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LeBarre JP, Chu W, Altern SH, Kocot AJ, Bhandari D, Barbieri E, Sly J, Crapanzano M, Cramer SM, Phillips M, Roush D, Carbonell R, Boi C, Menegatti S. Mixed-mode size-exclusion silica resin for polishing human antibodies in flow-through mode. J Chromatogr A 2024; 1720:464772. [PMID: 38452560 DOI: 10.1016/j.chroma.2024.464772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/07/2024] [Accepted: 02/25/2024] [Indexed: 03/09/2024]
Abstract
The polishing step in the downstream processing of therapeutic antibodies removes residual impurities from Protein A eluates. Among the various classes of impurities, antibody fragments are especially challenging to remove due to the broad biomolecular diversity generated by a multitude of fragmentation patterns. The current approach to fragment removal relies on ion exchange or mixed-mode adsorbents operated in bind-and-gradient-elution mode. However, fragments that bear strong similarity to the intact product or whose biophysical features deviate from the ensemble average can elude these adsorbents, and the lack of a chromatographic technology enabling robust antibody polishing is recognized as a major gap in downstream bioprocessing. Responding to this challenge, this study introduces size-exclusion mixed-mode (SEMM) silica resins as a novel chromatographic adsorbent for the capture of antibody fragments irrespective of their biomolecular features. The pore diameter of the silica beads features a narrow distribution and is selected to exclude monomeric antibodies, while allowing their fragments to access the pores where they are captured by the mixed-mode ligands. The static and dynamic binding capacity of the adsorbent ranged respectively between 30-45 and 25-33 gs of antibody fragments per liter of resin. Selected SEMM-silica resins also demonstrated the ability to capture antibody aggregates, which adsorb on the outer layer of the beads. Optimization of the SEMM-silica design and operation conditions - namely, pore size (10 nm) and ligand composition (quaternary amine and alkyl chain) as well as the linear velocity (100 cm/h), ionic strength (5.7 mS/cm), and pH (7) of the mobile phase - afforded a significant reduction of both fragments and aggregates, resulting into a final antibody yield up to 80% and monomeric purity above 97%.
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Affiliation(s)
- Jacob P LeBarre
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Scott H Altern
- The Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY, 12180, USA
| | - Andrew J Kocot
- The Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY, 12180, USA
| | - Dipendra Bhandari
- LigaTrap Technologies, Raleigh, 1791 Varsity Dr, Raleigh, NC, 27606, USA
| | - Eduardo Barbieri
- LigaTrap Technologies, Raleigh, 1791 Varsity Dr, Raleigh, NC, 27606, USA
| | - Jae Sly
- LigaTrap Technologies, Raleigh, 1791 Varsity Dr, Raleigh, NC, 27606, USA
| | - Michael Crapanzano
- LigaTrap Technologies, Raleigh, 1791 Varsity Dr, Raleigh, NC, 27606, USA
| | - Steven M Cramer
- The Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY, 12180, USA
| | | | - David Roush
- Merck & Co., Inc., 2000 Galloping Hill Rd, Kenilworth, Roush Biopharma Panacea, 20 Squire Terrace, Colts Neck, NJ, 07033, USA
| | - Ruben Carbonell
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA
| | - Cristiana Boi
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA; Department of Civil, Chemical Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131, Bologna, Italy
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA; LigaTrap Technologies, Raleigh, 1791 Varsity Dr, Raleigh, NC, 27606, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA; North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA.
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Altern SH, Kocot AJ, LeBarre JP, Boi C, Phillips MW, Roush DJ, Menegatti S, Cramer SM. Mechanistic model-based characterization of size-exclusion-mixed-mode resins for removal of monoclonal antibody fragments. J Chromatogr A 2024; 1718:464717. [PMID: 38354506 DOI: 10.1016/j.chroma.2024.464717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/22/2024] [Accepted: 02/03/2024] [Indexed: 02/16/2024]
Abstract
Although antibody fragments are a critical impurity to remove from process streams, few platformable purification techniques have been developed to this end. In this work, a novel size-exclusion-mixed-mode (SEMM) resin was characterized with respect to its efficacy in mAb fragment removal. Inverse size-exclusion chromatography showed that the silica-based resin had a narrow pore size distribution and a median pore radius of roughly 6.2 nm. Model-based characterization was carried out with Chromatography Analysis and Design Toolkit (CADET), using the general rate model and the multicomponent Langmuir isotherm. Model parameters were obtained from fitting breakthrough curves, performed at multiple residence times, for a mixture of mAb, aggregates, and an array of fragments (varying in size). Accurate fits were obtained to the frontal chromatographic data across a range of residence times. Model validation was then performed with a scaled-up column, altering residence time and feed composition from the calibration run. Accurate predictions were obtained, thereby illustrating the model's interpolative and extrapolative capabilities. Additionally, the SEMM resin achieved 90% mAb yield, 37% aggregate removal, 29% [Formula: see text] removal, 54% Fab/Fc removal, 100% Fc fragments removal, and a productivity of 72.3 g mAbL×h. Model predictions for these statistics were all within 5%. Simulated batch uptake experiments showed that resin penetration depth was directly related to protein size, with the exception of the aggregate species, and that separation was governed by differential pore diffusion rates. Additional simulations were performed to characterize the dependence of fragment removal on column dimension, load density, and feed composition. Fragment removal was found to be highly dependent on column load density, where optimal purification was achieved below 100 mg protein/mL column. Furthermore, fragment removal was dependent on column volume (constant load mass), but agnostic to whether column length or diameter was changed. Lastly, the dependence on feed composition was shown to be complex. While fragment removal was inversely related to fragment mass fraction in the feed, the extent depended on fragment size. Overall, the results from this study illustrated the efficacy of the SEMM resin in fragment and aggregate removal and elucidated relationships with key operational parameters through model-based characterization.
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Affiliation(s)
- Scott H Altern
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Andrew J Kocot
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Jacob P LeBarre
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Cristiana Boi
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA; Department of Civil, Chemical, Environmental, and Materials Engineering, University of Bologna, Bologna, Italy
| | - Michael W Phillips
- Downstream Research and Development, EMD Millipore Corporation, Burlington, MA, USA
| | - David J Roush
- Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA; North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, NC, USA
| | - Steven M Cramer
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.
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Altern SH, Welsh JP, Lyall JY, Kocot AJ, Burgess S, Kumar V, Williams C, Lenhoff AM, Cramer SM. Isotherm model discrimination for multimodal chromatography using mechanistic models derived from high-throughput batch isotherm data. J Chromatogr A 2023; 1693:463878. [PMID: 36827799 DOI: 10.1016/j.chroma.2023.463878] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/05/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
In this work, we have examined an array of isotherm formalisms and characterized them based on their relative complexities and predictive abilities with multimodal chromatography. The set of isotherm models studied were all based on the stoichiometric displacement framework, with considerations for electrostatic interactions, hydrophobic interactions, and thermodynamic activities. Isotherm parameters for each model were first determined through twenty repeated fits to a set of mAb - Capto MMC batch isotherm data spanning a range of loading, ionic strength, and pH as well as a set of mAb - Capto Adhere batch data at constant pH. The batch isotherm data were used in two ways-spanning the full range of loading or consisting of only the high concentration data points. Predictive ability was defined through the model's capacity to capture prominent changes in salt gradient elution behavior with respect to pH for Capto MMC or unique elution patterns and yield losses with respect to gradient slope for Capto Adhere. In both cases, model performance was quantified using a scoring metric based on agreement in peak characteristics for column predictions and accuracy of fit for the batch data. These scores were evaluated for all twenty isotherm fits and their corresponding column predictions, thereby producing a statistical distribution of model performances. Model complexity (number of isotherm parameters) was then considered through use of the Akaike information criterion (AIC) calculated from the score distributions. While model performance for Capto MMC benefitted substantially from removal of low protein concentration data, this was not the case for Capto Adhere; this difference was likely due to the qualitatively different shapes of the isotherms between the two resins. Surprisingly, the top-performing (high accuracy with minimal number of parameters) isotherm model was the same for both resins. The extended steric mass action (SMA) isotherm (containing both protein-salt and protein-protein activity terms) accurately captured both the pH-dependent elution behavior for Capto MMC as well as loss in protein recovery with increasing gradient slope for Capto Adhere. In addition, this isotherm model achieved the highest median score in both resin systems, despite it lacking any explicit hydrophobic stoichiometric terms. The more complex isotherm models, which explicitly accounted for both electrostatic and hydrophobic interaction stoichiometries, were ill-suited for Capto MMC and had lower AIC model likelihoods for Capto Adhere due to their increased complexity. Interestingly, the ability of the extended SMA isotherm to predict the Capto Adhere results was largely due to the protein-salt activity coefficient, as determined via isotherm parameter sensitivity analyses. Further, parametric studies on this parameter demonstrated that it had a major impact on both binding affinity and elution behavior, therein fully capturing the impact of hydrophobic interactions. In summary, we were able to determine the isotherm formalisms most capable of consistently predicting a wide range of column behavior for both a multimodal cation-exchange and multimodal anion-exchange resin with high accuracy, while containing a minimized set of model parameters.
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Affiliation(s)
- Scott H Altern
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - John P Welsh
- Biologics Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Jessica Y Lyall
- Purification Development, Genentech, South San Francisco, CA, USA
| | - Andrew J Kocot
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Sean Burgess
- Purification Development, Genentech, South San Francisco, CA, USA
| | - Vijesh Kumar
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Chris Williams
- Purification Development, Genentech, South San Francisco, CA, USA
| | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Steven M Cramer
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA.
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Koley S, Altern SH, Vats M, Han X, Jang D, Snyder MA, Belisle C, Cramer SM. Evaluation of guanidine-based multimodal anion exchangers for protein selectivity and orthogonality. J Chromatogr A 2021; 1653:462398. [PMID: 34280791 DOI: 10.1016/j.chroma.2021.462398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 11/25/2022]
Abstract
In this paper, we examined the chromatographic behavior of a new class of guanidine-based multimodal anion exchange resins. The selectivities and protein recoveries on these resins were first evaluated using linear gradient chromatography with a model acidic protein library at pH 5, 6 and 7. While a single-guanidine based resin exhibited significant recovery issues at high ligand density, a bis-guanidine based resin showed high recoveries of all but two of the proteins evaluated in the study. In addition, the bis-guanidine resin showed a more pH dependent selectivity pattern as compared to the low density single-guanidine resin. The salt elution range for the low density single-guanidine and bis-guanidine resins was also observed to vary from 0.250 to 0.621 M and 0.162 to 0.828 M NaCl, respectively. A QSAR model was then developed to predict the elution behavior of these proteins on the guanidine prototypes at multiple pH with overall training and test scores of 0.88 and 0.85, respectively. In addition, molecular dynamics simulations were performed with these ligands immobilized on a self-assembled monolayer (SAM) to characterize their conformational preferences and to gain insight into the molecular basis of their chromatographic behavior. Finally, a recently developed framework was employed to evaluate the separability of the bis-guanidine resin as well as its orthogonality to the multimodal cation exchanger, Nuvia cPrime. This evaluation was carried out using a second model protein library which included both acidic and basic proteins. The results of this analysis indicated that the bis-guanidine prototype exhibited both higher pair separability (0.73) and pair enhancement (0.42) as compared to the less hydrophobic commercial Nuvia aPrime 4A with pair separability and enhancement factors of 0.57 and 0.22, respectively. The enhanced selectivity and orthogonality of this new multimodal anion exchange ligand may offer potential opportunities for bioprocessing applications.
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Affiliation(s)
- Sushmita Koley
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Scott H Altern
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Mayank Vats
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Xuan Han
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Dongyoun Jang
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Mark A Snyder
- Bio-Rad Laboratories, Hercules, CA 94547 United States
| | - Chris Belisle
- Bio-Rad Laboratories, Hercules, CA 94547 United States
| | - Steven M Cramer
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States.
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