1
|
Lan W, Valente JJ, Ilott A, Chennamsetty N, Liu Z, Rizzo JM, Yamniuk AP, Qiu D, Shackman HM, Bolgar MS. Investigation of anomalous charge variant profile reveals discrete pH-dependent conformations and conformation-dependent charge states within the CDR3 loop of a therapeutic mAb. MAbs 2021; 12:1763138. [PMID: 32432964 PMCID: PMC7299213 DOI: 10.1080/19420862.2020.1763138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During the development of a therapeutic monoclonal antibody (mAb-1), the charge variant profile obtained by pH-gradient cation exchange chromatography (CEX) contained two main peaks, each of which exhibited a unique intrinsic fluorescence profile and demonstrated inter-convertibility upon reinjection of isolated peak fractions. Domain analysis of mAb-1 by CEX and liquid chromatography-mass spectrometry indicated that the antigen-binding fragment chromatographed as two separate peaks that had identical mass. Surface plasmon resonance binding analysis to antigen demonstrated comparable kinetics/affinity between these fractionated peaks and unfractionated starting material. Subsequent molecular modeling studies revealed that the relatively long and flexible complementarity-determining region 3 (CDR3) loop on the heavy chain could adopt two discrete pH-dependent conformations: an “open” conformation at neutral pH where the HC-CDR3 is largely solvent exposed, and a “closed” conformation at lower pH where the solvent exposure of a neighboring tryptophan in the light chain is reduced and two aspartic acid residues near the ends of the HC-CDR3 loop have atypical pKa values. The pH-dependent equilibrium between “open” and “closed” conformations of the HC-CDR3, and its proposed role in the anomalous charge variant profile of mAb-1, were supported by further CEX and hydrophobic interaction chromatography studies. This work is an example of how pH-dependent conformational changes and conformation-dependent changes to net charge can unexpectedly contribute to perceived instability and require thorough analytical, biophysical, and functional characterization during biopharmaceutical drug product development.
Collapse
Affiliation(s)
- Wenkui Lan
- Drug Product Development, Bristol Myers Squibb, New Brunswick, United States
| | - Joseph J Valente
- Drug Product Development, Bristol Myers Squibb, New Brunswick, United States
| | - Andrew Ilott
- Drug Product Development, Bristol Myers Squibb, New Brunswick, United States
| | - Naresh Chennamsetty
- Biophysics Center of Excellence, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, United States
| | - Zhihua Liu
- Drug Product Development, Bristol Myers Squibb, New Brunswick, United States
| | - Joseph M Rizzo
- Discovery Biotherapeutics, Bristol Myers Squibb, Pennington, United States
| | - Aaron P Yamniuk
- Discovery Biotherapeutics, Bristol Myers Squibb, Pennington, United States
| | - Difei Qiu
- Chemical Process Department, Bristol Myers Squibb, New Brunswick, United States
| | - Holly M Shackman
- Chemical Process Department, Bristol Myers Squibb, New Brunswick, United States
| | - Mark S Bolgar
- Drug Product Development, Bristol Myers Squibb, New Brunswick, United States
| |
Collapse
|
2
|
Liu R, Shi Q. Protein retention in dextran-grafted cation exchange chromatography: The influence of pHs, counterions and polymer structure. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
3
|
Masuda Y, Ogino Y, Yamaichi K, Takahashi Y, Nonaka K, Wakamatsu K. The prevention of an anomalous chromatographic behavior and the resulting successful removal of viruses from monoclonal antibody with an asymmetric charge distribution by using a membrane adsorber in highly efficient, anion-exchange chromatography in flow-through mode. Biotechnol Prog 2020; 36:e2955. [PMID: 31894893 DOI: 10.1002/btpr.2955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/25/2019] [Accepted: 12/29/2019] [Indexed: 01/15/2023]
Abstract
Anion exchange (AEX) chromatography in the flow-through mode is a widely employed purification process for removal of process/product-related impurities and exogenous/endogenous viruses from monoclonal antibodies (mAbs). The pH of the mobile phase for AEX chromatography is typically set at half a unit below the isoelectric point (pI) of each mAb (i.e., pI - 0.5) or lower and, in combination with a low ionic strength, these conditions are usually satisfactory for both the recovery of the mAb and removal of impurities. However, we have recently encountered a tight binding of mAb1 to AEX resins under these standard chromatographic conditions. This anomalous adsorption behavior appears to be an effect of the asymmetric charge distribution on the surface of the mAb1. We found that mAb1 did not bind to the AEX resins if the mobile phase has a much lower pH and higher ionic strength, but those conditions would not allow adequate virus removal. We predicted that the use of membrane adsorbers might provide effective mAb1 purification, since the supporting matrix has a network structure that would be less susceptible to interactions with the asymmetric charge distribution on the protein surface. We tested the Natriflo HD-Q AEX membrane adsorber under standard chromatographic conditions and found that mAb1 flowed through the membrane adsorber, resulting in successful separation from murine leukemia virus. This AEX membrane adsorber is expected to be useful for process development because mAbs can be purified under similar standard chromatographic conditions regardless of their charge distributions.
Collapse
Affiliation(s)
- Yumiko Masuda
- Biologics Technology Research Laboratories, Daiichi Sankyo Co., Ltd, Ohra-gun, Gunma, Japan.,Graduate School of Science and Technology, Gunma University, Kiryu-shi, Gunma, Japan
| | - Yuka Ogino
- Biologics Technology Research Laboratories, Daiichi Sankyo Co., Ltd, Ohra-gun, Gunma, Japan
| | - Kozo Yamaichi
- Biologics Technology Research Laboratories, Daiichi Sankyo Co., Ltd, Ohra-gun, Gunma, Japan
| | - Yusuke Takahashi
- Biologics Technology Research Laboratories, Daiichi Sankyo Co., Ltd, Ohra-gun, Gunma, Japan
| | - Koichi Nonaka
- Biologics Technology Research Laboratories, Daiichi Sankyo Co., Ltd, Ohra-gun, Gunma, Japan
| | - Kaori Wakamatsu
- Graduate School of Science and Technology, Gunma University, Kiryu-shi, Gunma, Japan
| |
Collapse
|
4
|
Domain contributions to antibody retention in multimodal chromatography systems. J Chromatogr A 2018; 1563:89-98. [DOI: 10.1016/j.chroma.2018.05.058] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/16/2018] [Accepted: 05/27/2018] [Indexed: 11/17/2022]
|
5
|
Parr MK, Schmidt AH. Life cycle management of analytical methods. J Pharm Biomed Anal 2018; 147:506-517. [DOI: 10.1016/j.jpba.2017.06.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 06/10/2017] [Accepted: 06/12/2017] [Indexed: 11/30/2022]
|
6
|
Robinson JR, Karkov HS, Woo JA, Krogh BO, Cramer SM. QSAR models for prediction of chromatographic behavior of homologous Fab variants. Biotechnol Bioeng 2017; 114:1231-1240. [DOI: 10.1002/bit.26236] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/16/2016] [Accepted: 12/04/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Julie R. Robinson
- Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; Center for Biotechnology and Interdisciplinary Studies; 110 8th Street Troy New York 12180
| | - Hanne S. Karkov
- Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; Center for Biotechnology and Interdisciplinary Studies; 110 8th Street Troy New York 12180
- Downstream Technology; Novo Nordisk A/S; DK-2760 Maaloev Denmark
| | - James A. Woo
- Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; Center for Biotechnology and Interdisciplinary Studies; 110 8th Street Troy New York 12180
| | - Berit O. Krogh
- Expression Technologies; Novo Nordisk A/S; DK-2760 Maaloev Denmark
| | - Steven M. Cramer
- Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; Center for Biotechnology and Interdisciplinary Studies; 110 8th Street Troy New York 12180
| |
Collapse
|
7
|
Makhatadze GI. Linking computation and experiments to study the role of charge-charge interactions in protein folding and stability. Phys Biol 2017; 14:013002. [PMID: 28169222 DOI: 10.1088/1478-3975/14/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past two decades there has been an increase in appreciation for the role of surface charge-charge interactions in protein folding and stability. The perception shifted from the belief that charge-charge interactions are not important for protein folding and stability to the near quantitative understanding of how these interactions shape the folding energy landscape. This led to the ability of computational approaches to rationally redesign surface charge-charge interactions to modulate thermodynamic properties of proteins. Here we summarize our progress in understanding the role of charge-charge interactions for protein stability using examples drawn from my own laboratory and touch upon unanswered questions.
Collapse
Affiliation(s)
- George I Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, and Department of Biological Sciences, Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180 USA
| |
Collapse
|
8
|
Li Z, Zhang Y, Wang Q, Li Z, Liu Y, Zhang S, Zhang G, Ma G, Luo J, Su Z. Purification design and practice for pertactin, the third component of acellular pertussis vaccine, from Bordetella pertussis. Vaccine 2016; 34:4032-9. [DOI: 10.1016/j.vaccine.2016.06.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/13/2016] [Accepted: 06/04/2016] [Indexed: 11/30/2022]
|
9
|
Tyteca E, Veuthey JL, Desmet G, Guillarme D, Fekete S. Computer assisted liquid chromatographic method development for the separation of therapeutic proteins. Analyst 2016; 141:5488-501. [DOI: 10.1039/c6an01520d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This review summarizes the use of computer assisted liquid chromatographic method development for the analytical characterization of protein biopharmaceuticals.
Collapse
Affiliation(s)
- Eva Tyteca
- Vrije Universiteit Brussel
- Department of Chemical Engineering
- B-1050 Brussels
- Belgium
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences
- University of Geneva
- University of Lausanne
- 1211 Geneva 4
- Switzerland
| | - Gert Desmet
- Vrije Universiteit Brussel
- Department of Chemical Engineering
- B-1050 Brussels
- Belgium
| | - Davy Guillarme
- School of Pharmaceutical Sciences
- University of Geneva
- University of Lausanne
- 1211 Geneva 4
- Switzerland
| | - Szabolcs Fekete
- School of Pharmaceutical Sciences
- University of Geneva
- University of Lausanne
- 1211 Geneva 4
- Switzerland
| |
Collapse
|
10
|
Levy NE, Valente KN, Lee KH, Lenhoff AM. Host cell protein impurities in chromatographic polishing steps for monoclonal antibody purification. Biotechnol Bioeng 2015; 113:1260-72. [DOI: 10.1002/bit.25882] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 10/19/2015] [Accepted: 11/05/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Nicholas E. Levy
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware19716
| | - Kristin N. Valente
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware19716
- Delaware Biotechnology InstituteNewarkDelaware19711
| | - Kelvin H. Lee
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware19716
- Delaware Biotechnology InstituteNewarkDelaware19711
| | - Abraham M. Lenhoff
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware19716
| |
Collapse
|
11
|
Salvalaglio M, Paloni M, Guelat B, Morbidelli M, Cavallotti C. A two level hierarchical model of protein retention in ion exchange chromatography. J Chromatogr A 2015; 1411:50-62. [DOI: 10.1016/j.chroma.2015.07.101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/23/2015] [Accepted: 07/27/2015] [Indexed: 10/23/2022]
|
12
|
Fekete S, Beck A, Veuthey JL, Guillarme D. Ion-exchange chromatography for the characterization of biopharmaceuticals. J Pharm Biomed Anal 2015; 113:43-55. [PMID: 25800161 DOI: 10.1016/j.jpba.2015.02.037] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/18/2015] [Accepted: 02/19/2015] [Indexed: 12/28/2022]
Abstract
Ion-exchange chromatography (IEX) is a historical technique widely used for the detailed characterization of therapeutic proteins and can be considered as a reference and powerful technique for the qualitative and quantitative evaluation of charge heterogeneity. The goal of this review is to provide an overview of theoretical and practical aspects of modern IEX applied for the characterization of therapeutic proteins including monoclonal antibodies (Mabs) and antibody drug conjugates (ADCs). The section on method development describes how to select a suitable stationary phase chemistry and dimensions, the mobile phase conditions (pH, nature and concentration of salt), as well as the temperature and flow rate, considering proteins isoelectric point (pI). In addition, both salt-gradient and pH-gradient approaches were critically reviewed and benefits as well as limitations of these two strategies were provided. Finally, several applications, mostly from pharmaceutical industries, illustrate the potential of IEX for the characterization of charge variants of various types of biopharmaceutical products.
Collapse
Affiliation(s)
- Szabolcs Fekete
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Boulevard d'Yvoy 20, 1211 Geneva 4, Switzerland.
| | - Alain Beck
- Center of Immunology Pierre Fabre, 5 Avenue Napoléon III, BP 60497, 74160 Saint-Julien-en-Genevois, France(1)
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Boulevard d'Yvoy 20, 1211 Geneva 4, Switzerland
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Boulevard d'Yvoy 20, 1211 Geneva 4, Switzerland
| |
Collapse
|
13
|
Yu L, Zhang L, Sun Y. Protein behavior at surfaces: Orientation, conformational transitions and transport. J Chromatogr A 2015; 1382:118-34. [DOI: 10.1016/j.chroma.2014.12.087] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/26/2014] [Accepted: 12/31/2014] [Indexed: 12/18/2022]
|
14
|
Srinivasan K, Parimal S, Lopez MM, McCallum SA, Cramer SM. Investigation into the molecular and thermodynamic basis of protein interactions in multimodal chromatography using functionalized nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:13205-16. [PMID: 25310519 DOI: 10.1021/la502141q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although multimodal chromatography offers significant potential for bioseparations, there is a lack of molecular level understanding of the nature of protein binding in these systems. In this study a nanoparticle system is employed that can simulate a chromatographic resin surface while also being amenable to isothermal titration calorimetry (ITC) and solution NMR. ITC and NMR titration experiments are carried out with (15)N-labeled ubiquitin to investigate the interactions of ubiquitin with nanoparticles functionalized with two industrially important multimodal ligands. The ITC results suggest that binding to both multimodal ligand surfaces is entropically driven over a range of temperatures and that this is due primarily to the release of surface bound waters. In order to reveal structural details of the interaction process, binding-induced chemical shift changes obtained from the NMR experiments are employed to obtain dissociation constants of individual amino acid residues on the protein surface. The residue level information obtained from NMR is then used to identify a preferred binding face on ubiquitin for interaction to both multimodal ligand surfaces. In addition, electrostatic potential and spatial aggregation propensity maps are used to determine important protein surface property data that are shown to correlate well with the molecular level information obtained from NMR. Importantly, the data demonstrate that the cluster of interacting residues on the protein surface act co-operatively to give rise to multimodal binding affinities several orders of magnitude greater than those obtained previously for interactions with free solution ligands. The use of NMR and ITC to study protein interactions with functionalized nanoparticles offers a new tool for obtaining important molecular and thermodynamic insights into protein affinity in multimodal chromatographic systems.
Collapse
Affiliation(s)
- Kartik Srinivasan
- Howard P. Isermann Department of Chemical and Biological Engineering, ‡Center for Biotechnology and Interdisciplinary Studies, and §Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | | | | | | | | |
Collapse
|
15
|
Enthalpy contributions to adsorption of highly charged lysozyme onto a cation-exchanger under linear and overloaded conditions. J Chromatogr A 2014; 1352:46-54. [DOI: 10.1016/j.chroma.2014.05.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/17/2014] [Accepted: 05/19/2014] [Indexed: 11/22/2022]
|
16
|
Chmielowski RA, Meissner S, Roush D, Linden TO, Glowacki E, Konietzko J, Nti-Gyabaah J. Resolution of heterogeneous charged antibody aggregates via multimodal chromatography: A comparison to conventional approaches. Biotechnol Prog 2014; 30:636-45. [DOI: 10.1002/btpr.1908] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/28/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Rebecca A. Chmielowski
- Merck and Co., MSD, Biologics Process Development, Process Development and Engineering; Kenilworth NJ 07033
| | - Sandra Meissner
- Merck and Co., MSD, Biologics Process Development, Process Development and Engineering; Kenilworth NJ 07033
| | - David Roush
- Merck and Co., MSD, Biologics Process Development, Process Development and Engineering; Kenilworth NJ 07033
| | - Thomas O. Linden
- Merck and Co., MSD, Biologics Process Development, Process Development and Engineering; Kenilworth NJ 07033
| | - Edward Glowacki
- Merck and Co., MSD, Biologics Process Development, Process Development and Engineering; Kenilworth NJ 07033
| | - Janelle Konietzko
- Merck and Co., MSD, Vaccine Process Development; West Point PA 19486
| | | |
Collapse
|
17
|
Bolduc D, Rahdar M, Tu-Sekine B, Sivakumaren SC, Raben D, Amzel LM, Devreotes P, Gabelli SB, Cole P. Phosphorylation-mediated PTEN conformational closure and deactivation revealed with protein semisynthesis. eLife 2013; 2:e00691. [PMID: 23853711 PMCID: PMC3707082 DOI: 10.7554/elife.00691] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/07/2013] [Indexed: 12/23/2022] Open
Abstract
The tumor suppressor PIP3 phosphatase PTEN is phosphorylated on four clustered Ser/Thr on its C-terminal tail (aa 380–385) and these phosphorylations are proposed to induce a reduction in PTEN’s plasma membrane recruitment. How these phosphorylations affect the structure and enzymatic function of PTEN is poorly understood. To gain insight into the mechanistic basis of PTEN regulation by phosphorylation, we generated semisynthetic site-specifically tetra-phosphorylated PTEN using expressed protein ligation. By employing a combination of biophysical and enzymatic approaches, we have found that purified tail-phosphorylated PTEN relative to its unphosphorylated counterpart shows reduced catalytic activity and membrane affinity and undergoes conformational compaction likely involving an intramolecular interaction between its C-tail and the C2 domain. Our results suggest that there is a competition between membrane phospholipids and PTEN phospho-tail for binding to the C2 domain. These findings reveal a key aspect of PTEN’s regulation and suggest pharmacologic approaches for direct PTEN activation. DOI:http://dx.doi.org/10.7554/eLife.00691.001 PTEN is an enzyme that is found in almost every tissue in the body, and its job is to stop cells dividing. If it fails to perform this job, the uncontrolled proliferation of cells can lead to the growth of tumors. PTEN stops cells dividing by localizing at the plasma membrane of a cell and removing a phosphate group from a lipid called PIP3: this sends a signal, via the PI3K pathway, that suppresses the replication and survival of cells. Three regions of PTEN are thought to be central to its biological functions: one of these regions, the phosphatase domain, is directly responsible for removing a phosphate group from the lipid PIP3; a second region, called the C2 domain, is known to be critical for PTEN binding to the cell membrane; however, the role of third region, called the C-terminal domain, is poorly understood. Many proteins are regulated by the addition and removal of phosphate groups, and PTEN is no exception. In particular, it seems as if the addition of phosphate groups to four amino acid residues in the C-terminal domain can switch off the activity of PTEN, but the details of this process have been elusive. Now, Bolduc et al. have employed a variety of biochemical and biophysical techniques to explore this process, finding that the addition of the phosphate groups reduced PTEN’s affinity for the plasma membrane. At the same time, interactions between the C-terminal and C2 domains of the PTEN cause the shape of the enzyme to change in a way that ‘buries’ the residues to which the phosphate groups have been added. In addition to offering new insights into PTEN, the work of Bolduc et al. could help efforts to identify compounds with clinical anti-cancer potential. DOI:http://dx.doi.org/10.7554/eLife.00691.002
Collapse
Affiliation(s)
- David Bolduc
- Department of Pharmacology and Molecular Sciences , Johns Hopkins University School of Medicine , Baltimore , United States
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Guélat B, Delegrange L, Valax P, Morbidelli M. Model-based prediction of monoclonal antibody retention in ion-exchange chromatography. J Chromatogr A 2013; 1298:17-25. [DOI: 10.1016/j.chroma.2013.04.048] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 04/05/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
|
19
|
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]
|
20
|
Guélat B, Ströhlein G, Lattuada M, Delegrange L, Valax P, Morbidelli M. Simulation model for overloaded monoclonal antibody variants separations in ion-exchange chromatography. J Chromatogr A 2012; 1253:32-43. [DOI: 10.1016/j.chroma.2012.06.081] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 06/21/2012] [Accepted: 06/25/2012] [Indexed: 12/18/2022]
|
21
|
Freed AS, Garde S, Cramer SM. Molecular Simulations of Multimodal Ligand–Protein Binding: Elucidation of Binding Sites and Correlation with Experiments. J Phys Chem B 2011; 115:13320-7. [DOI: 10.1021/jp2038015] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander S. Freed
- The Howard P. Isermann Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Shekhar Garde
- The Howard P. Isermann Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Steven M. Cramer
- The Howard P. Isermann Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| |
Collapse
|
22
|
Evaluation of selectivity in multimodal anion exchange systems: A priori prediction of protein retention and examination of mobile phase modifier effects. J Chromatogr A 2011; 1218:7813-20. [DOI: 10.1016/j.chroma.2011.08.080] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 07/25/2011] [Accepted: 08/26/2011] [Indexed: 11/23/2022]
|
23
|
Conley GP, Viswanathan M, Hou Y, Rank DL, Lindberg AP, Cramer SM, Ladner RC, Nixon AE, Chen J. Evaluation of protein engineering and process optimization approaches to enhance antibody drug manufacturability. Biotechnol Bioeng 2011; 108:2634-44. [PMID: 21618474 DOI: 10.1002/bit.23220] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 04/28/2011] [Accepted: 05/12/2011] [Indexed: 11/11/2022]
Abstract
A potent single digit picomolar fully human monoclonal antibody (hMAb) inhibitor with a high degree of specificity to the antigen of interest was identified from a phage display library. The hMAb, however, exhibited a high degree of hydrophobicity and easily formed insoluble aggregates when purified using a Protein A based generic process. Strategies were designed using both protein engineering and process development approaches to optimize the molecule's amino acid sequence and its behavior in process conditions. The insoluble aggregation issue was brought under control by one single amino acid mutation in CDR region or by switching to non-ProA based purification process. Our study therefore presents the rational manufacturability design for future monoclonal antibody product and its purification process under the quality by design concept by either engineering the drug molecule to adapt existing platform process or optimizing the process to fit the specific properties of the drug product.
Collapse
Affiliation(s)
- Greg P Conley
- Discovery Research, Dyax Corp., Cambridge, Massachusetts 02139, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Freed AS, Cramer SM. Protein-surface interaction maps for ion-exchange chromatography. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:3561-3568. [PMID: 21375221 DOI: 10.1021/la104641z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this paper, protein-surface interaction maps were generated by performing coarse-grained protein-surface calculations. This approach allowed for the rapid determination of the protein-surface interaction energies at a range of orientations and distances. Interaction maps of lysozyme indicated that there was a contiguous series of orientations corresponding to several adjacent preferred binding regions on the protein surface. Examination of these orientations provided insight into the residues involved in surface interactions, which qualitatively agreed with the retention data for single-site mutants. Interaction maps of lysozyme single-site mutants were also generated and provided significant insight into why these variants exhibited significant differences in their chromatographic behavior. This approach was also employed to study the binding behavior of CspB and related mutants. The results indicated that, in addition to describing general trends in the data, these maps provided significant insight into retention data of the single-site mutants. In particular, subtle retention trends observed with the K12 and K13 mutants were well-described using this interaction map approach. Finally, the number of interaction points with energies stronger than -2 kcal/mol was shown to be able to semi-quantitatively predict the behavior of most of the mutants. This rapid approach for calculating protein-surface interaction maps is expected to facilitate future method development for separating closely related protein variants in ion-exchange systems.
Collapse
Affiliation(s)
- Alexander S Freed
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | | |
Collapse
|
25
|
Chung WK, Holstein MA, Freed AS, Evans ST, Baer ZC, Cramer SM. Ion Exchange Chromatographic Behavior of a Homologous Cytochrome C Variant Library Obtained by Controlled Succinylation. SEP SCI TECHNOL 2010. [DOI: 10.1080/01496395.2010.507432] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
26
|
Effects of urea induced protein conformational changes on ion exchange chromatographic behavior. J Chromatogr A 2010; 1217:7393-400. [PMID: 20956007 DOI: 10.1016/j.chroma.2010.09.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 09/16/2010] [Accepted: 09/20/2010] [Indexed: 11/23/2022]
Abstract
Urea is widely employed to facilitate protein separations in ion exchange chromatography at various scales. In this work, five model proteins were used to examine the chromatographic effects of protein conformational changes induced by urea in ion exchange chromatography. Linear gradient experiments were carried out at various urea concentrations and the protein secondary and tertiary structures were evaluated by far UV CD and fluorescence measurements, respectively. The results indicated that chromatographic retention times were well correlated with structural changes and that they were more sensitive to tertiary structural change. Steric Mass Action (SMA) isotherm parameters were also examined and the results indicated that urea induced protein conformational changes could affect both the characteristic charge and equilibrium constants in these systems. Dynamic light scattering analysis of changes in protein size due to urea-induced unfolding indicated that the size of the protein was not correlated with SMA parameter changes. These results indicate that while urea-induced structural changes can have a marked effect on protein chromatographic behavior in IEX, this behavior can be quite complicated and protein specific. These differences in protein behavior may provide insight into how these partially unfolded proteins are interacting with the resin material.
Collapse
|
27
|
Alpert AJ, Petritis K, Kangas L, Smith RD, Mechtler K, Mitulović G, Mohammed S, Heck AJR. Peptide orientation affects selectivity in ion-exchange chromatography. Anal Chem 2010; 82:5253-9. [PMID: 20481592 PMCID: PMC2884984 DOI: 10.1021/ac100651k] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we demonstrate that separation of proteolytic peptides, having the same net charge and one basic residue, is affected by their specific orientation toward the stationary phase in ion-exchange chromatography. In electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) with an anion-exchange material, the C-terminus of the peptides is, on average, oriented toward the stationary phase. In cation exchange, the average peptide orientation is the opposite. Data with synthetic peptides, serving as orientation probes, indicate that in tryptic/Lys-C peptides the C-terminal carboxyl group appears to be in a zwitterionic bond with the side chain of the C-terminal Lys/Arg residue. In effect, the side chain is then less basic than the N-terminus, accounting for the specific orientation of tryptic and Lys-C peptides. Analyses of larger sets of peptides, generated from lysates by either Lys-N, Lys-C, or trypsin, reveal that specific peptide orientation affects the ability of charged side chains, such as phosphate residues, to influence retention. Phosphorylated residues that are remote in the sequence from the binding site affect retention less than those that are closer. When a peptide contains multiple charged sites, then orientation is observed to be less rigid and retention tends to be governed by the peptide's net charge rather than its sequence. These general observations could be of value in confirming a peptide's identification and, in particular, phosphosite assignments in proteomics analyses. More generally, orientation accounts for the ability of chromatography to separate peptides of the same composition but different sequence.
Collapse
Affiliation(s)
- Andrew J Alpert
- PolyLC Inc., 9151 Rumsey Road, Ste. 180, Columbia, Maryland 21045, USA.
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Chung WK, Evans ST, Freed AS, Keba JJ, Baer ZC, Rege K, Cramer SM. Utilization of lysozyme charge ladders to examine the effects of protein surface charge distribution on binding affinity in ion exchange systems. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:759-768. [PMID: 19678624 DOI: 10.1021/la902135t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A lysozyme library was employed to study the effects of protein surface modification on protein retention and to elucidate preferred protein binding orientations for cation exchange chromatography. Acetic anhydride was used as an acetylating agent to modify protein surface lysine residues. Partial acetylation of lysozyme resulted in the formation of a homologous set of modified proteins with varying charge densities and distribution. The resulting protein charge ladder was separated on a cation exchange column, and eluent fractions were subsequently analyzed using capillary zone electrophoresis and direct infusion electrospray ionization mass spectrometry. The ion exchange separation showed a significant degree of variation in the retention time of the different variants. Several fractions contained coelution of variants, some with differing net charge. In addition, several cases were observed where variants with more positive surface charge eluted from the column prior to variants with less positive charge. Enzymatic digest followed by mass spectrometry was performed to determine the sites of acetylation on the surface of the variants eluting in various fractions. Electrostatic potential maps of these variants were then generated to provide further insight into the elution order of the variants.
Collapse
Affiliation(s)
- Wai Keen Chung
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | | | | | | | | | | | | |
Collapse
|
29
|
Chung WK, Hou Y, Holstein M, Freed A, Makhatadze GI, Cramer SM. Investigation of protein binding affinity in multimodal chromatographic systems using a homologous protein library. J Chromatogr A 2010; 1217:191-8. [DOI: 10.1016/j.chroma.2009.08.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/29/2009] [Accepted: 08/04/2009] [Indexed: 11/30/2022]
|
30
|
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]
|