1
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Han Y, Desai AA, Zupancic JM, Smith MD, Tessier PM, Ruotolo BT. Native ion mobility-mass spectrometry reveals the binding mechanisms of anti-amyloid therapeutic antibodies. Protein Sci 2024; 33:e5008. [PMID: 38723181 PMCID: PMC11081520 DOI: 10.1002/pro.5008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/02/2024] [Accepted: 04/13/2024] [Indexed: 05/13/2024]
Abstract
One of the most important attributes of anti-amyloid antibodies is their selective binding to oligomeric and amyloid aggregates. However, current methods of examining the binding specificities of anti-amyloid β (Aβ) antibodies have limited ability to differentiate between complexes that form between antibodies and monomeric or oligomeric Aβ species during the dynamic Aβ aggregation process. Here, we present a high-resolution native ion-mobility mass spectrometry (nIM-MS) method to investigate complexes formed between a variety of Aβ oligomers and three Aβ-specific IgGs, namely two antibodies with relatively high conformational specificity (aducanumab and A34) and one antibody with low conformational specificity (crenezumab). We found that crenezumab primarily binds Aβ monomers, while aducanumab preferentially binds Aβ monomers and dimers and A34 preferentially binds Aβ dimers, trimers, and tetrameters. Through collision induced unfolding (CIU) analysis, our data indicate that antibody stability is increased upon Aβ binding and, surprisingly, this stabilization involves the Fc region. Together, we conclude that nIM-MS and CIU enable the identification of Aβ antibody binding stoichiometries and provide important details regarding antibody binding mechanisms.
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Affiliation(s)
- Yilin Han
- Department of ChemistryUniversity of MichiganAnn ArborMichiganUSA
| | - Alec A. Desai
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Jennifer M. Zupancic
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Matthew D. Smith
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Peter M. Tessier
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
- Department of Pharmaceutical SciencesUniversity of MichiganAnn ArborMichiganUSA
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMichiganUSA
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2
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Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
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Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
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3
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Zheng Z, Ma M, Jia Y, Cui Y, Zhao R, Li S, Wenthur C, Li L, Li G. Expedited Evaluation of Conformational Stability-Heterogeneity Associations for Crude Polyclonal Antibodies in Response to Conjugate Vaccines. Anal Chem 2023; 95:10895-10902. [PMID: 37433088 PMCID: PMC10695093 DOI: 10.1021/acs.analchem.3c00223] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Conjugate vaccines have been demonstrated to be a promising strategy for immunotherapeutic intervention in substance use disorder, wherein a hapten structurally similar to the target drug is conjugated to an immunogenic carrier protein. The antibodies generated following immunization with these species can provide long-lasting protection against overdose through sequestration of the abused drug in the periphery, which mitigates its ability to cross the blood-brain barrier. However, these antibodies exhibit a high degree of heterogeneity in structure. The resultant variations in chemical and structural compositions have not yet been clearly linked to the stability that directly affects their in vivo functional performance. In this work, we describe a rapid mass-spectrometry-based analytical workflow capable of simultaneous and comprehensive interrogation of the carrier protein-dependent heterogeneity and stability of crude polyclonal antibodies in response to conjugate vaccines. Quantitative collision-induced unfolding-ion mobility-mass spectrometry with an all-ion mode is adapted to rapidly assess the conformational heterogeneity and stability of crude serum antibodies collected from four different vaccine conditions, in an unprecedented manner. A series of bottom-up glycoproteomic experiments was performed to reveal the driving force underlying these observed heterogeneities. Overall, this study not only presents a generally applicable workflow for fast assessment of crude antibody conformational stability and heterogeneity at the intact protein level but also leverages carrier protein optimization as a simple solution to antibody quality control.
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Affiliation(s)
- Zhen Zheng
- State Key Laboratory of Pharmaceutical Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yifei Jia
- State Key Laboratory of Pharmaceutical Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Rui Zhao
- State Key Laboratory of Pharmaceutical Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Shuangshuang Li
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Cody Wenthur
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Gongyu Li
- State Key Laboratory of Pharmaceutical Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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4
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Villafuerte-Vega RC, Li HW, Slaney TR, Chennamsetty N, Chen G, Tao L, Ruotolo BT. Ion Mobility-Mass Spectrometry and Collision-Induced Unfolding of Designed Bispecific Antibody Therapeutics. Anal Chem 2023; 95:6962-6970. [PMID: 37067470 DOI: 10.1021/acs.analchem.3c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Bispecific antibodies (bsAbs) represent a critically important class of emerging therapeutics capable of targeting two different antigens simultaneously. As such, bsAbs have been developed as effective treatment agents for diseases that remain challenging for conventional monoclonal antibody (mAb) therapeutics to access. Despite these advantages, bsAbs are intricate molecules, requiring both the appropriate engineering and pairing of heavy and light chains derived from separate parent mAbs. Current analytical tools for tracking the bsAb construction process have demonstrated a limited ability to robustly probe the higher-order structure (HOS) of bsAbs. Native ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU) have proven to be useful tools in probing the HOS of mAb therapeutics. In this report, we describe a series of detailed and quantitative IM-MS and CIU data sets that reveal HOS details associated with a knob-into-hole (KiH) bsAb model system and its corresponding parent mAbs. We find that quantitative analysis of CIU data indicates that global KiH bsAb stability occupies an intermediate space between the stabilities recorded for its parent mAbs. Furthermore, our CIU data identify the hole-containing half of the KiH bsAb construct to be the least stable, thus driving much of the overall stability of the KiH bsAb. An analysis of both intact bsAb and enzymatic fragments allows us to associate the first and second CIU transitions observed for the intact KiH bsAb to the unfolding Fab and Fc domains, respectively. This result is likely general for CIU data collected for low charge state mAb ions and is supported by data acquired for deglycosylated KiH bsAb and mAb constructs, each of which indicates greater destabilization of the second CIU transition observed in our data. When integrated, our CIU analysis allows us to link changes in the first CIU transition primarily to the Fab region of the hole-containing halfmer, while the second CIU transition is likely strongly connected to the Fc region of the knob-containing halfmer. Taken together, our results provide an unprecedented road map for evaluating the domain-level stabilities and HOS of both KiH bsAb and mAb constructs using CIU.
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Affiliation(s)
| | - Henry W Li
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thomas R Slaney
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Naresh Chennamsetty
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Guodong Chen
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Li Tao
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Deslignière E, Ollivier S, Beck A, Ropartz D, Rogniaux H, Cianférani S. Benefits and Limitations of High-Resolution Cyclic IM-MS for Conformational Characterization of Native Therapeutic Monoclonal Antibodies. Anal Chem 2023; 95:4162-4171. [PMID: 36780376 DOI: 10.1021/acs.analchem.2c05265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Monoclonal antibodies (mAbs) currently represent the main class of therapeutic proteins. mAbs approved by regulatory agencies are selected from IgG1, IgG2, and IgG4 subclasses, which possess different interchain disulfide connectivities. Ion mobility coupled to native mass spectrometry (IM-MS) has emerged as a valuable approach to tackle the challenging characterization of mAbs' higher order structures. However, due to the limited resolution of first-generation IM-MS instruments, subtle conformational differences on large proteins have long been hard to capture. Recent technological developments have aimed at increasing available IM resolving powers and acquisition mode capabilities, namely, through the release of high-resolution IM-MS (HR-IM-MS) instruments, like cyclic IM-MS (cIM-MS). Here, we outline the advantages and drawbacks of cIM-MS for better conformational characterization of intact mAbs (∼150 kDa) in native conditions compared to first-generation instruments. We first assessed the extent to which multipass cIM-MS experiments could improve the separation of mAbs' conformers. These initial results evidenced some limitations of HR-IM-MS for large native biomolecules which possess rich conformational landscapes that remain challenging to decipher even with higher IM resolving powers. Conversely, for collision-induced unfolding (CIU) approaches, higher resolution proved to be particularly useful (i) to reveal new unfolding states and (ii) to enhance the separation of coexisting activated states, thus allowing one to apprehend gas-phase CIU behaviors of mAbs directly at the intact level. Altogether, this study offers a first panoramic overview of the capabilities of cIM-MS for therapeutic mAbs, paving the way for more widespread HR-IM-MS/CIU characterization of mAb-derived formats.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67000, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg 67087, France
| | - Simon Ollivier
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Alain Beck
- IRPF Centre d'Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois 74160, France
| | - David Ropartz
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Hélène Rogniaux
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67000, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg 67087, France
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6
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Deslignière E, Ollivier S, Ehkirch A, Martelet A, Ropartz D, Lechat N, Hernandez-Alba O, Menet JM, Clavier S, Rogniaux H, Genet B, Cianférani S. Combination of IM-Based Approaches to Unravel the Coexistence of Two Conformers on a Therapeutic Multispecific mAb. Anal Chem 2022; 94:7981-7989. [PMID: 35604400 PMCID: PMC9178554 DOI: 10.1021/acs.analchem.2c00928] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Multispecific antibodies,
which target multiple antigens at once,
are emerging as promising therapeutic entities to offer more effective
treatment than conventional monoclonal antibodies (mAbs). However,
these highly complex mAb formats pose significant analytical challenges.
We report here on the characterization of a trispecific antibody (tsAb),
which presents two isomeric forms clearly separated and identified
with size exclusion chromatography coupled to native mass spectrometry
(SEC-nMS). Previous studies showed that these isomers might originate
from a proline cis/trans isomerization
in one Fab subunit of the tsAb. We combined several innovative ion
mobility (IM)-based approaches to confirm the isomeric nature of the
two species and to gain new insights into the conformational landscape
of both isomers. Preliminary SEC-nIM-MS measurements performed on
a low IM resolution instrument provided the first hints of the coexistence
of different conformers, while complementary collision-induced unfolding
(CIU) experiments evidenced distinct gas-phase unfolding behaviors
upon activation for the two isomers. As subtle conformational differences
remained poorly resolved on our early generation IM platform, we performed
high-resolution cyclic IM (cIM-MS) to unambiguously conclude on the
coexistence of two conformers. The cis/trans equilibrium was further tackled by exploiting the IMn slicing capabilities of the cIM-MS instrument. Altogether, our results
clearly illustrate the benefits of combining state-of-the-art nMS
and IM-MS approaches to address challenging issues encountered in
biopharma. As engineered antibody constructs become increasingly sophisticated,
CIU and cIM-MS methodologies undoubtedly have the potential to integrate
the drug development analytical toolbox to achieve in-depth conformational
characterization of these products.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Simon Ollivier
- INRAE, UR BIA, F-44316 Nantes, France.,INRAE, BIBS Facility, F-44316 Nantes, France
| | - Anthony Ehkirch
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Armelle Martelet
- CMC Development, BioAnalytics department France, SANOFI R&D, 94400 Vitry-sur-Seine, France
| | - David Ropartz
- INRAE, UR BIA, F-44316 Nantes, France.,INRAE, BIBS Facility, F-44316 Nantes, France
| | - Nelly Lechat
- CMC Development, BioAnalytics department France, SANOFI R&D, 94400 Vitry-sur-Seine, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Jean-Michel Menet
- CMC Development, BioAnalytics department France, SANOFI R&D, 94400 Vitry-sur-Seine, France
| | - Séverine Clavier
- CMC Development, BioAnalytics department France, SANOFI R&D, 94400 Vitry-sur-Seine, France
| | - Hélène Rogniaux
- INRAE, UR BIA, F-44316 Nantes, France.,INRAE, BIBS Facility, F-44316 Nantes, France
| | - Bruno Genet
- CMC Development, BioAnalytics department France, SANOFI R&D, 94400 Vitry-sur-Seine, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
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7
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Vallejo DD, Jeon CK, Parson KF, Herderschee HR, Eschweiler JD, Filoti DI, Ruotolo BT. Ion Mobility-Mass Spectrometry Reveals the Structures and Stabilities of Biotherapeutic Antibody Aggregates. Anal Chem 2022; 94:6745-6753. [PMID: 35475624 DOI: 10.1021/acs.analchem.2c00160] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Stability is a key critical quality attribute monitored throughout the development of monoclonal antibody (mAb) therapeutics. Minor changes in their higher order structure (HOS) caused by stress or environment may alter mAb aggregation, immunogenicity, and efficacy. In addition, the structures of the resulting mAb aggregates are largely unknown, as are their dependencies on conditions under which they are created. In this report, we investigate the HOS of mAb monomers and dimers under a variety of forced degradation conditions with ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU) technologies. We evaluate two model IgG1 antibodies that differ significantly only in their complementarity-determinant regions: IgG1α and IgG1β. Our data covering both heat- and pH-based forced degradation conditions, aquired on two different IM-MS platforms, show that these mAbs undergo global HOS changes at both monomer and dimer levels upon degradation, but shifts in collision cross section (CCS) differ under pH or heat degradation conditions. In addition, the level of CCS change detected is different between IgG1α and IgG1β, suggesting that differences in the CDR drive differential responses to degradation that influence the antibody HOS. Dramatically different CIU fingerprints are obtained for IgG1α and IgG1β monomers and dimers for both degradation conditions. Finally, we constructed a series of computational models of mAb dimers for comparison with experimental CCS values and found evidence for a compact, overlapped dimer structure under native and heat degradation conditions, possibly adopting an inverted or nonoverlapped quaternary structure when produced through pH degredation. We conclude by discussing the potential impact of our findings on ongoing biotherapeutic discovery and development efforts.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chae Kyung Jeon
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hayley R Herderschee
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Dana I Filoti
- AbbVie, North Chicago, Illinois 60064, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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8
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Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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9
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Vallejo DD, Kang J, Coghlan J, Ramírez CR, Polasky DA, Kurulugama RT, Fjeldsted JC, Schwendeman AA, Ruotolo BT. Collision-Induced Unfolding Reveals Stability Differences in Infliximab Therapeutics under Native and Heat Stress Conditions. Anal Chem 2021; 93:16166-16174. [PMID: 34808055 DOI: 10.1021/acs.analchem.1c03946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU) assays of monoclonal antibody (mAb)-based biotherapeutics have proven sensitive to disulfide bridge structures, glycosylation patterns, and small molecule conjugation levels. Despite promising prior reports detailing the capabilities of IM-MS and CIU to differentiate biosimilars, generic mAb therapeutics, there remain questions surrounding the sensitivity of CIU to mAb structure changes that occur upon stress, the reproducibility of such measurements across IM-MS platforms, and the correlation between CIU and differential scanning calorimetry (DSC) datasets. In this report, we describe a comprehensive IM-MS and CIU dataset acquired for three Infliximabs: Remicade, Inflectra, and Renflexis. We subject each infliximab sample to forced degradation through heat stress and observe broadly similar yet subtly different stability patterns for these three biotherapeutics. We find that CIU is capable of tracking differences in mAb higher-order structure (HOS) imparted during forced heat stress degradation and that DSC is less sensitive to these alterations in comparison. Furthermore, we collected our comprehensive IM-MS and CIU data across two instrument platforms (Waters G2 and Agilent 6560), with both producing similar abilities to differentiate mAbs while also revealing minor differences between the results obtained on the two instruments. Finally, we demonstrate that CIU-based heatmaps and classification allow for rapid assessment of the most differentiating charge states for the analysis of infliximab, and using multiplexed classification, we conservatively estimate a 30-fold improvement in the time required to perform mAb stability and HOS measurements over standard DSC tools.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jukyung Kang
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jill Coghlan
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Daniel A Polasky
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - John C Fjeldsted
- Agilent Technologies, Santa Clara, California 95051, United States
| | - Anna A Schwendeman
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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10
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Abstract
Recent advancements place a comprehensive catalog of protein structure, oligomeric state, sequence, and modification status tentatively within reach, thus providing an unprecedented roadmap to therapies for many human diseases. To achieve this goal, revolutionary technologies capable of bridging key gaps in our ability to simultaneously measure protein composition and structure must be developed. Much of the current progress in this area has been catalyzed by mass spectrometry (MS) tools, which have become an indispensable resource for interrogating the structural proteome. For example, methods associated with native proteomics seek to comprehensively capture and quantify the endogenous assembly states for all proteins within an organism. Such technologies have often been partnered with ion mobility (IM) separation, from which collision cross section (CCS) information can be rapidly extracted to provide protein size information. IM technologies are also being developed that utilize CCS values to enhance the confidence of protein identification workflows derived from liquid chromatography-IM-MS analyses of enzymatically produced peptide mixtures. Such parallel advancements in technology beg the question: can CCS values prove similarly useful for the identification of intact proteins and their complexes in native proteomics? In this perspective, I examine current evidence and technology trends to explore the promise and limitations of such CCS information for the comprehensive analysis of multiprotein complexes from cellular mixtures.
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Affiliation(s)
- Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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11
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Abstract
![]()
Native mass spectrometry
(MS) involves the analysis and characterization
of macromolecules, predominantly intact proteins and protein complexes,
whereby as much as possible the native structural features of the
analytes are retained. As such, native MS enables the study of secondary,
tertiary, and even quaternary structure of proteins and other biomolecules.
Native MS represents a relatively recent addition to the analytical
toolbox of mass spectrometry and has over the past decade experienced
immense growth, especially in enhancing sensitivity and resolving
power but also in ease of use. With the advent of dedicated mass analyzers,
sample preparation and separation approaches, targeted fragmentation
techniques, and software solutions, the number of practitioners and
novel applications has risen in both academia and industry. This review
focuses on recent developments, particularly in high-resolution native
MS, describing applications in the structural analysis of protein
assemblies, proteoform profiling of—among others—biopharmaceuticals
and plasma proteins, and quantitative and qualitative analysis of
protein–ligand interactions, with the latter covering lipid,
drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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12
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Zhou L, Wang D, Iftikhar M, Lu Y, Zhou M. Conformational changes and binding property of the periplasmic binding protein BtuF during vitamin B 12 transport revealed by collision-induced unfolding, hydrogen-deuterium exchange mass spectrometry and molecular dynamic simulation. Int J Biol Macromol 2021; 187:350-360. [PMID: 34303738 DOI: 10.1016/j.ijbiomac.2021.07.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/05/2021] [Accepted: 07/18/2021] [Indexed: 10/20/2022]
Abstract
The periplasmic binding protein (PBP) BtuF plays a key role in transporting vitamin B12 from periplasm to the ATP-binding cassette (ABC) transporter BtuCD. Conformational changes of BtuF during transport can hardly be captured by traditional biophysical methods and the exact mechanism regarding B12 and BtuF recognition is still under debate. In the present work, conformational changes of BtuF upon B12 binding and release were investigated using hybrid approaches including collision-induced unfolding (CIU), hydrogen deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulation. It was found that B12 binding increased the stability of BtuF. In addition, fast exchange regions of BtuF were localized. Most importantly, midpoint of hinge helix in BtuF was found highly flexible, and binding of B12 proceed in a manner similar to the Venus flytrap mechanism. Our study therefore delineates a clear view of BtuF delivering B12, and demonstrated a hybrid approach encompassing MS and computer based methods that holds great potential to the probing of conformational dynamics of proteins in action.
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Affiliation(s)
- Lijun Zhou
- Institute of Bio-analytical Chemistry, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China
| | - Defu Wang
- Institute of Bio-analytical Chemistry, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China
| | - Mehwish Iftikhar
- Institute of Bio-analytical Chemistry, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China
| | - Yinghong Lu
- Institute of Bio-analytical Chemistry, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China.
| | - Min Zhou
- Institute of Bio-analytical Chemistry, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China.
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13
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Wilson KM, Burkus-Matesevac A, Maddox SW, Chouinard CD. Native Ubiquitin Structural Changes Resulting from Complexation with β-Methylamino-l-alanine (BMAA). J Am Soc Mass Spectrom 2021; 32:895-900. [PMID: 33735566 DOI: 10.1021/jasms.0c00372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The objective of this research was to investigate potential changes to unfolding energy barriers for ubiquitin in the presence of the noncanonical amino acid β-methylamino-l-alanine (BMAA). Although BMAA has been implicated in neurodegenerative disease, its specific role remains unclear. We hypothesized that formation of a ubiquitin + BMAA noncovalent complex would alter the protein's unfolding dynamics in comparison with native ubiquitin alone or in noncovalent complexes with other amino acids. Ion mobility-mass spectrometry (IM-MS) revealed that at sufficiently high concentrations BMAA did in fact form a noncovalent complex with ubiquitin, and similar complexes were identified for a range of additional amino acids. Collision-induced unfolding (CIU) was used to interrogate the unfolding of native ubiquitin and these Ubq-amino acid complexes, showing a major transition from its compact native state (∼1200 Å2) to an unfolded state (∼1400 Å2) at activation energies in the range from 8.0 to 9.0 V (entrance grid delta). The Ubq-BMAA complex, on the other hand, was observed to have a significantly higher energy barrier to unfolding, requiring more than 10.5 V. This indicates that the complex remains more stable under native conditions and this may indicate that BMAA has attached to a critical binding location worthy of further study for its potential role in the onset of neurodegenerative disease.
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Affiliation(s)
- Katie Mae Wilson
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, Florida 32904, United States
| | - Aurora Burkus-Matesevac
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, Florida 32904, United States
| | - Samuel W Maddox
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, Florida 32904, United States
| | - Christopher D Chouinard
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, Florida 32904, United States
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14
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Deslignière E, Ehkirch A, Botzanowski T, Beck A, Hernandez-Alba O, Cianférani S. Toward Automation of Collision-Induced Unfolding Experiments through Online Size Exclusion Chromatography Coupled to Native Mass Spectrometry. Anal Chem 2020; 92:12900-12908. [DOI: 10.1021/acs.analchem.0c01426] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Anthony Ehkirch
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Alain Beck
- IRPF—Centre d’Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
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15
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Yen H, Liko I, Gault J, Wu D, Struwe WB, Robinson CV. Correlating Glycoforms of DC-SIGN with Stability Using a Combination of Enzymatic Digestion and Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2020; 59:15560-15564. [PMID: 33462887 PMCID: PMC7496578 DOI: 10.1002/anie.202005727] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/05/2020] [Indexed: 01/03/2023]
Abstract
The immune scavenger protein DC-SIGN interacts with glycosylated proteins and has a putative role in facilitating viral infection. How these recognition events take place with different viruses is not clear and the effects of glycosylation on the folding and stability of DC-SIGN have not been reported. Herein, we report the development and application of a mass-spectrometry-based approach to both uncover and characterise the effects of O-glycans on the stability of DC-SIGN. We first quantify the Core 1 and 2 O-glycan structures on the carbohydrate recognition and extracellular domains of the protein using sequential exoglycosidase sequencing. Using ion mobility mass spectrometry, we show how specific O-glycans, and/or single monosaccharide substitutions, alter both the overall collision cross section and the gas-phase stability of the DC-SIGN isoforms. We find that rather than the mass or length of glycoprotein modifications, the stability of DC-SIGN is better correlated with the number of glycosylation sites.
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Affiliation(s)
- Hsin‐Yung Yen
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
- Present address: OMass TherapeuticsThe Schrodinger Building, Oxford Science ParkOxfordOX4 4GEUK
| | - Idlir Liko
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
- Present address: OMass TherapeuticsThe Schrodinger Building, Oxford Science ParkOxfordOX4 4GEUK
| | - Joseph Gault
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Di Wu
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Carol V. Robinson
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
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16
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Abstract
Metallothioneins (MTs) constitute a family of cysteine-rich proteins that play key biological roles for a wide range of metal ions, but unlike many other metalloproteins, the structures of apo- and partially metalated MTs are not well understood. Here, we combine nano-electrospray ionization-mass spectrometry (ESI-MS) and nano-ESI-ion mobility (IM)-MS with collision-induced unfolding (CIU), chemical labeling using N-ethylmaleimide (NEM), and both bottom-up and top-down proteomics in an effort to better understand the metal binding sites of the partially metalated forms of human MT-2A, viz., Ag4-MT. The results for Ag4-MT are then compared to similar results obtained for Cd4-MT. The results show that Ag4-MT is a cooperative product, and data from top-down and bottom-up proteomics mass spectrometry analysis combined with NEM labeling revealed that all four Ag+ ions of Ag4-MT are bound to the β-domain. The binding sites are identified as Cys13, Cys15, Cys19, Cys21, Cys24, and Cys26. While both Ag+ and Cd2+ react with MT to yield cooperative products, i.e., Ag4-MT and Cd4-MT, these products are very different; Ag+ ions of Ag4-MT are located in the β-domain, whereas Cd2+ ions of Cd4-MT are located in the α-domain. Ag6-MT has been reported to be fully metalated in the β-domain, but our data suggest the two additional Ag+ ions are more weakly bound than are the other four. Higher order Agi-MT complexes (i = 7-17) are formed in solutions that contain excess Ag+ ions, and these are assumed to be bound to the α-domain or shared between the two domains. Interestingly, the excess Ag+ ions are displaced upon addition of NEM to this solution to yield predominantly Ag4NEM14-MT. Results from CIU suggest that Agi-MT complexes are structurally more ordered and that the energy required to unfold these complexes increases as the number of coordinated Ag+ increases.
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Affiliation(s)
- Shiyu Dong
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Liqi Fan
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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17
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Yen H, Liko I, Gault J, Wu D, Struwe WB, Robinson CV. Correlating Glycoforms of DC‐SIGN with Stability Using a Combination of Enzymatic Digestion and Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hsin‐Yung Yen
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
- Present address: OMass Therapeutics The Schrodinger Building, Oxford Science Park Oxford OX4 4GE UK
| | - Idlir Liko
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
- Present address: OMass Therapeutics The Schrodinger Building, Oxford Science Park Oxford OX4 4GE UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
| | - Di Wu
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
| | - Weston B. Struwe
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
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18
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Groves K, Cryar A, Cowen S, Ashcroft AE, Quaglia M. Mass Spectrometry Characterization of Higher Order Structural Changes Associated with the Fc-glycan Structure of the NISTmAb Reference Material, RM 8761. J Am Soc Mass Spectrom 2020; 31:553-564. [PMID: 32008322 DOI: 10.1021/jasms.9b00022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
As monoclonal antibodies (mAbs) rapidly emerge as a dominant class of therapeutics, so does the need for suitable analytical technologies to monitor for changes in protein higher order structure (HOS) of these biomolecules. Reference materials (RM) serve a key analytical purpose of benchmarking the suitability and robustness of both established and emerging analytical procedures for both drug producers and regulators. Here, two simple enzymatic protocols for generating Fc-glycan variants from the NISTmAb RM are described and both global and localized changes in HOS between the RM and these Fc-glycan variants are characterized using hydrogen deuterium exchange-mass spectrometry (HDX-MS) and ion mobility spectrometry-mass spectrometry (IMS-MS) measurements. An alternative statistical approach is described where measurement thresholds that differentiate between measurement variability and significant structural changes were established on the basis of experimental data. Measurements revealed decreases in structural stability correlating with the degree of Fc-glycan structure loss, especially at the CH2/CH3 domain interface. These data promote the use of this RM and these Fc-glycan variants for establishing the sensitivity of and validating analytical methods for the detection of HOS measurements of mAbs.
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Affiliation(s)
- Kate Groves
- LGC, Queens Road, Teddington TW11 0LY, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Adam Cryar
- LGC, Queens Road, Teddington TW11 0LY, UK
| | | | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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19
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Kang J, Kim SY, Vallejo D, Hageman TS, White DR, Benet A, Coghlan J, Sen KI, Ford M, Saveliev S, Tolbert TJ, Weis DD, Schwendeman SP, Ruotolo BT, Schwendeman A. Multifaceted assessment of rituximab biosimilarity: The impact of glycan microheterogeneity on Fc function. Eur J Pharm Biopharm 2020; 146:111-124. [PMID: 31841688 DOI: 10.1016/j.ejpb.2019.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 12/04/2019] [Accepted: 12/08/2019] [Indexed: 01/08/2023]
Abstract
Biosimilars are poised to reduce prices and increase patient access to expensive, but highly effective biologic products. However, questions still remain about the degree of similarity and scarcity of information on biosimilar products from outside of the US/EU in the public domain. Thus, as an independent entity, we performed a comparative analysis between the innovator, Rituxan® (manufactured by Genentech/Roche), and a Russian rituximab biosimilar, Acellbia® (manufactured by Biocad). We evaluated biosimilarity of these two products by a variety of state-of-the-art analytical mass spectrometry techniques, including tandem MS mapping, HX-MS, IM-MS, and intact MS. Both were found to be generally similar regarding primary and higher order structure, though differences were identified in terms of glycoform distribution levels of C-terminal Lys, N-terminal pyroGlu, charge variants and soluble aggregates. Notably, we confirmed that the biosimilar had a higher level of afucosylated glycans, resulting in a stronger FcγIIIa binding affinity and increased ADCC activity. Taken together, our work provides a comprehensive comparison of Rituxan® and Acellbia®.
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Affiliation(s)
- Jukyung Kang
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, United States; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Sang Yeop Kim
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, United States; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Daniel Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Tyler S Hageman
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, United States
| | - Derek R White
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, United States
| | - Alexander Benet
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, United States; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Jill Coghlan
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, United States; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - K Ilker Sen
- Protein Metrics Inc., San Carlos, CA 94070, United States
| | | | | | - Thomas J Tolbert
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, United States
| | - David D Weis
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, United States; Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, United States
| | - Steven P Schwendeman
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, United States; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Anna Schwendeman
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, United States; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, United States.
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20
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Watanabe Y, Bowden TA, Wilson IA, Crispin M. Exploitation of glycosylation in enveloped virus pathobiology. Biochim Biophys Acta Gen Subj 2019; 1863:1480-1497. [PMID: 31121217 PMCID: PMC6686077 DOI: 10.1016/j.bbagen.2019.05.012] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 12/12/2022]
Abstract
Glycosylation is a ubiquitous post-translational modification responsible for a multitude of crucial biological roles. As obligate parasites, viruses exploit host-cell machinery to glycosylate their own proteins during replication. Viral envelope proteins from a variety of human pathogens including HIV-1, influenza virus, Lassa virus, SARS, Zika virus, dengue virus, and Ebola virus have evolved to be extensively glycosylated. These host-cell derived glycans facilitate diverse structural and functional roles during the viral life-cycle, ranging from immune evasion by glycan shielding to enhancement of immune cell infection. In this review, we highlight the imperative and auxiliary roles glycans play, and how specific oligosaccharide structures facilitate these functions during viral pathogenesis. We discuss the growing efforts to exploit viral glycobiology in the development of anti-viral vaccines and therapies.
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Affiliation(s)
- Yasunori Watanabe
- School of Biological Sciences and Institute of Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford OX3 7BN, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas A Bowden
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences and Institute of Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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21
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Abstract
Neutralizing antibodies against human immunodeficiency virus subtype 1 (HIV-1) bind to its envelope glycoprotein (Env). Half of the molecular mass of Env is carbohydrate making it one of the most heavily glycosylated proteins known in nature. HIV-1 Env glycans are derived from the host and present a formidable challenge for host anti-glycan antibody induction. Anti-glycan antibody induction is challenging because anti-HIV-1 glycan antibodies should recognize Env antigen while not acquiring autoreactivity. Thus, the glycan network on HIV-1 Env is referred to as the glycan shield. Despite the challenges presented by immune recognition of host-derived glycans, neutralizing antibodies capable of binding the glycans on HIV-1 Env can be generated by the host immune system in the setting of HIV-1 infection. In particular, a cluster of high mannose glycans, including an N-linked glycan at position 332, form the high mannose patch and are targeted by a variety of broadly neutralizing antibodies. These high mannose patch-directed HIV-1 antibodies can be categorized into distinct categories based on their antibody paratope structure, neutralization activity, and glycan and peptide reactivity. Below we will compare and contrast each of these classes of HIV-1 glycan-dependent antibodies and describe vaccine design efforts to elicit each of these antibody types.
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22
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Struwe WB, Robinson CV. Relating glycoprotein structural heterogeneity to function - insights from native mass spectrometry. Curr Opin Struct Biol 2019; 58:241-8. [PMID: 31326232 DOI: 10.1016/j.sbi.2019.05.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 01/08/2023]
Abstract
Glycosylation is the most complex and prevalent protein modification that influences attributes ranging from cellular localization and signaling to half-life and proteolysis. Glycoconjugates are fundamental for cellular function and alterations in their structure are often observed in pathological states. Most biotherapeutic proteins are glycosylated, which influences drug safety and efficacy. Therefore, the ability to characterize glycoproteins is important in all areas of biomolecular and medicinal research. Here we discuss recent advances in native mass spectrometry that have significantly improved our ability to characterize heterogeneous glycoproteins and to relate glycan structure to protein function.
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23
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Polasky DA, Dixit SM, Vallejo DD, Kulju KD, Ruotolo BT. An Algorithm for Building Multi-State Classifiers Based on Collision-Induced Unfolding Data. Anal Chem 2019; 91:10407-10412. [DOI: 10.1021/acs.analchem.9b02650] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sugyan M. Dixit
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Daniel D. Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kathryn D. Kulju
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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24
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Vallejo DD, Polasky DA, Kurulugama RT, Eschweiler JD, Fjeldsted JC, Ruotolo BT. A Modified Drift Tube Ion Mobility-Mass Spectrometer for Charge-Multiplexed Collision-Induced Unfolding. Anal Chem 2019; 91:8137-8146. [PMID: 31194508 DOI: 10.1021/acs.analchem.9b00427] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Collision-induced unfolding (CIU) of protein ions and their noncovalent complexes offers relatively rapid access to a rich portfolio of biophysical information, without the need to tag or purify proteins prior to analysis. Such assays have been characterized extensively for a range of therapeutic proteins, proving exquisitely sensitive to alterations in protein sequence, structure, and post-translational modification state. Despite advantages over traditional probes of protein stability, improving the throughput and information content of gas-phase protein unfolding assays remains a challenge for current instrument platforms. In this report, we describe modifications to an Agilent 6560 drift tube ion mobility-mass spectrometer in order to perform robust, simultaneous CIU across all precursor ions detected. This approach dramatically increases the speed associated with typical CIU assays, which typically involve mass selection of narrow m/ z regions prior to collisional activation, and thus their development requires a comprehensive assessment of charge-stripping reactions that can unintentionally pollute CIU data with chemical noise when more than one precursor ion is allowed to undergo simultaneous activation. By studying the unfolding and dissociation of intact antibody ions, a key analyte class associated with biotherapeutics, we reveal a predictive relationship between the precursor charge state, the amount of buffer components bound to the ions of interest, and the amount of charge stripping detected. We then utilize our knowledge of antibody charge stripping to rapidly capture CIU data for a range of antibody subclasses and subtypes across all charge states simultaneously, demonstrating a strong charge state dependence on the information content of CIU. Finally, we demonstrate that CIU data collection times can be further reduced by scanning fewer voltage steps, enabling us to optimize the throughput of our improved CIU methods and confidently differentiate antibody variant ions using ∼20% of the data typically collected during CIU. Taken together, our results characterize a new instrument platform for biotherapeutic stability measurements with dramatically improved throughput and information content.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Daniel A Polasky
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | | | - Joseph D Eschweiler
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States.,AbbVie , North Chicago , Illinois 60064 , United States
| | - John C Fjeldsted
- Agilent Technologies , Santa Clara , California 95051 , United States
| | - Brandon T Ruotolo
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
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25
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Brown KA, Rajendran S, Dowd J, Wilson DJ. Rapid characterization of structural and functional similarity for a candidate bevacizumab (Avastin) biosimilar using a multipronged mass‐spectrometry‐based approach. Drug Test Anal 2019; 11:1207-1217. [DOI: 10.1002/dta.2609] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Kerene A. Brown
- Chemistry DepartmentYork University Toronto ON Canada
- The Centre for Research in Mass SpectrometryYork University Toronto ON Canada
| | | | - Jason Dowd
- Apobiologix (division of Apotex Inc.) Toronto ON Canada
| | - Derek J. Wilson
- Chemistry DepartmentYork University Toronto ON Canada
- The Centre for Research in Mass SpectrometryYork University Toronto ON Canada
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26
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Beck A, D’Atri V, Ehkirch A, Fekete S, Hernandez-Alba O, Gahoual R, Leize-Wagner E, François Y, Guillarme D, Cianférani S. Cutting-edge multi-level analytical and structural characterization of antibody-drug conjugates: present and future. Expert Rev Proteomics 2019; 16:337-362. [DOI: 10.1080/14789450.2019.1578215] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alain Beck
- Biologics CMC and Developability, IRPF - Centre d’Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois, France
| | - Valentina D’Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU, Geneva, Switzerland
| | - Anthony Ehkirch
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
| | - Szabolcs Fekete
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU, Geneva, Switzerland
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
| | - Rabah Gahoual
- Unité de Technologies Biologiques et Chimiques pour la Santé (UTCBS), Paris 5-CNRS UMR8258 Inserm U1022, Faculté de Pharmacie, Université Paris Descartes, Paris, France
| | - Emmanuel Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140, Université de Strasbourg, CNRS, Strasbourg, France
| | - Yannis François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- Biologics CMC and Developability, IRPF - Centre d’Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
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27
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Allison TM, Bechara C. Structural mass spectrometry comes of age: new insight into protein structure, function and interactions. Biochem Soc Trans 2019; 47:317-27. [DOI: 10.1042/bst20180356] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022]
Abstract
Abstract
Mass spectrometry (MS) provides an impressive array of information about the structure, function and interactions of proteins. In recent years, many new developments have been in the field of native MS and these exemplify a new coming of age of this field. In this mini review, we connect the latest methodological and instrumental developments in native MS to the new insights these have enabled. We highlight the prominence of an increasingly common strategy of using hybrid approaches, where multiple MS-based techniques are used in combination, and integrative approaches, where MS is used alongside other techniques such as ion-mobility spectrometry. We also review how the emergence of a native top-down approach, which combines native MS with top-down proteomics into a single experiment, is the pièce de résistance of structural mass spectrometry's coming of age. Finally, we outline key developments that have enabled membrane protein native MS to shift from being extremely challenging to routine, and how this technique is uncovering inaccessible details of membrane protein–lipid interactions.
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28
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Tian Y, Lippens JL, Netirojjanakul C, Campuzano IDG, Ruotolo BT. Quantitative collision-induced unfolding differentiates model antibody-drug conjugates. Protein Sci 2018; 28:598-608. [PMID: 30499138 DOI: 10.1002/pro.3560] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022]
Abstract
Antibody-drug conjugates (ADCs) are antibody-based therapeutics that have proven to be highly effective cancer treatment platforms. They are composed of monoclonal antibodies conjugated with highly potent drugs via chemical linkers. Compared to cysteine-targeted chemistries, conjugation at native lysine residues can lead to a higher degree of structural heterogeneity, and thus it is important to evaluate the impact of conjugation on antibody conformation. Here, we present a workflow involving native ion mobility (IM)-MS and gas-phase unfolding for the structural characterization of lysine-linked monoclonal antibody (mAb)-biotin conjugates. Following the determination of conjugation states via denaturing Liquid Chromatography-Mass Spectrometry (LC-MS) measurements, we performed both size exclusion chromatography (SEC) and native IM-MS measurements in order to compare the structures of biotinylated and unmodified IgG1 molecules. Hydrodynamic radii (Rh) and collision cross-sectional (CCS) values were insufficient to distinguish the conformational changes in these antibody-biotin conjugates owing to their flexible structures and limited instrument resolution. In contrast, collision induced unfolding (CIU) analyses were able to detect subtle structural and stability differences in the mAb upon biotin conjugation, exhibiting a sensitivity to mAb conjugation that exceeds native MS analysis alone. Destabilization of mAb-biotin conjugates was detected by both CIU and differential scanning calorimetry (DSC) data, suggesting a previously unknown correlation between the two measurement tools. We conclude by discussing the impact of IM-MS and CIU technologies on the future of ADC development pipelines.
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Affiliation(s)
- Yuwei Tian
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Jennifer L Lippens
- Amgen Discovery Research, Discovery Attribute Sciences, Amgen, Thousand Oaks, California, 91320
| | - Chawita Netirojjanakul
- Amgen Discovery Research, Hybrid Modality Engineering, Amgen, Thousand Oaks, California, 91320
| | - Iain D G Campuzano
- Amgen Discovery Research, Discovery Attribute Sciences, Amgen, Thousand Oaks, California, 91320
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
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29
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Hansen K, Lau AM, Giles K, McDonnell JM, Struwe WB, Sutton BJ, Politis A. A Mass-Spectrometry-Based Modelling Workflow for Accurate Prediction of IgG Antibody Conformations in the Gas Phase. Angew Chem Int Ed Engl 2018; 57:17194-17199. [PMID: 30408305 PMCID: PMC6392142 DOI: 10.1002/anie.201812018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Indexed: 11/09/2022]
Abstract
Immunoglobulins are biomolecules involved in defence against foreign substances. Flexibility is key to their functional properties in relation to antigen binding and receptor interactions. We have developed an integrative strategy combining ion mobility mass spectrometry (IM-MS) with molecular modelling to study the conformational dynamics of human IgG antibodies. Predictive models of all four human IgG subclasses were assembled and their dynamics sampled in the transition from extended to collapsed state during IM-MS. Our data imply that this collapse of IgG antibodies is related to their intrinsic structural features, including Fab arm flexibility, collapse towards the Fc region, and the length of their hinge regions. The workflow presented here provides an accurate structural representation in good agreement with the observed collision cross section for these flexible IgG molecules. These results have implications for studying other nonglobular flexible proteins.
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Affiliation(s)
- Kjetil Hansen
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Andy M. Lau
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | | | | | | | - Brian J. Sutton
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonUK
| | - Argyris Politis
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
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30
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Hansen K, Lau AM, Giles K, McDonnell JM, Struwe WB, Sutton BJ, Politis A. A Mass‐Spectrometry‐Based Modelling Workflow for Accurate Prediction of IgG Antibody Conformations in the Gas Phase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kjetil Hansen
- Department of Chemistry King's College London 7 Trinity Street London SE1 1DB UK
| | - Andy M. Lau
- Department of Chemistry King's College London 7 Trinity Street London SE1 1DB UK
| | - Kevin Giles
- Waters Corp. Stamford Road Wilmslow SK9 4AX UK
| | - James M. McDonnell
- Randall Centre for Cell and Molecular Biophysics King's College London UK
| | | | - Brian J. Sutton
- Randall Centre for Cell and Molecular Biophysics King's College London UK
| | - Argyris Politis
- Department of Chemistry King's College London 7 Trinity Street London SE1 1DB UK
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