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Wittkopp F, Welsh J, Todd R, Staby A, Roush D, Lyall J, Karkov S, Hunt S, Griesbach J, Bertran MO, Babi D. Current state of implementation of in silico tools in the biopharmaceutical industry-Proceedings of the 5th modeling workshop. Biotechnol Bioeng 2024; 121:2952-2973. [PMID: 38853778 DOI: 10.1002/bit.28768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024]
Abstract
The fifth modeling workshop (5MW) was held in June 2023 at Favrholm, Denmark and sponsored by Recovery of Biological Products Conference Series. The goal of the workshop was to assemble modeling practitioners to review and discuss the current state, progress since the last fourth mini modeling workshop (4MMW), gaps and opportunities for development, deployment and maintenance of models in bioprocess applications. Areas of focus were four categories: biophysics and molecular modeling, mechanistic modeling, computational fluid dynamics (CFD) and plant modeling. Highlights of the workshop included significant advancements in biophysical/molecular modeling to novel protein constructs, mechanistic models for filtration and initial forays into modeling of multiphase systems using CFD for a bioreactor and mapped strategically to cell line selection/facility fit. A significant impediment to more fully quantitative and calibrated models for biophysics is the lack of large, anonymized datasets. A potential solution would be the use of specific descriptors in a database that would allow for detailed analyzes without sharing proprietary information. Another gap identified was the lack of a consistent framework for use of models that are included or support a regulatory filing beyond the high-level guidance in ICH Q8-Q11. One perspective is that modeling can be viewed as a component or precursor of machine learning (ML) and artificial intelligence (AI). Another outcome was alignment on a key definition for "mechanistic modeling." Feedback from participants was that there was progression in all of the fields of modeling within scope of the conference. Some areas (e.g., biophysics and molecular modeling) have opportunities for significant research investment to realize full impact. However, the need for ongoing research and development for all model types does not preclude the application to support process development, manufacturing and use in regulatory filings. Analogous to ML and AI, given the current state of the four modeling types, a prospective investment in educating inter-disciplinary subject matter experts (e.g., data science, chromatography) is essential to advancing the modeling community.
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Affiliation(s)
- Felix Wittkopp
- Roche Diagnostics GmbH, Gene Therapy Technical Development, Penzberg, Germany
| | - John Welsh
- Rivanna Bioprocess Solutions, Charlottesville, Virginia, USA
| | - Robert Todd
- Digital Process Design, Boulder, Colorado, USA
| | - Arne Staby
- CMC Development, Novo Nordisk, Bagsværd, Denmark
| | - David Roush
- Roush Biopharma Panacea, Colts Neck, New Jersey, USA
| | - Jessica Lyall
- Purification Development, Genentech, South San Francisco, California, USA
| | - Sophie Karkov
- Purification Research, Global Research Technologies, Novo Nordisk, Måløv, Denmark
| | - Stephen Hunt
- Allogene Therapeutics, Inc., South San Francisco, California, USA
| | | | - Maria-Ona Bertran
- Product Supply API Manufacturing Development, Novo Nordisk, Bagsværd, Denmark
| | - Deenesh Babi
- Product Supply API Manufacturing Development, Novo Nordisk, Bagsværd, Denmark
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2
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Hess R, Faessler J, Yun D, Mama A, Saleh D, Grosch JH, Wang G, Schwab T, Hubbuch J. Predicting multimodal chromatography of therapeutic antibodies using multiscale modeling. J Chromatogr A 2024; 1718:464706. [PMID: 38335881 DOI: 10.1016/j.chroma.2024.464706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
Multimodal chromatography has emerged as a powerful method for the purification of therapeutic antibodies. However, process development of this separation technique remains challenging because of an intricate and molecule-specific interaction towards multimodal ligands, leading to time-consuming and costly experimental optimization. This study presents a multiscale modeling approach to predict the multimodal chromatographic behavior of therapeutic antibodies based on their sequence information. Linear gradient elution (LGE) experiments were performed on an anionic multimodal resin for 59 full-length antibodies, including five different antibody formats at pH 5.0, 6.0, and 7.0 that were used for parameter determination of a linear adsorption model at low loading density conditions. Quantitative structure-property relationship (QSPR) modeling was utilized to correlate the adsorption parameters with up to 1374 global and local physicochemical descriptors calculated from antibody homology models. The final QSPR models employed less than eight descriptors per model and demonstrated high training accuracy (R² > 0.93) and reasonable test set prediction accuracy (Q² > 0.83) for the adsorption parameters. Model evaluation revealed the significance of electrostatic interaction and hydrophobicity in determining the chromatographic behavior of antibodies, as well as the importance of the HFR3 region in antibody binding to the multimodal resin. Chromatographic simulations using the predicted adsorption parameters showed good agreement with the experimental data for the vast majority of antibodies not employed during the model training. The results of this study demonstrate the potential of sequence-based prediction for determining chromatographic behavior in therapeutic antibody purification. This approach leads to more efficient and cost-effective process development, providing a valuable tool for the biopharmaceutical industry.
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Affiliation(s)
- Rudger Hess
- Karlsruhe Institute of Technology (KIT), Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe, Germany; DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jan Faessler
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Doil Yun
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Ahmed Mama
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - David Saleh
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jan-Hendrik Grosch
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Gang Wang
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Thomas Schwab
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jürgen Hubbuch
- Karlsruhe Institute of Technology (KIT), Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe, Germany.
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3
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Qu Y, Baker I, Black J, Fabri L, Gras SL, Lenhoff AM, Kentish SE. Application of mechanistic modelling in membrane and fiber chromatography for purification of biotherapeutics - A review. J Chromatogr A 2024; 1716:464588. [PMID: 38217959 DOI: 10.1016/j.chroma.2023.464588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/03/2023] [Accepted: 12/17/2023] [Indexed: 01/15/2024]
Abstract
Mechanistic modelling is a simulation tool which has been effectively applied in downstream bioprocessing to model resin chromatography. Membrane and fiber chromatography are newer approaches that offer higher rates of mass transfer and consequently higher flow rates and reduced processing times. This review describes the key considerations in the development of mechanistic models for these unit operations. Mass transfer is less complex than in resin columns, but internal housing volumes can make modelling difficult, particularly for laboratory-scale devices. Flow paths are often non-linear and the dead volume is often a larger fraction of the overall volume, which may require more complex hydrodynamic models to capture residence time distributions accurately. In this respect, the combination of computational fluid dynamics with appropriate protein binding models is emerging as an ideal approach.
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Affiliation(s)
- Yiran Qu
- Department of Chemical Engineering, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Irene Baker
- Cell Culture and Purification Development, CSL Innovation, Melbourne, Victoria 3000, Australia
| | - Jamie Black
- Cell Culture and Purification Development, CSL Innovation, Melbourne, Victoria 3000, Australia
| | - Louis Fabri
- Cell Culture and Purification Development, CSL Innovation, Melbourne, Victoria 3000, Australia
| | - Sally L Gras
- Department of Chemical Engineering, University of Melbourne, Melbourne, Victoria 3010, Australia; Bio21 Institute of Molecular Science and Biotechnology, Melbourne, Victoria 3052, Australia
| | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Sandra E Kentish
- Department of Chemical Engineering, University of Melbourne, Melbourne, Victoria 3010, Australia.
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4
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Understanding adsorption behavior of antiviral labyrinthopeptin peptides in anion exchange chromatography. J Chromatogr A 2023; 1690:463792. [PMID: 36681006 DOI: 10.1016/j.chroma.2023.463792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Lantipeptides from bacterial sources are increasingly important as biopharmaceuticals because of their broad range of applications. However, the availability of most lantipeptides is low, and systematic approaches for downstream processing of this group of peptides is still lacking. Model-based development for chromatographic separations has proven to be a useful tool for developing reliable purification processes. One important compound of such a model is the adsorption behavior of the components of interest. In ion-exchange chromatography, the adsorption equilibrium between salt and proteins can be described using the steric mass action (SMA) formalism. Beyond, the model parameters may be related to the lanthipeptides physico-chemical properties. In this study, the antiviral lantipeptides labyrinthopeptin A1 and A2, purified from Actinomadura namibiensis culture broth, were characterized for their adsorption behavior in anion-exchange chromatography in the range from pH 5.0-7.4. The experiments necessary to determine the three SMA parameters were chosen in a way to limit the amount of peptides needed. Linear gradient elution was applied successfully to separate A1 and A2 and to determine the characteristic charge νi and the equilibrium constant [Formula: see text] . Batch adsorption experiments using a robotic workstation for high throughput and accuracy provided non-linear adsorption isotherms and the steric factor σi. Labyrinthopeptin A1 and A2 show a very different adsorption behavior even though the fundamental structure of the two peptides is similar. keq of A1 ranging from 0.18 to 0.88 are approximately one order of magnitude smaller than that of A2 ranging from 3.44 to 9.73 indicating the higher affinity of A2 to the stationary phase. At pH 7.0 σ was 1.12 and 0.60 for A1 and A2, respectively which was expected based on the molecular weight of the peptides. The characteristic charge for both peptides was also theoretically estimated from the amino acids involved in electrostatic interactions which was in good agreement with experimental data. Thereby, this work provides an useful approach to estimate SMA parameters based on simple structural information that can be applied early in chromatographic ion-exchange process development for peptides and may help adapting the processes for future designed lanthipeptides.
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Chen YC, Yao SJ, Lin DQ. Parameter-by-parameter method for steric mass action model of ion exchange chromatography: Simplified estimation for steric shielding factor. J Chromatogr A 2023; 1687:463655. [PMID: 36442298 DOI: 10.1016/j.chroma.2022.463655] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
Abstract
Mechanistic models play a crucial role in the process development and optimization of ion-exchange chromatography (IEC). Recent researches in steric mass action (SMA) model have heightened the need for better estimation of nonlinear parameter, steric shielding factor σ. In this work, a straightforward approach combination of simplified linear approximation (SLA) and inverse method (IM) was proposed to initialize and further determine σ, respectively. An existed, unique, and positive σ can be derived from SLA. Compared with linear approximation (LA) developed in our previous study, σ of the multi-component system can be calculated easily without solving the complex system of linear equations, leading to a time complexity reduction from O(n3) to O(n). The proposed method was verified first in numerical experiments about the separation of three charge variants. The calculated σ was more reasonable than that of LA, and the error of elution profiles with the parameters estimated by SLA+IM was only one-sixth of that by LA in numerical experiments. Moreover, the error accumulation effect could also be reduced. The proposed method was further confirmed in real-world experiments about the separation of monomer-dimer mixtures of monoclonal antibody. The results gave a lower error and better physical understanding compared to LA. In conclusion, SLA+IM developed in the present work provides a novel and straightforward way to determine σ. This simplification would help to save the effort of calibration experiments and accelerate the process development for the multi-component IEC separation.
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Affiliation(s)
- Yu-Cheng Chen
- Zhejiang Key Laboratory of Smart Biomaterials, Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Shan-Jing Yao
- Zhejiang Key Laboratory of Smart Biomaterials, Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Dong-Qiang Lin
- Zhejiang Key Laboratory of Smart Biomaterials, Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.
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Saleh D, Hess R, Ahlers-Hesse M, Rischawy F, Wang G, Grosch JH, Schwab T, Kluters S, Studts J, Hubbuch J. A multiscale modeling method for therapeutic antibodies in ion exchange chromatography. Biotechnol Bioeng 2023; 120:125-138. [PMID: 36226467 DOI: 10.1002/bit.28258] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/09/2022] [Accepted: 10/08/2022] [Indexed: 11/10/2022]
Abstract
The development of biopharmaceutical downstream processes relies on exhaustive experimental studies. The root cause is the poorly understood relationship between the protein structure of monoclonal antibodies (mAbs) and their macroscopic process behavior. Especially the development of preparative chromatography processes is challenged by the increasing structural complexity of novel antibody formats and accelerated development timelines. This study introduces a multiscale in silico model consisting of homology modeling, quantitative structure-property relationships (QSPR), and mechanistic chromatography modeling leading from the amino acid sequence of a mAb to the digital representation of its cation exchange chromatography (CEX) process. The model leverages the mAbs' structural characteristics and experimental data of a diverse set of 21 therapeutic antibodies to predict elution profiles of two mAbs that were removed from the training data set. QSPR modeling identified mAb-specific protein descriptors relevant for the prediction of the thermodynamic equilibrium and the stoichiometric coefficient of the adsorption reaction. The consideration of two discrete conformational states of IgG4 mAbs enabled prediction of split-peak elution profiles. Starting from the sequence, the presented multiscale model allows in silico development of chromatography processes before protein material is available for experimental studies.
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Affiliation(s)
- David Saleh
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Rudger Hess
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Michelle Ahlers-Hesse
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Federico Rischawy
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gang Wang
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Jan-Hendrik Grosch
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Thomas Schwab
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Simon Kluters
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Joey Studts
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Jürgen Hubbuch
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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7
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Seelinger F, Wittkopp F, von Hirschheydt T, Hafner M, Frech C. Application of the Steric Mass Action formalism for modeling under high loading conditions: Part 1. Investigation of the influence of pH on the steric shielding factor. J Chromatogr A 2022; 1676:463265. [DOI: 10.1016/j.chroma.2022.463265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/28/2022]
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8
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Seelinger F, Wittkopp F, von Hirschheydt T, Frech C. Application of the Steric Mass Action formalism for modeling under high loading conditions: Part 2. Investigation of high loading and column overloading effects. J Chromatogr A 2022; 1676:463266. [DOI: 10.1016/j.chroma.2022.463266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/29/2022]
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9
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Opportunities and challenges for model utilization in the biopharmaceutical industry: current versus future state. Curr Opin Chem Eng 2022. [DOI: 10.1016/j.coche.2022.100813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Heymann W, Glaser J, Schlegel F, Johnson W, Rolandi P, von Lieres E. Advanced score system and automated search strategies for parameter estimation in mechanistic chromatography modeling. J Chromatogr A 2021; 1661:462693. [PMID: 34863063 DOI: 10.1016/j.chroma.2021.462693] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/29/2021] [Accepted: 11/16/2021] [Indexed: 01/04/2023]
Abstract
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).
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Affiliation(s)
- William Heymann
- Institute of Geo- and Biosciences 1 (IBG-1), Forschungszentrum Jülich, Wilhelm-Johnen-Str. 1, 52428 Jülich, Germany; RWTH Aachen University, 52062 Aachen, Germany
| | - Juliane Glaser
- Digital Integration and Predictive Technologies (DIPT), Amgen Research Munich, Staffelseestr. 2, 81477 München, Germany
| | - Fabrice Schlegel
- Digital Integration and Predictive Technologies (DIPT), Amgen, 360 Binney St, Cambridge, MA 02142, United States
| | - Will Johnson
- Digital Integration and Predictive Technologies (DIPT), Amgen, 360 Binney St, Cambridge, MA 02142, United States
| | - Pablo Rolandi
- Digital Integration and Predictive Technologies (DIPT), Amgen, 360 Binney St, Cambridge, MA 02142, United States
| | - Eric von Lieres
- Institute of Geo- and Biosciences 1 (IBG-1), Forschungszentrum Jülich, Wilhelm-Johnen-Str. 1, 52428 Jülich, Germany.
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11
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Bernau CR, Jäpel RC, Hübbers JW, Nölting S, Opdensteinen P, Buyel JF. Precision analysis for the determination of steric mass action parameters using eight tobacco host cell proteins. J Chromatogr A 2021; 1652:462379. [PMID: 34256268 DOI: 10.1016/j.chroma.2021.462379] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 12/12/2022]
Abstract
Plants are advantageous as biopharmaceutical manufacturing platforms because they allow the economical and scalable upstream production of proteins, including those requiring post-translational modifications, but do not support the replication of human viruses. However, downstream processing can be more labor-intensive compared to fermenter-based systems because the product is often mixed with abundant host cell proteins (HCPs). Modeling chromatographic separation can minimize the number of process development experiments and thus reduce costs. An important part of such modeling is the sorption isotherm, such as the steric mass action (SMA) model, which describes the multicomponent protein-salt equilibria established in ion-exchange systems. Here we purified ten HCPs, including 2-Cys-peroxiredoxin, from tobacco (Nicotiana tabacum and N. benthamiana). For eight of these HCPs, we obtained sufficient quantities to determine the SMA binding parameters (KSMA and ν) under different production-relevant conditions. We studied the parameters for 2-Cys-peroxiredoxin on Q-Sepharose HP in detail, revealing that pH, resin batch and buffer batch had little influence on KSMA and ν, with coefficients of variation (COVs) less than 0.05 and 0.21, respectively. In contrast, the anion-exchange resins SuperQ-650S, Q-Sepharose FF and QAE-550C led to COVs of 0.69 for KSMA and 0.05 for ν, despite using the same quaternary amine functional group as Q-Sepharose HP. Plant cultivation in summer vs winter resulted in COVs of 0.09 for KSMA and 0.02 for ν, revealing a small impact compared to COVs of 17.15 for KSMA and 0.20 for ν when plants were grown in different settings (climate-controlled phytotron vs greenhouse). We conclude that plant cultivation can substantially affect protein properties and the resulting SMA parameters. Accordingly, plant growth but also protein purification and characterization for chromatography model building should be tightly controlled and well documented.
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Affiliation(s)
- C R Bernau
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, Aachen 52074, Germany.
| | - R C Jäpel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, Aachen 52074, Germany.
| | - J W Hübbers
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, Aachen 52074, Germany.
| | - S Nölting
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, Aachen 52074, Germany.
| | - P Opdensteinen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, Aachen 52074, Germany; Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, Aachen 52074, Germany.
| | - J F Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, Aachen 52074, Germany; Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, Aachen 52074, Germany.
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12
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Briskot T, Hahn T, Huuk T, Wang G, Kluters S, Studts J, Wittkopp F, Winderl J, Schwan P, Hagemann I, Kaiser K, Trapp A, Stamm SM, Koehn J, Malmquist G, Hubbuch J. Analysis of complex protein elution behavior in preparative ion exchange processes using a colloidal particle adsorption model. J Chromatogr A 2021; 1654:462439. [PMID: 34384923 DOI: 10.1016/j.chroma.2021.462439] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 12/28/2022]
Abstract
A fundamental understanding of the protein retention mechanism in preparative ion exchange (IEX) chromatography columns is essential for a model-based process development approach. For the past three decades, the mechanistic description of protein retention has been based predominantly on the steric mass action (SMA) model. In recent years, however, retention profiles of proteins have been reported more frequently for preparative processes that are not consistent with the mechanistic understanding relying on the SMA model. In this work, complex elution behavior of proteins in preparative IEX processes is analyzed using a colloidal particle adsorption (CPA) model. The CPA model is found to be capable of reproducing elution profiles that cannot be described by the traditional SMA model. According to the CPA model, the reported complex behavior can be ascribed to a strong compression and concentration of the elution front in the lower unsaturated part of the chromatography column. As the unsaturated part of the column decreases with increasing protein load density, exceeding a critical load density can lead to the formation of a shoulder in the peak front. The general applicability of the model in describing preparative IEX processes is demonstrated using several industrial case studies including multiple monoclonal antibodies on different IEX adsorber systems. In this context, the work covers both salt controlled and pH-controlled protein elution.
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Affiliation(s)
- Till Briskot
- GoSilico GmbH, Kriegsstr. 240, Karlsruhe 76135, Germany; Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, Karlsruhe 76131, Germany
| | - Tobias Hahn
- GoSilico GmbH, Kriegsstr. 240, Karlsruhe 76135, Germany
| | - Thiemo Huuk
- GoSilico GmbH, Kriegsstr. 240, Karlsruhe 76135, Germany
| | - Gang Wang
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß 88397, Germany
| | - Simon Kluters
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß 88397, Germany
| | - Joey Studts
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß 88397, Germany
| | - Felix Wittkopp
- Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg 82377, Germany
| | - Johannes Winderl
- Roche Pharma Technical Development, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg 82377, Germany
| | | | | | | | - Anja Trapp
- Process Science & Innovation, Rentschler Biopharma SE, Erwin Rentschler Str. 21, Laupheim 88471, Germany
| | - Serge M Stamm
- Process Science & Innovation, Rentschler Biopharma SE, Erwin Rentschler Str. 21, Laupheim 88471, Germany
| | - Jadranka Koehn
- Process Science & Innovation, Rentschler Biopharma SE, Erwin Rentschler Str. 21, Laupheim 88471, Germany
| | | | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, Karlsruhe 76131, Germany.
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13
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Saleh D, Hess R, Ahlers-Hesse M, Beckert N, Schönberger M, Rischawy F, Wang G, Bauer J, Blech M, Kluters S, Studts J, Hubbuch J. Modeling the impact of amino acid substitution in a monoclonal antibody on cation exchange chromatography. Biotechnol Bioeng 2021; 118:2923-2933. [PMID: 33871060 DOI: 10.1002/bit.27798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/23/2021] [Accepted: 04/15/2021] [Indexed: 01/03/2023]
Abstract
A vital part of biopharmaceutical research is decision making around which lead candidate should be progressed in early-phase development. When multiple antibody candidates show similar biological activity, developability aspects are taken into account to ease the challenges of manufacturing the potential drug candidate. While current strategies for developability assessment mainly focus on drug product stability, only limited information is available on how antibody candidates with minimal differences in their primary structure behave during downstream processing. With increasing time-to-market pressure and an abundance of monoclonal antibodies (mAbs) in development pipelines, developability assessments should also consider the ability of mAbs to integrate into the downstream platform. This study investigates the influence of amino acid substitutions in the complementarity-determining region (CDR) of a full-length IgG1 mAb on the elution behavior in preparative cation exchange chromatography. Single amino acid substitutions within the investigated mAb resulted in an additional positive charge in the light chain (L) and heavy chain (H) CDR, respectively. The mAb variants showed an increased retention volume in linear gradient elution compared with the wild-type antibody. Furthermore, the substitution of tryptophan with lysine in the H-CDR3 increased charge heterogeneity of the product. A multiscale in silico analysis, consisting of homology modeling, protein surface analysis, and mechanistic chromatography modeling increased understanding of the adsorption mechanism. The results reveal the potential effects of lead optimization during antibody drug discovery on downstream processing.
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Affiliation(s)
- David Saleh
- Late Stage DSP Development, Boehringer Ingelheim, Biberach, Germany.,Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Rudger Hess
- Late Stage DSP Development, Boehringer Ingelheim, Biberach, Germany.,Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | | | - Nicole Beckert
- Pharmaceutical Development Biologics, Boehringer Ingelheim, Biberach, Germany
| | | | - Federico Rischawy
- Late Stage DSP Development, Boehringer Ingelheim, Biberach, Germany.,Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Gang Wang
- Late Stage DSP Development, Boehringer Ingelheim, Biberach, Germany
| | - Joschka Bauer
- Pharmaceutical Development Biologics, Boehringer Ingelheim, Biberach, Germany
| | - Michaela Blech
- Pharmaceutical Development Biologics, Boehringer Ingelheim, Biberach, Germany
| | - Simon Kluters
- Late Stage DSP Development, Boehringer Ingelheim, Biberach, Germany
| | - Joey Studts
- Late Stage DSP Development, Boehringer Ingelheim, Biberach, Germany
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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14
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Saleh D, Wang G, Müller B, Rischawy F, Kluters S, Studts J, Hubbuch J. Straightforward method for calibration of mechanistic cation exchange chromatography models for industrial applications. Biotechnol Prog 2020; 36:e2984. [DOI: 10.1002/btpr.2984] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/03/2020] [Accepted: 02/19/2020] [Indexed: 12/31/2022]
Affiliation(s)
- David Saleh
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT) Karlsruhe Germany
| | - Gang Wang
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Benedict Müller
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Federico Rischawy
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT) Karlsruhe Germany
| | - Simon Kluters
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Joey Studts
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT) Karlsruhe Germany
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15
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Moringo NA, Bishop LDC, Shen H, Misiura A, Carrejo NC, Baiyasi R, Wang W, Ye F, Robinson JT, Landes CF. A mechanistic examination of salting out in protein-polymer membrane interactions. Proc Natl Acad Sci U S A 2019; 116:22938-22945. [PMID: 31659038 PMCID: PMC6859367 DOI: 10.1073/pnas.1909860116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Developing a mechanistic understanding of protein dynamics and conformational changes at polymer interfaces is critical for a range of processes including industrial protein separations. Salting out is one example of a procedure that is ubiquitous in protein separations yet is optimized empirically because there is no mechanistic description of the underlying interactions that would allow predictive modeling. Here, we investigate peak narrowing in a model transferrin-nylon system under salting out conditions using a combination of single-molecule tracking and ensemble separations. Distinct surface transport modes and protein conformational changes at the negatively charged nylon interface are quantified as a function of salt concentration. Single-molecule kinetics relate macroscale improvements in chromatographic peak broadening with microscale distributions of surface interaction mechanisms such as continuous-time random walks and simple adsorption-desorption. Monte Carlo simulations underpinned by the stochastic theory of chromatography are performed using kinetic data extracted from single-molecule observations. Simulations agree with experiment, revealing a decrease in peak broadening as the salt concentration increases. The results suggest that chemical modifications to membranes that decrease the probability of surface random walks could reduce peak broadening in full-scale protein separations. More broadly, this work represents a proof of concept for combining single-molecule experiments and a mechanistic theory to improve costly and time-consuming empirical methods of optimization.
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Affiliation(s)
| | | | - Hao Shen
- Department of Chemistry, Rice University, Houston, TX 77251
| | | | | | - Rashad Baiyasi
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251
| | - Wenxiao Wang
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251
| | - Fan Ye
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251
| | - Jacob T Robinson
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251
- Department of Bioengineering, Rice University, Houston, TX 77251
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, TX 77251;
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251
- Smalley-Curl Institute, Rice University, Houston, TX 77251
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77251
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16
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Singh N, Herzer S. Downstream Processing Technologies/Capturing and Final Purification : Opportunities for Innovation, Change, and Improvement. A Review of Downstream Processing Developments in Protein Purification. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 165:115-178. [PMID: 28795201 DOI: 10.1007/10_2017_12] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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).
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Affiliation(s)
- Nripen Singh
- Bristol-Myers Squibb, Global Manufacturing and Supply, Devens, MA, 01434, USA.
| | - Sibylle Herzer
- Bristol-Myers Squibb, Global Manufacturing and Supply, Hopewell, NJ, 01434, USA
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17
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Karlberg M, von Stosch M, Glassey J. Exploiting mAb structure characteristics for a directed QbD implementation in early process development. Crit Rev Biotechnol 2018. [DOI: 10.1080/07388551.2017.1421899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Micael Karlberg
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne, UK
| | - Moritz von Stosch
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne, UK
| | - Jarka Glassey
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne, UK
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18
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Khalaf R, Heymann J, LeSaout X, Monard F, Costioli M, Morbidelli M. Model-based high-throughput design of ion exchange protein chromatography. J Chromatogr A 2016; 1459:67-77. [DOI: 10.1016/j.chroma.2016.06.076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/19/2016] [Accepted: 06/24/2016] [Indexed: 01/11/2023]
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19
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Miryala B, Zhen Z, Potta T, Breneman CM, Rege K. Parallel Synthesis and Quantitative Structure–Activity Relationship (QSAR) Modeling of Aminoglycoside-Derived Lipopolymers for Transgene Expression. ACS Biomater Sci Eng 2015; 1:656-668. [DOI: 10.1021/acsbiomaterials.5b00045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bhavani Miryala
- Chemical
Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287-6106, United States
| | - Zhuo Zhen
- Department
of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Thrimoorthy Potta
- Chemical
Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287-6106, United States
| | - Curt M. Breneman
- Department
of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Kaushal Rege
- Chemical
Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287-6106, United States
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20
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Nestola P, Peixoto C, Silva RRJS, Alves PM, Mota JPB, Carrondo MJT. Improved virus purification processes for vaccines and gene therapy. Biotechnol Bioeng 2015; 112:843-57. [PMID: 25677990 DOI: 10.1002/bit.25545] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 01/05/2015] [Accepted: 01/13/2015] [Indexed: 01/10/2023]
Abstract
The downstream processing of virus particles for vaccination or gene therapy is becoming a critical bottleneck as upstream titers keep improving. Moreover, the growing pressure to develop cost-efficient processes has brought forward new downstream trains. This review aims at analyzing the state-of-the-art in viral downstream purification processes, encompassing the classical unit operations and their recent developments. Emphasis is given to novel strategies for process intensification, such as continuous or semi-continuous systems based on multicolumn technology, opening up process efficiency. Process understanding in the light of the pharmaceutical quality by design (QbD) initiative is also discussed. Finally, an outlook of the upcoming breakthrough technologies is presented.
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Affiliation(s)
- Piergiuseppe Nestola
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal; Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
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21
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Lang KMH, Kittelmann J, Dürr C, Osberghaus A, Hubbuch J. A comprehensive molecular dynamics approach to protein retention modeling in ion exchange chromatography. J Chromatogr A 2015; 1381:184-93. [PMID: 25618359 DOI: 10.1016/j.chroma.2015.01.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/19/2014] [Accepted: 01/08/2015] [Indexed: 11/29/2022]
Abstract
In downstream processing, the underlying adsorption mechanism of biomolecules to adsorbent material are still subject of extensive research. One approach to more mechanistic understanding is simulating this adsorption process and hereby the possibility to identify the parameters with strongest impact. So far this method was applied with all-atom molecular dynamics simulations of two model proteins on one cation exchanger. In this work we developed a molecular dynamics tool to simulate protein-adsorber interaction for various proteins on an anion exchanger and ran gradient elution experiments to relate the simulation results to experimental data. We were able to show that simulation results yield similar results as experimental data regarding retention behavior as well as binding orientation. We could identify arginines in case of cation exchangers and aspartic acids in case of anion exchangers as major contributors to binding.
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Affiliation(s)
- Katharina M H Lang
- Section IV: Biomolecular Separation Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 1, 76131 Karlsruhe, Germany
| | - Jörg Kittelmann
- Section IV: Biomolecular Separation Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 1, 76131 Karlsruhe, Germany
| | - Cathrin Dürr
- Section IV: Biomolecular Separation Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 1, 76131 Karlsruhe, Germany
| | - Anna Osberghaus
- Section IV: Biomolecular Separation Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 1, 76131 Karlsruhe, Germany
| | - Jürgen Hubbuch
- Section IV: Biomolecular Separation Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 1, 76131 Karlsruhe, Germany.
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22
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Insaidoo FK, Rauscher MA, Smithline SJ, Kaarsholm NC, Feuston BP, Ortigosa AD, Linden TO, Roush DJ. Targeted purification development enabled by computational biophysical modeling. Biotechnol Prog 2014; 31:154-64. [DOI: 10.1002/btpr.2023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/02/2014] [Indexed: 01/12/2023]
Affiliation(s)
| | | | | | - Niels C. Kaarsholm
- Merck Research Laboratories, Merck & Co., Inc; Whitehouse Station NJ 08889
| | - Bradley P. Feuston
- Merck Research Laboratories, Merck & Co., Inc; Whitehouse Station NJ 08889
| | | | - Thomas O. Linden
- Merck Research Laboratories, Merck & Co., Inc; Whitehouse Station NJ 08889
| | - David J. Roush
- Merck Research Laboratories, Merck & Co., Inc; Whitehouse Station NJ 08889
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23
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Huuk TC, Hahn T, Osberghaus A, Hubbuch J. Model-based integrated optimization and evaluation of a multi-step ion exchange chromatography. Sep Purif Technol 2014. [DOI: 10.1016/j.seppur.2014.09.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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24
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Thermodynamic description of peptide adsorption on mixed-mode resins. J Chromatogr A 2014; 1341:41-9. [DOI: 10.1016/j.chroma.2014.03.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 03/07/2014] [Accepted: 03/10/2014] [Indexed: 11/22/2022]
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25
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Buyel JF, Woo JA, Cramer SM, Fischer R. The use of quantitative structure-activity relationship models to develop optimized processes for the removal of tobacco host cell proteins during biopharmaceutical production. J Chromatogr A 2013; 1322:18-28. [PMID: 24268820 DOI: 10.1016/j.chroma.2013.10.076] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/23/2013] [Accepted: 10/24/2013] [Indexed: 01/06/2023]
Abstract
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.
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Affiliation(s)
- J F Buyel
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany.
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26
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Potta T, Zhen Z, Grandhi TSP, Christensen MD, Ramos J, Breneman CM, Rege K. Discovery of antibiotics-derived polymers for gene delivery using combinatorial synthesis and cheminformatics modeling. Biomaterials 2013; 35:1977-88. [PMID: 24331709 DOI: 10.1016/j.biomaterials.2013.10.069] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/27/2013] [Indexed: 01/06/2023]
Abstract
We describe the combinatorial synthesis and cheminformatics modeling of aminoglycoside antibiotics-derived polymers for transgene delivery and expression. Fifty-six polymers were synthesized by polymerizing aminoglycosides with diglycidyl ether cross-linkers. Parallel screening resulted in identification of several lead polymers that resulted in high transgene expression levels in cells. The role of polymer physicochemical properties in determining efficacy of transgene expression was investigated using Quantitative Structure-Activity Relationship (QSAR) cheminformatics models based on Support Vector Regression (SVR) and 'building block' polymer structures. The QSAR model exhibited high predictive ability, and investigation of descriptors in the model, using molecular visualization and correlation plots, indicated that physicochemical attributes related to both, aminoglycosides and diglycidyl ethers facilitated transgene expression. This work synergistically combines combinatorial synthesis and parallel screening with cheminformatics-based QSAR models for discovery and physicochemical elucidation of effective antibiotics-derived polymers for transgene delivery in medicine and biotechnology.
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Affiliation(s)
- Thrimoorthy Potta
- Chemical Engineering, Arizona State University, Tempe, AZ 85287-6106, USA
| | - Zhuo Zhen
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | | | | | - James Ramos
- Harrington Biomedical Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Curt M Breneman
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kaushal Rege
- Chemical Engineering, Arizona State University, Tempe, AZ 85287-6106, USA; Harrington Biomedical Engineering, Arizona State University, Tempe, AZ 85287, USA.
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27
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Kröner F, Hanke AT, Nfor BK, Pinkse MWH, Verhaert PDEM, Ottens M, Hubbuch J. Analytical characterization of complex, biotechnological feedstocks by pH gradient ion exchange chromatography for purification process development. J Chromatogr A 2013; 1311:55-64. [PMID: 24016717 DOI: 10.1016/j.chroma.2013.08.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 07/22/2013] [Accepted: 08/09/2013] [Indexed: 11/30/2022]
Abstract
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.
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Affiliation(s)
- Frieder Kröner
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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28
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Kallberg K, Johansson HO, Bulow L. Multimodal chromatography: An efficient tool in downstream processing of proteins. Biotechnol J 2012; 7:1485-95. [DOI: 10.1002/biot.201200074] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/26/2012] [Accepted: 10/09/2012] [Indexed: 11/06/2022]
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29
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Proteomics-based, multivariate random forest method for prediction of protein separation behavior during cation-exchange chromatography. J Chromatogr A 2012; 1249:103-14. [DOI: 10.1016/j.chroma.2012.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 05/31/2012] [Accepted: 06/03/2012] [Indexed: 01/01/2023]
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30
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Nfor BK, Ahamed T, Pinkse MW, van der Wielen LA, Verhaert PD, van Dedem GW, Eppink MH, van de Sandt EJ, Ottens M. Multi-dimensional fractionation and characterization of crude protein mixtures: Toward establishment of a database of protein purification process development parameters. Biotechnol Bioeng 2012; 109:3070-83. [DOI: 10.1002/bit.24576] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Revised: 04/20/2012] [Accepted: 05/30/2012] [Indexed: 11/08/2022]
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31
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Osberghaus A, Drechsel K, Hansen S, Hepbildikler S, Nath S, Haindl M, von Lieres E, Hubbuch J. Model-integrated process development demonstrated on the optimization of a robotic cation exchange step. Chem Eng Sci 2012. [DOI: 10.1016/j.ces.2012.04.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Josch J, Strube J. Characterization of Feed Properties for Conceptual Process Design Involving Complex Mixtures. CHEM-ING-TECH 2012. [DOI: 10.1002/cite.201200030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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33
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Optimizing a chromatographic three component separation: A comparison of mechanistic and empiric modeling approaches. J Chromatogr A 2012; 1237:86-95. [DOI: 10.1016/j.chroma.2012.03.029] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 02/29/2012] [Accepted: 03/09/2012] [Indexed: 11/18/2022]
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34
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Osberghaus A, Hepbildikler S, Nath S, Haindl M, von Lieres E, Hubbuch J. Determination of parameters for the steric mass action model—A comparison between two approaches. J Chromatogr A 2012; 1233:54-65. [DOI: 10.1016/j.chroma.2012.02.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/18/2012] [Accepted: 02/01/2012] [Indexed: 10/14/2022]
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35
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Josch JP, Both S, Strube J. Characterization of Feed Properties for Conceptual Process Design Involving Complex Mixtures, Such as Natural Extracts. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/fns.2012.36112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Lienqueo ME, Mahn A, Salgado JC, Shene C. Mathematical Modeling of Protein Chromatograms. Chem Eng Technol 2011. [DOI: 10.1002/ceat.201100282] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Vicente T, Mota JP, Peixoto C, Alves PM, Carrondo MJ. Rational design and optimization of downstream processes of virus particles for biopharmaceutical applications: Current advances. Biotechnol Adv 2011; 29:869-78. [DOI: 10.1016/j.biotechadv.2011.07.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 07/07/2011] [Accepted: 07/11/2011] [Indexed: 12/11/2022]
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39
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Model simulation and experimental verification of a cation-exchange IgG capture step in batch and continuous chromatography. J Chromatogr A 2011; 1218:5195-204. [DOI: 10.1016/j.chroma.2011.05.103] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 05/24/2011] [Accepted: 05/30/2011] [Indexed: 11/21/2022]
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40
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Wilken LR, Nikolov ZL. Process evaluations and economic analyses of recombinant human lysozyme and hen egg-white lysozyme purifications. Biotechnol Prog 2011; 27:733-43. [PMID: 21574265 DOI: 10.1002/btpr.593] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 02/26/2011] [Indexed: 11/12/2022]
Abstract
Human lysozyme and hen egg-white lysozyme have antibacterial, antiviral, and antifungal properties with numerous potential commercial applications. Currently, hen egg-white lysozyme dominates low cost applications but the recent high-level expression of human lysozyme in rice could provide an economical source of lysozyme. This work compares human lysozyme and hen egg-white lysozyme adsorption to the cation exchange resin, SP-Sepharose FF, and the effect of rice extract components on lysozyme purification. With one exception, the dynamic binding capacities of human lysozyme were lower than those of hen egg-white at pH 4.5, 6, and 7.5 with ionic strengths ranging from 0 to 100 mM (5-20 mS). Ionic strength and pH had a similar effect on the adsorption capacities, but human lysozyme was more sensitive to these two factors than hen egg-white lysozyme. In the presence of rice extract, the dynamic binding capacities of human and hen egg-white lysozymes were reduced by 20-30% and by 32-39% at pH 6. Hen egg-white lysozyme was used as a benchmark to compare the effectiveness of human lysozyme purification from transgenic rice extract. Process simulation and cost analyses for human lysozyme purification from rice and hen egg-white lysozyme purification from egg-white resulted in similar unit production costs at 1 ton per year scale.
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Affiliation(s)
- Lisa R Wilken
- Dept. of Biological & Agricultural Engineering, Texas A&M University, College Station, TX 77843, USA
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41
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Dismer F, Hubbuch J. 3D structure-based protein retention prediction for ion-exchange chromatography. J Chromatogr A 2010; 1217:1343-53. [DOI: 10.1016/j.chroma.2009.12.061] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 12/03/2009] [Accepted: 12/22/2009] [Indexed: 11/25/2022]
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42
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Nakagawa T, Ishihara T, Yoshida H, Yoneya T, Wakamatsu K, Kadoya T. Relationship between human IgG structure and retention time in hydroxyapatite chromatography with sodium-phosphate gradient elution. J Sep Sci 2009; 33:37-45. [DOI: 10.1002/jssc.200900543] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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43
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Pabst TM, Suda EJ, Thomas KE, Mensah P, Ramasubramanyan N, Gustafson ME, Hunter AK. Binding and elution behavior of proteins on strong cation exchangers. J Chromatogr A 2009; 1216:7950-6. [DOI: 10.1016/j.chroma.2009.09.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 09/12/2009] [Accepted: 09/17/2009] [Indexed: 10/20/2022]
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44
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Understanding the mechanism of virus removal by Q sepharose fast flow chromatography during the purification of CHO-cell derived biotherapeutics. Biotechnol Bioeng 2009; 104:371-80. [DOI: 10.1002/bit.22416] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Chung WK, Hou Y, Freed A, Holstein M, Makhatadze GI, Cramer SM. Investigation of protein binding affinity and preferred orientations in ion exchange systems using a homologous protein library. Biotechnol Bioeng 2009; 102:869-81. [PMID: 18821632 DOI: 10.1002/bit.22100] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A library of cold shock protein B (CspB) mutant variants was employed to study protein binding affinity and preferred orientations in cation exchange chromatography. Single site mutations introduced at charged amino acids on the protein surface resulted in a homologous protein set with varying charge density and distribution. The retention times of the mutants varied significantly during linear gradient chromatography. While the expected trends were observed with increasing or decreasing positive charge on the protein surface, the degree of change was a strong function of the location and microenvironment of the mutated amino acid. Quantitative structure-property relationship (QSPR) models were generated using a support vector regression technique that was able to give good predictions of the retention times of the various mutants. Molecular descriptors selected during model generation were used to elucidate the factors affecting protein retention. Electrostatic potential maps were also employed to provide insight into the effects of protein surface topography, charge density and charge distribution on protein binding affinity and possible preferred binding orientations. The use of this protein mutant library in concert with the qualitative and quantitative analyses presented in the article provides an improved understanding of protein behavior in ion exchange systems.
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Affiliation(s)
- Wai Keen Chung
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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46
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Xu X, Lenhoff AM. Binary adsorption of globular proteins on ion-exchange media. J Chromatogr A 2009; 1216:6177-95. [DOI: 10.1016/j.chroma.2009.06.082] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 06/24/2009] [Accepted: 06/30/2009] [Indexed: 10/20/2022]
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47
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Maddula SR, Kharkar M, Manudhane K, Kale S, Bhori A, Lali A, Dubey PK, Sarma KRJ, Bhattacharya A, Bandichhor R. Preparative Chromatography Technique in the Removal of Isostructural Genotoxic Impurity in Rizatriptan: Use of Physicochemical Descriptors of Solute and Adsorbent. Org Process Res Dev 2009. [DOI: 10.1021/op9000093] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Srinivasula Reddy Maddula
- Center of Excellence, Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Survey Nos. 42, 45, 46, and 54 Bachupally, Qutubullapur, Ranga Reddy District 500072, Andhra Pradesh, India, Bioprocessing Lab, Chemical Engineering Department, U. I. C. T., Mumbai - 400 019, India, and College of Engineering, J. N. T. U., Hyderabad - 500072 A.P., India
| | - Manoj Kharkar
- Center of Excellence, Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Survey Nos. 42, 45, 46, and 54 Bachupally, Qutubullapur, Ranga Reddy District 500072, Andhra Pradesh, India, Bioprocessing Lab, Chemical Engineering Department, U. I. C. T., Mumbai - 400 019, India, and College of Engineering, J. N. T. U., Hyderabad - 500072 A.P., India
| | - Kushal Manudhane
- Center of Excellence, Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Survey Nos. 42, 45, 46, and 54 Bachupally, Qutubullapur, Ranga Reddy District 500072, Andhra Pradesh, India, Bioprocessing Lab, Chemical Engineering Department, U. I. C. T., Mumbai - 400 019, India, and College of Engineering, J. N. T. U., Hyderabad - 500072 A.P., India
| | - Sandeep Kale
- Center of Excellence, Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Survey Nos. 42, 45, 46, and 54 Bachupally, Qutubullapur, Ranga Reddy District 500072, Andhra Pradesh, India, Bioprocessing Lab, Chemical Engineering Department, U. I. C. T., Mumbai - 400 019, India, and College of Engineering, J. N. T. U., Hyderabad - 500072 A.P., India
| | - Abijar Bhori
- Center of Excellence, Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Survey Nos. 42, 45, 46, and 54 Bachupally, Qutubullapur, Ranga Reddy District 500072, Andhra Pradesh, India, Bioprocessing Lab, Chemical Engineering Department, U. I. C. T., Mumbai - 400 019, India, and College of Engineering, J. N. T. U., Hyderabad - 500072 A.P., India
| | - Arvind Lali
- Center of Excellence, Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Survey Nos. 42, 45, 46, and 54 Bachupally, Qutubullapur, Ranga Reddy District 500072, Andhra Pradesh, India, Bioprocessing Lab, Chemical Engineering Department, U. I. C. T., Mumbai - 400 019, India, and College of Engineering, J. N. T. U., Hyderabad - 500072 A.P., India
| | - P. K. Dubey
- Center of Excellence, Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Survey Nos. 42, 45, 46, and 54 Bachupally, Qutubullapur, Ranga Reddy District 500072, Andhra Pradesh, India, Bioprocessing Lab, Chemical Engineering Department, U. I. C. T., Mumbai - 400 019, India, and College of Engineering, J. N. T. U., Hyderabad - 500072 A.P., India
| | - K. R. Janardana Sarma
- Center of Excellence, Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Survey Nos. 42, 45, 46, and 54 Bachupally, Qutubullapur, Ranga Reddy District 500072, Andhra Pradesh, India, Bioprocessing Lab, Chemical Engineering Department, U. I. C. T., Mumbai - 400 019, India, and College of Engineering, J. N. T. U., Hyderabad - 500072 A.P., India
| | - Apurba Bhattacharya
- Center of Excellence, Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Survey Nos. 42, 45, 46, and 54 Bachupally, Qutubullapur, Ranga Reddy District 500072, Andhra Pradesh, India, Bioprocessing Lab, Chemical Engineering Department, U. I. C. T., Mumbai - 400 019, India, and College of Engineering, J. N. T. U., Hyderabad - 500072 A.P., India
| | - Rakeshwar Bandichhor
- Center of Excellence, Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Survey Nos. 42, 45, 46, and 54 Bachupally, Qutubullapur, Ranga Reddy District 500072, Andhra Pradesh, India, Bioprocessing Lab, Chemical Engineering Department, U. I. C. T., Mumbai - 400 019, India, and College of Engineering, J. N. T. U., Hyderabad - 500072 A.P., India
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Vasina EN, Paszek E, Nicolau DV, Nicolau DV. The BAD project: data mining, database and prediction of protein adsorption on surfaces. LAB ON A CHIP 2009; 9:891-900. [PMID: 19294299 DOI: 10.1039/b813475h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Protein adsorption at solid-liquid interfaces is critical to many applications, including biomaterials, protein microarrays and lab-on-a-chip devices. Despite this general interest, and a large amount of research in the last half a century, protein adsorption cannot be predicted with an engineering level, design-orientated accuracy. Here we describe a Biomolecular Adsorption Database (BAD), freely available online, which archives the published protein adsorption data. Piecewise linear regression with breakpoint applied to the data in the BAD suggests that the input variables to protein adsorption, i.e., protein concentration in solution; protein descriptors derived from primary structure (number of residues, global protein hydrophobicity and range of amino acid hydrophobicity, isoelectric point); surface descriptors (contact angle); and fluid environment descriptors (pH, ionic strength), correlate well with the output variable-the protein concentration on the surface. Furthermore, neural network analysis revealed that the size of the BAD makes it sufficiently representative, with a neural network-based predictive error of 5% or less. Interestingly, a consistently better fit is obtained if the BAD is divided in two separate sub-sets representing protein adsorption on hydrophilic and hydrophobic surfaces, respectively. Based on these findings, selected entries from the BAD have been used to construct neural network-based estimation routines, which predict the amount of adsorbed protein, the thickness of the adsorbed layer and the surface tension of the protein-covered surface. While the BAD is of general interest, the prediction of the thickness and the surface tension of the protein-covered layers are of particular relevance to the design of microfluidics devices.
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Affiliation(s)
- Elena N Vasina
- Department of Electrical Engineering & Electronics, The University of Liverpool, Liverpool, L69 3GJ, UK
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49
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Xu L, Glatz CE. Predicting protein retention time in ion-exchange chromatography based on three-dimensional protein characterization. J Chromatogr A 2009; 1216:274-80. [DOI: 10.1016/j.chroma.2008.11.075] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 11/21/2008] [Accepted: 11/26/2008] [Indexed: 11/26/2022]
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50
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Sharma R, Lee JS, Bettencourt RC, Xiao C, Konieczny SF, Won YY. Effects of the incorporation of a hydrophobic middle block into a PEG-polycation diblock copolymer on the physicochemical and cell interaction properties of the polymer-DNA complexes. Biomacromolecules 2008; 9:3294-307. [PMID: 18942877 DOI: 10.1021/bm800876v] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
One-component homopolymers of cationic monomers (polycations) and diblock copolymers comprising poly(ethylene glycol) (PEG) and a polycation block have been the most widely used types of polymers for the formulation of polymer-based gene delivery systems. In this study, we incorporate a hydrophobic middle block into the conventional PEG-polycation architecture and investigate the effects of this hydrophobic modification on the physicochemical and cell-level biological properties of the polymer-DNA complexes that are relevant to gene delivery applications. The ABC-type triblock copolymer used in this study consists of (A) PEG, (B) hydrophobic poly( n-butyl acrylate) (PnBA), and (C) cationic poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) component polymers. The properties of the triblock copolymer/DNA complexes are compared with those of two other more conventional DNA carriers derived, respectively, using a PDMAEMA homopolymer and a PEG-PDMAEMA diblock copolymer that had comparable molecular weights for individual blocks. In aqueous solution, the PEG-PnBA-PDMAEMA polymer forms positively charged spherical micelles. The electrostatic complexation of these micelles with plasmid DNA molecules results in the formation of stable small-sized DNA particles that are coated with a micelle monolayer, as confirmed by agarose gel electrophoresis, dynamic light scattering (DLS), and cryogenic transmission electron microscopy (cryo-TEM). Proton nuclear magnetic resonance ( (1)H NMR) spectroscopy measurements indicate that the whole micelle-DNA assembly (named "micelleplex" for convenience) is shielded predominantly by the PEG chains. DLS and optical microscopy imaging measurements indicate that compared with PDMAEMA-DNA polyplexes, the micelleplexes have a significantly lower tendency to aggregate under physiological salt concentrations and show reduced interactions with negatively charged components in serum such as albumin and erythrocytes. While the micelleplexes are comparable to the PEG-PDMAEMA-based DNA polyplexes in terms of their stability against aggregation under high salt concentrations and in the presence of the albumin protein, they have a slightly higher tendency to interact with erythrocytes than the diblock copolymer polyplexes. Agarose gel electrophoresis measurements indicate that relative to the PEG-PDMAEMA polyplexes, the micelleplexes provide better protection of the encapsulated DNA from enzymatic degradation and also exhibit greater stability against disintegration induced by polyanionic additives; in these respects, the PDMAEMA homopolymer-based polyplexes show the best performance. In vitro studies in HeLa cells indicate that the PDMAEMA polyplexes show the highest gene transfection efficiency among the three different gene delivery systems. Between the micelleplexes and the PEG-PDMAEMA polyplexes, a higher gene transfection efficiency is observed with the latter system. All three formulations show comparable levels of cytotoxicity in HeLa cells.
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Affiliation(s)
- Rahul Sharma
- School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
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