidic) from the first dimension were trapped on PS-DVB RP trap columns prior to back-flushed elution onto the analytical RP column for fast separation of the proteins with UV/MS detection.

Fractionation and separation of human salivary proteins by pH-gradient ion exchange and reversed phase chromatography coupled to mass spectrometry

In the present work, a 2-D capillary liquid chromatography method for fractionation and separation of human salivary proteins is demonstrated. Fractionation of proteins according to their pI values was performed in the 1-D employing a strong anion exchange (SAX) column subjected to a wide-range descending pH gradient. Polystyrene-divinylbenzene (PS-DVB) RP columns were used for focusing and subsequent separation of the proteins in the 2-D. The SAX column was presaturated with a high pH buffer (A) consisting of 10 mM amine buffering species, pH 9.0, and elution was performed with a low pH elution buffer (B) having the same buffer composition and concentration as buffer A, but pH 3.5. Isoelectric point fractions eluting from the 1-D column were trapped on PS-DVB trap columns prior to back-flushed elution onto the PS-DVB analytical column for separation of the proteins. The 1-D fraction eluting at pH 9.0-8.7 was chosen for further analysis. After separation on the RP analytical column, nine RP protein fractions were collected and tryptic digested for subsequent analyses by MALDI TOF MS and column switching capillary LC coupled to ESI TOF MS and ESI QTOF MS. Eight proteins and two peptides were identified in the pH 9.0-8.7 fraction using peptide mass fingerprinting and uninterpreted MS/MS data.

Controlling the retention in capillary LC with solvents, temperature, and electric fields

Once a suitable stationary phase and column dimensions have been selected, the retention in liquid chromatography (LC) is traditionally adjusted by controlling the mobile phase composition. Solvent gradients enable achievement of good separation selectivity while decreasing the separation time as compared to isocratic elution. Capillary columns allow use of other programming parameters, i.e. temperature and applied electric fields, in addition to solvent gradient elution. This paper presents a review of programmed separation techniques in miniaturized LC, including retention modeling and method transfer from the conventional to micro- and capillary scales. The impact of miniaturized instrumentation on retention and the limitations of capillary LC are discussed. Special attention is focused on the gradient dwell volume effects, which are more important in micro-LC techniques than in conventional analytical LC and may cause significant increase in the time of analysis, unless special instrumentation and (or) pre-column flow-splitting is used. The influence of temperature upon retention is also discussed, and applications where the temperature has been actively used for retention control in capillary LC are included together with the instrumentation utilized. Finally the possibilities of additional selectivity control by applying an electric field over a packed capillary LC column are discussed.