1
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Li B, Ustyugova IV, Szymkowicz L, Zhu S, Ming M, Fung KYY, Cortés G, James DA, Hrynyk M, Rahman N, Brookes RH, Ausar SF. Formulation development of a stable influenza recombinant neuraminidase vaccine candidate. Hum Vaccin Immunother 2024; 20:2304393. [PMID: 38497413 PMCID: PMC10950269 DOI: 10.1080/21645515.2024.2304393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/09/2024] [Indexed: 03/19/2024] Open
Abstract
Current influenza vaccines could be augmented by including recombinant neuraminidase (rNA) protein antigen to broaden protective immunity and improve efficacy. Toward this goal, we investigated formulation conditions to optimize rNA physicochemical stability. When rNA in sodium phosphate saline buffer (NaPBS) was frozen and thawed (F/T), the tetrameric structure transitioned from a "closed" to an "open" conformation, negatively impacting functional activity. Hydrogen deuterium exchange experiments identified differences in anchorage binding sites at the base of the open tetramer, offering a structural mechanistic explanation for the change in conformation and decreased functional activity. Change to the open configuration was triggered by the combined stresses of acidic pH and F/T. The desired closed conformation was preserved in a potassium phosphate buffer (KP), minimizing pH drop upon freezing and including 10% sucrose to control F/T stress. Stability was further evaluated in thermal stress studies where changes in conformation were readily detected by ELISA and size exclusion chromatography (SEC). Both tests were suitable indicators of stability and antigenicity and considered potential critical quality attributes (pCQAs). To understand longer-term stability, the pCQA profiles from thermally stressed rNA at 6 months were modeled to predict stability of at least 24-months at 5°C storage. In summary, a desired rNA closed tetramer was maintained by formulation selection and monitoring of pCQAs to produce a stable rNA vaccine candidate. The study highlights the importance of understanding and controlling vaccine protein structural and functional integrity.
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Affiliation(s)
- Bing Li
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
| | | | | | | | - Marin Ming
- Sanofi Analytical Sciences, Toronto, ON, Canada
| | - Karen Y. Y. Fung
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
| | - Guadalupe Cortés
- Sanofi mRNA & Translational Medicine COVID Franchise, Global Clinical Development, Waltham, MA, USA
| | - D. Andrew James
- Sanofi External Research and Development, Toronto, ON, Canada
| | | | - Nausheen Rahman
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
| | - Roger H. Brookes
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
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2
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Olaleye O, Graf C, Spanov B, Govorukhina N, Groves MR, van de Merbel NC, Bischoff R. Determination of Binding Sites on Trastuzumab and Pertuzumab to Selective Affimers Using Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:775-783. [PMID: 36960982 PMCID: PMC10080681 DOI: 10.1021/jasms.3c00069] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a method to probe the solvent accessibility and conformational dynamics of a protein or a protein-ligand complex with respect to exchangeable amide hydrogens. Here, we present the application of HDX-MS to determine the binding sites of Affimer reagents to the monoclonal antibodies trastuzumab and pertuzumab, respectively. Intact and subunit level HDX-MS analysis of antibody-affimer complexes showed significant protection from HDX in the antibody Fab region upon affimer binding. Bottom-up HDX-MS experiments including online pepsin digestion revealed that the binding sites of the affimer reagents were mainly located in the complementarity-determining region (CDR) 2 of the heavy chain of the respective antibodies. Three-dimensional models of the binding interaction between the affimer reagents and the antibodies were built by homology modeling and molecular docking based on the HDX data.
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Affiliation(s)
- Oladapo Olaleye
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Christian Graf
- Novartis
Technical Research & Development Biologics, Hexal AG, Keltenring
1 + 3, 82041 Oberhaching, Germany
| | - Baubek Spanov
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Natalia Govorukhina
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Matthew R. Groves
- Drug
Design, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Nico C. van de Merbel
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- ICON
Bioanalytical Laboratories, Amerikaweg 18, 9407 TK Assen, The Netherlands
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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3
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Cleaver S, Gardner M, Barlow A, Ferrari E, Soloviev M. Fast Protocols for Characterizing Antibody-Peptide Binding. Methods Mol Biol 2023; 2578:83-101. [PMID: 36152282 DOI: 10.1007/978-1-0716-2732-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microarray assay formats gained popularity in the 1990s, first implemented in DNA-based arrays but later adopted for use with proteins, namely antibodies, peptides, low molecular weight (LMW) molecules, such as lipids, and even tissues. In nucleic acid-based affinity assays and arrays, but not in protein or peptide arrays, the specificity and affinity of complementary strand interactions can be deduced from or adjusted through modifications to the nucleotide sequence. Arrays of LMW molecules are characterized by largely uniform but low binding affinities. Multiplexed protein-based affinity assays, such as microarrays, might present an additional challenge due to heterogeneity of antigen properties and of their binding affinities. The use of peptides instead of proteins reduces physical heterogeneity of these reagents through either the widened peptide selection options or rational sequence engineering. However, rational engineering of binding affinities remains an unmet need, and peptide-binding affinities to the respective antipeptide antibodies could vary by orders of magnitude. Hence, multiplexing of such assays by using a microarray format and data analysis and interpretation requires some knowledge of their binding affinities. Low-throughput binding assays to characterize such peptide-antipeptide antibodies interactions are widely available, but scaling-up of traditional protein- and peptide-binding assays might present practical challenges. Here, we describe fast label-free practical approach especially suitable for estimating peptide-binding affinities. The method in question relies on commercially available biolayer interferometry-based equipment with a protocol which can be easily scaled-up, subject to user needs and equipment availability.
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Affiliation(s)
- Sophie Cleaver
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Matthew Gardner
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Anthony Barlow
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Enrico Ferrari
- School of Life Sciences, University of Lincoln, Lincoln, UK
| | - Mikhail Soloviev
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK.
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4
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Shin G, Lim SI. Unveiling the biological interface of protein complexes by mass spectrometry-coupled methods. Proteins 2022; 91:593-607. [PMID: 36573681 DOI: 10.1002/prot.26459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Most biomolecules become functional and bioactive by forming protein complexes through interaction with ligands that are diverse in size, shape, and physicochemical properties. In the complex biological milieu, the interaction is ligand-specific, driven by molecular sensing, and involves the recognition of a binding interface localized within a protein structure. Mapping interfaces of protein complexes is a highly sought area of research as it delivers fundamental insights into proteomes and pathology and hence strategies for therapeutics. While X-ray crystallography and electron microscopy remain the gold standard for structural elucidation of protein complexes, their artificial and static analytic nature often produces a non-native interface that otherwise might be negligible or non-existent in a biological environment. Recently, the mass spectrometry-coupled approaches, chemical crosslinking (CLMS) and hydrogen-deuterium exchange (HDMS) have become valuable analytic complements to the traditional techniques. These methods explicitly identify hot residues and motifs embedded in binding interfaces, especially when the interaction is predominantly dynamic, transient, and/or caused by an intrinsically disordered domain. Here, we review the principal role of CLMS and HDMS in protein structural biology with a particular emphasis on the contribution of recent examples to exploring biological interfaces. Additionally, we describe recent studies that utilized these methods to expand our understanding of protein complex formation and the related biological processes, to increase the probability of structure-based drug design.
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Affiliation(s)
- Goeun Shin
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
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5
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Tajoddin NN, Konermann L. Structural Dynamics of a Thermally Stressed Monoclonal Antibody Characterized by Temperature-Dependent H/D Exchange Mass Spectrometry. Anal Chem 2022; 94:15499-15509. [DOI: 10.1021/acs.analchem.2c03931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nastaran N. Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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6
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Biavasco R, De Giovanni M. The Relative Positioning of B and T Cell Epitopes Drives Immunodominance. Vaccines (Basel) 2022; 10:vaccines10081227. [PMID: 36016115 PMCID: PMC9413633 DOI: 10.3390/vaccines10081227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 12/05/2022] Open
Abstract
Humoral immunity is crucial for protection against invading pathogens. Broadly neutralizing antibodies (bnAbs) provide sterilizing immunity by targeting conserved regions of viral variants and represent the goal of most vaccination approaches. While antibodies can be selected to bind virtually any region of a given antigen, the consistent induction of bnAbs in the context of influenza and HIV has represented a major roadblock. Many possible explanations have been considered; however, none of the arguments proposed to date seem to fully recapitulate the observed counter-selection for broadly protective antibodies. Antibodies can influence antigen presentation by enhancing the processing of CD4 epitopes adjacent to the binding region while suppressing the overlapping ones. We analyze the relative positioning of dominant B and T cell epitopes in published antigens that elicit strong and poor humoral responses. In strong immunogenic antigens, regions bound by immunodominant antibodies are frequently adjacent to CD4 epitopes, potentially boosting their presentation. Conversely, poorly immunogenic regions targeted by bnAbs in HIV and influenza overlap with clusters of dominant CD4 epitopes, potentially conferring an intrinsic disadvantage for bnAb-bearing B cells in germinal centers. Here, we propose the theory of immunodominance relativity, according to which the relative positioning of immunodominant B and CD4 epitopes within a given antigen drives immunodominance. Thus, we suggest that the relative positioning of B-T epitopes may be one additional mechanism that cooperates with other previously described processes to influence immunodominance. If demonstrated, this theory can improve the current understanding of immunodominance, provide a novel explanation for HIV and influenza escape from humoral responses, and pave the way for a new rational design of universal vaccines.
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Affiliation(s)
- Riccardo Biavasco
- Department of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Marco De Giovanni
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Correspondence:
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7
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Tran MH, Schoeder CT, Schey KL, Meiler J. Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook. Front Immunol 2022; 13:859964. [PMID: 35720345 PMCID: PMC9204306 DOI: 10.3389/fimmu.2022.859964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022] Open
Abstract
Although computational structure prediction has had great successes in recent years, it regularly fails to predict the interactions of large protein complexes with residue-level accuracy, or even the correct orientation of the protein partners. The performance of computational docking can be notably enhanced by incorporating experimental data from structural biology techniques. A rapid method to probe protein-protein interactions is hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS has been increasingly used for epitope-mapping of antibodies (Abs) to their respective antigens (Ags) in the past few years. In this paper, we review the current state of HDX-MS in studying protein interactions, specifically Ab-Ag interactions, and how it has been used to inform computational structure prediction calculations. Particularly, we address the limitations of HDX-MS in epitope mapping and techniques and protocols applied to overcome these barriers. Furthermore, we explore computational methods that leverage HDX-MS to aid structure prediction, including the computational simulation of HDX-MS data and the combination of HDX-MS and protein docking. We point out challenges in interpreting and incorporating HDX-MS data into Ab-Ag complex docking and highlight the opportunities they provide to build towards a more optimized hybrid method, allowing for more reliable, high throughput epitope identification.
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Affiliation(s)
- Minh H. Tran
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, United States
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Clara T. Schoeder
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
| | - Kevin L. Schey
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Jens Meiler
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
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8
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Hydrogen-Deuterium Exchange Mass Spectrometry Reveals a Novel Binding Region of a Neutralizing Fully Human Monoclonal Antibody to Anthrax Protective Antigen. Toxins (Basel) 2022; 14:toxins14020092. [PMID: 35202120 PMCID: PMC8877668 DOI: 10.3390/toxins14020092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/14/2022] [Accepted: 01/21/2022] [Indexed: 12/04/2022] Open
Abstract
Anthrax vaccine adsorbed (AVA) containing protective antigen (PA) is the only FDA-approved anthrax vaccine in the United States. Characterization of the binding of AVA-induced anti-PA human antibodies against the PA antigen after vaccination is crucial to understanding mechanisms of the AVA-elicited humoral immune response. Hydrogen deuterium exchange mass spectrometry (HDX-MS) is often coupled with a short liquid chromatography gradient (e.g., 5–10 min) for the characterization of protein interactions. We recently developed a long-gradient (e.g., 90 min), sub-zero temperature, ultra-high performance liquid chromatography HDX-MS (UPLC-HDX-MS) platform that has significantly increased separation power and limited back-exchange for the analysis of protein samples with high complexity. In this study, we demonstrated the utility of this platform for mapping antibody–antigen epitopes by examining four fully human monoclonal antibodies to anthrax PA. Antibody p1C03, with limited neutralizing activity in vivo, bound to a region on domain 1A of PA. p6C04 and p1A06, with no neutralizing activities, bound to the same helix on domain 3 to prevent oligomerization of PA. We found p6C01 strongly bound to domain 3 on a different helix region. We also identified a secondary epitope for p6C01, which likely leads to the blocking of furin cleavage of PA after p6C01 binding. This novel binding of p6C01 results in highly neutralizing activity. This is the first report of this distinct binding mechanism for a highly neutralizing fully human antibody to anthrax protective antigen. Studying such epitopes can facilitate the development of novel therapeutics against anthrax.
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9
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Sheff JG, Kelly JF, Robotham A, Sulea T, Malenfant F, L'Abbé D, Duchesne M, Pelletier A, Lefebvre J, Acel A, Parat M, Gosselin M, Wu C, Fortin Y, Baardsnes J, Van Faassen H, Awrey S, Chafe SC, McDonald PC, Dedhar S, Lenferink AEG. Hydrogen-deuterium exchange mass spectrometry reveals three unique binding responses of mAbs directed to the catalytic domain of hCAIX. MAbs 2021; 13:1997072. [PMID: 34812124 PMCID: PMC8632303 DOI: 10.1080/19420862.2021.1997072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human carbonic anhydrase (hCAIX), an extracellular enzyme that catalyzes the reversible hydration of CO2, is often overexpressed in solid tumors. This enzyme is instrumental in maintaining the survival of cancer cells in a hypoxic and acidic tumor microenvironment. Absent in most normal tissues, hCAIX is a promising therapeutic target for detection and treatment of solid tumors. Screening of a library of anti-hCAIX monoclonal antibodies (mAbs) previously identified three therapeutic candidates (mAb c2C7, m4A2 and m9B6) with distinct biophysical and functional characteristics. Selective binding to the catalytic domain was confirmed by yeast surface display and isothermal calorimetry, and deeper insight into the dynamic binding profiles of these mAbs upon binding were highlighted by bottom-up hydrogen-deuterium exchange mass spectrometry (HDX-MS). Here, a conformational and allosterically silent epitope was identified for the antibody-drug conjugate candidate c2C7. Unique binding profiles are described for both inhibitory antibodies, m4A2 and m9B6. M4A2 reduces the ability of the enzyme to hydrate CO2 by steric gating at the entrance of the catalytic cavity. Conversely, m9B6 disrupts the secondary structure that is necessary for substrate binding and hydration. The synergy of these two inhibitory mechanisms is demonstrated in in vitro activity assays and HDX-MS. Finally, the ability of m4A2 to modulate extracellular pH and intracellular metabolism is reported. By highlighting three unique modes by which hCAIX can be targeted, this study demonstrates both the utility of HDX-MS as an important tool in the characterization of anti-cancer biotherapeutics, and the underlying value of CAIX as a therapeutic target.
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Affiliation(s)
- Joey G Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - John F Kelly
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anna Robotham
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Félix Malenfant
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Denis L'Abbé
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mélanie Duchesne
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Alex Pelletier
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jean Lefebvre
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Andrea Acel
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Marie Parat
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mylene Gosselin
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Cunle Wu
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yves Fortin
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Henk Van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Shannon Awrey
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada
| | - Shawn C Chafe
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada
| | - Paul C McDonald
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada
| | - Shoukat Dedhar
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Anne E G Lenferink
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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10
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Zhu S, Liuni P, Chen T, Houy C, Wilson DJ, James DA. Epitope screening using Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS): An accelerated workflow for evaluation of lead monoclonal antibodies. Biotechnol J 2021; 17:e2100358. [PMID: 34747565 DOI: 10.1002/biot.202100358] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND Epitope mapping is an increasingly important aspect of biotherapeutic and vaccine development. Recent advances in therapeutic antibody design and production have enabled candidate mAbs to be identified at a rapidly increasing rate, resulting in a significant bottleneck in the characterization of "structural" epitopes, that are challenging to determine using existing high throughput epitope mapping tools. Here, a Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) epitope screening workflow was introduced that is well suited for accelerated characterization of epitopes with a common antigen. MAIN METHODS AND MAJOR RESULTS The method is demonstrated on set of six candidate mAbs targeting Pertactin (PRN). Using this approach, five of the six epitopes were unambiguously determined using two HDX mixing timepoints in 24 h total run time, which is equivalent to the instrument time required to map a single epitope using the conventional workflow. CONCLUSION An accelerated HDX-MS epitope screening workflow was developed. The "screening" workflow successfully characterized five (out of six attempted) novel epitopes on the PRN antigen; information that can be used to support vaccine antigenicity assays.
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Affiliation(s)
- Shaolong Zhu
- Analytical Sciences, Sanofi Pasteur Ltd, Toronto, Ontario, Canada
| | - Peter Liuni
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, Ontario, Canada
| | - Tricia Chen
- Analytical Sciences, Sanofi Pasteur Ltd, Toronto, Ontario, Canada
| | - Camille Houy
- Analytical Sciences, Sanofi Pasteur Ltd, Toronto, Ontario, Canada
| | - Derek J Wilson
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, Ontario, Canada
| | - D Andrew James
- Analytical Sciences, Sanofi Pasteur Ltd, Toronto, Ontario, Canada
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, Ontario, Canada
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11
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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12
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Huang RYC, Wang Y, Jhatakia AD, Deng AX, Bee C, Deshpande S, Rangan VS, Bezman N, Gudmundsson O, Chen G. Higher-Order Structure Characterization of NKG2A/CD94 Protein Complex and Anti-NKG2A Antibody Binding Epitopes by Mass Spectrometry-Based Protein Footprinting Strategies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1567-1574. [PMID: 33415981 DOI: 10.1021/jasms.0c00399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
NK group 2 member A (NKG2A), an immune checkpoint inhibitor, is an emerging therapeutic target in immuno-oncology. NKG2A forms a heterodimer with CD94 on the cell surface of NK and a subset of T cells and recognizes the nonclassical human leukocyte antigen (HLA-E) in humans. Therapeutic blocking antibodies that block the ligation between HLA-E and NKG2A/CD94 have been shown to enhance antitumor immunity in mice and humans. In this study, we illustrate the practical utilities of mass spectrometry (MS)-based protein footprinting in areas from reagent characterization to antibody epitope mapping. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) in the higher-order structure characterization of NKG2A in complex with CD94 provides novel insights into the conformational dynamics of NKG2A/CD94 heterodimer. To fully understand antibody/target interactions, we employed complementary protein footprinting methods, including HDX-MS and fast photochemical oxidation of proteins (FPOP)-MS, to determine the binding epitopes of therapeutic monoclonal antibodies targeting NKG2A. Such a combination approach provides molecular insights into the binding mechanisms of antibodies to NKG2A with high specificity, demonstrating the blockade of NKG2A/HLA-E interaction.
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Affiliation(s)
- Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey United States
| | - Yun Wang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey United States
| | - Amy D Jhatakia
- Discovery Biology, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Andy X Deng
- Discovery Biotherapeutics, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Christine Bee
- Discovery Biotherapeutics, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Shrikant Deshpande
- Discovery Biotherapeutics, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Vangipuram S Rangan
- Discovery Biotherapeutics, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Natalie Bezman
- Discovery Biology, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Olafur Gudmundsson
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey United States
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13
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De-Simone SG, Gomes LR, Napoleão-Pêgo P, Lechuga GC, de Pina JS, da Silva FR. Epitope Mapping of the Diphtheria Toxin and Development of an ELISA-Specific Diagnostic Assay. Vaccines (Basel) 2021; 9:313. [PMID: 33810325 PMCID: PMC8066203 DOI: 10.3390/vaccines9040313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 01/06/2023] Open
Abstract
Background: The diphtheria toxoid antigen is a major component in pediatric and booster combination vaccines and is known to raise a protective humoral immune response upon vaccination. Although antibodies are considered critical for diphtheria protection, little is known about the antigenic determinants that maintain humoral immunity. Methods: One-hundred and twelve 15 mer peptides covering the entire sequence of diphtheria toxin (DTx) protein were prepared by SPOT synthesis. The immunoreactivity of membrane-bound peptides with sera from mice immunized with a triple DTP vaccine allowed mapping of continuous B-cell epitopes, topological studies, multiantigen peptide (MAP) synthesis, and Enzyme-Linked Immunosorbent Assay (ELISA) development. Results: Twenty epitopes were identified, with two being in the signal peptide, five in the catalytic domain (CD), seven in the HBFT domain, and five in the receptor-binding domain (RBD). Two 17 mer (CB/Tx-2/12 and CB/DTx-4-13) derived biepitope peptides linked by a Gly-Gly spacer were chemically synthesized. The peptides were used as antigens to coat ELISA plates and assayed with human (huVS) and mice vaccinated sera (miVS) for in vitro diagnosis of diphtheria. The assay proved to be highly sensitive (99.96%) and specific (100%) for huVS and miVS and, when compared with a commercial ELISA test, demonstrated a high performance. Conclusions: Our work displayed the complete picture of the linear B cell IgG response epitope of the DTx responsible for the protective effect and demonstrated sufficient specificity and eligibility for phase IIB studies of some epitopes to develop new and fast diagnostic assays.
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Affiliation(s)
- Salvatore Giovanni De-Simone
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDNP), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (P.N.-P.); (G.C.L.); (J.S.d.P.); (F.R.d.S.)
- Molecular and Cellular Biology Department, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil
| | - Larissa Rodrigues Gomes
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDNP), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (P.N.-P.); (G.C.L.); (J.S.d.P.); (F.R.d.S.)
| | - Paloma Napoleão-Pêgo
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDNP), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (P.N.-P.); (G.C.L.); (J.S.d.P.); (F.R.d.S.)
| | - Guilherme Curty Lechuga
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDNP), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (P.N.-P.); (G.C.L.); (J.S.d.P.); (F.R.d.S.)
| | - Jorge Soares de Pina
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDNP), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (P.N.-P.); (G.C.L.); (J.S.d.P.); (F.R.d.S.)
| | - Flavio Rocha da Silva
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDNP), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (P.N.-P.); (G.C.L.); (J.S.d.P.); (F.R.d.S.)
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14
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Sheff J, Wang P, Xu P, Arbour M, Masson L, van Faassen H, Hussack G, Kemmerich K, Brunette E, Stanimirovic D, Hill JJ, Kelly J, Ni F. Defining the epitope of a blood-brain barrier crossing single domain antibody specific for the type 1 insulin-like growth factor receptor. Sci Rep 2021; 11:4284. [PMID: 33608571 PMCID: PMC7896052 DOI: 10.1038/s41598-021-83198-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
Ligand-activated signaling through the type 1 insulin-like growth factor receptor (IGF1R) is implicated in many physiological processes ranging from normal human growth to cancer proliferation and metastasis. IGF1R has also emerged as a target for receptor-mediated transcytosis, a transport phenomenon that can be exploited to shuttle biotherapeutics across the blood–brain barrier (BBB). We employed differential hydrogen–deuterium exchange mass spectrometry (HDX-MS) and nuclear magnetic resonance (NMR) to characterize the interactions of the IGF1R ectodomain with a recently discovered BBB-crossing single-domain antibody (sdAb), VHH-IR5, in comparison with IGF-1 binding. HDX-MS confirmed that IGF-1 induced global conformational shifts in the L1/FnIII-1/-2 domains and α-CT helix of IGF1R. In contrast, the VHH-IR5 sdAb-mediated changes in conformational dynamics were limited to the α-CT helix and its immediate vicinity (L1 domain). High-resolution NMR spectroscopy titration data and linear peptide scanning demonstrated that VHH-IR5 has high-affinity binding interactions with a peptide sequence around the C-terminal region of the α-CT helix. Taken together, these results define a core linear epitope for VHH-IR5 within the α-CT helix, overlapping the IGF-1 binding site, and suggest a potential role for the α-CT helix in sdAb-mediated transcytosis.
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Affiliation(s)
- Joey Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Ping Wang
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Ping Xu
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Melanie Arbour
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Luke Masson
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Kristin Kemmerich
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Eric Brunette
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Danica Stanimirovic
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Jennifer J Hill
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - John Kelly
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Feng Ni
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada.
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15
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HDXmodeller: an online webserver for high-resolution HDX-MS with auto-validation. Commun Biol 2021; 4:199. [PMID: 33589746 PMCID: PMC7884430 DOI: 10.1038/s42003-021-01709-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022] Open
Abstract
The extent to which proteins are protected from hydrogen deuterium exchange (HDX) provides valuable insight into their folding, dynamics and interactions. Characterised by mass spectrometry (MS), HDX benefits from negligible mass restrictions and exceptional throughput and sensitivity but at the expense of resolution. Exchange mechanisms which naturally transpire for individual residues cannot be accurately located or understood because amino acids are characterised in differently sized groups depending on the extent of proteolytic digestion. Here we report HDXmodeller, the world's first online webserver for high-resolution HDX-MS. HDXmodeller accepts low-resolution HDX-MS input data and returns high-resolution exchange rates quantified for each residue. Crucially, HDXmodeller also returns a set of unique statistics that can correctly validate exchange rate models to an accuracy of 99%. Remarkably, these statistics are derived without any prior knowledge of the individual exchange rates and facilitate unparallel user confidence and the capacity to evaluate different data optimisation strategies.
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16
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Sun H, Ma L, Wang L, Xiao P, Li H, Zhou M, Song D. Research advances in hydrogen-deuterium exchange mass spectrometry for protein epitope mapping. Anal Bioanal Chem 2021; 413:2345-2359. [PMID: 33404742 DOI: 10.1007/s00216-020-03091-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/01/2022]
Abstract
With the development of biomedical technology, epitope mapping of proteins has become critical for developing and evaluating new protein drugs. The application of hydrogen-deuterium exchange for protein epitope mapping holds great potential. Although several reviews addressed the hydrogen-deuterium exchange, to date, only a few systematic reviews have focused on epitope mapping using this technology. Here, we introduce the basic principles, development history, and review research progress in hydrogen-deuterium exchange epitope mapping technology and discuss its advantages. We summarize the main hurdles in applying hydrogen-deuterium exchange epitope mapping technology, combined with relevant examples to provide specific solutions. We describe the epitope mapping of virus assemblies, disease-associated proteins, and polyclonal antibodies as examples of pattern introduction. Finally, we discuss the outlook of hydrogen-deuterium exchange epitope mapping technology. This review will help researchers studying protein epitopes to gain a more comprehensive understanding of this technology.
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Affiliation(s)
- Haofeng Sun
- National Institute of Metrology, Beijing, 100029, China
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lingyun Ma
- National Institute of Metrology, Beijing, 100029, China
| | - Leyu Wang
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Peng Xiao
- National Institute of Metrology, Beijing, 100029, China
| | - Hongmei Li
- National Institute of Metrology, Beijing, 100029, China
| | - Min Zhou
- School of Chemical and Engineering, Nanjing University of Science and Technology, Jiangsu, 210094, China.
| | - Dewei Song
- National Institute of Metrology, Beijing, 100029, China.
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17
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Mehaffey MR, Lee J, Jung J, Lanzillotti MB, Escobar EE, Morgenstern KR, Georgiou G, Brodbelt JS. Mapping a Conformational Epitope of Hemagglutinin A Using Native Mass Spectrometry and Ultraviolet Photodissociation. Anal Chem 2020; 92:11869-11878. [PMID: 32867493 PMCID: PMC7808878 DOI: 10.1021/acs.analchem.0c02237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As the importance of effective vaccines and the role of protein therapeutics in the drug industry continue to expand, alternative strategies to characterize protein complexes are needed. Mass spectrometry (MS) in conjunction with enzymatic digestion or chemical probes has been widely used for mapping binding epitopes at the molecular level. However, advances in instrumentation and application of activation methods capable of accessing higher energy dissociation pathways have recently allowed direct analysis of protein complexes. Here we demonstrate a workflow utilizing native MS and ultraviolet photodissociation (UVPD) to map the antigenic determinants of a model antibody-antigen complex involving hemagglutinin (HA), the primary immunogenic antigen of the influenza virus, and the D1 H1-17/H3-14 antibody which has been shown to confer potent protection to lethal infection in mice despite lacking neutralization activity. Comparison of sequence coverages upon UV photoactivation of HA and of the HA·antibody complex indicates the elimination of some sequence ions that originate from backbone cleavages exclusively along the putative epitope regions of HA in the presence of the antibody. Mapping the number of sequence ions covering the HA antigen versus the HA·antibody complex highlights regions with suppressed backbone cleavage and allows elucidation of unknown epitopes. Moreover, examining the observed fragment ion types generated by UVPD demonstrates a loss in diversity exclusively along the antigenic determinants upon MS/MS of the antibody-antigen complex. UVPD-MS shows promise as a method to rapidly map epitope regions along antibody-antigen complexes as novel antibodies are discovered or developed.
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Affiliation(s)
| | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
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18
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Ausar SF, Zhu S, Duprez J, Cohen M, Bertrand T, Steier V, Wilson DJ, Li S, Sheung A, Brookes RH, Pedyczak A, Rak A, Andrew James D. Genetically detoxified pertussis toxin displays near identical structure to its wild-type and exhibits robust immunogenicity. Commun Biol 2020; 3:427. [PMID: 32759959 PMCID: PMC7406505 DOI: 10.1038/s42003-020-01153-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
The mutant gdPT R9K/E129G is a genetically detoxified variant of the pertussis toxin (PTx) and represents an attractive candidate for the development of improved pertussis vaccines. The impact of the mutations on the overall protein structure and its immunogenicity has remained elusive. Here we present the crystal structure of gdPT and show that it is nearly identical to that of PTx. Hydrogen-deuterium exchange mass spectrometry revealed dynamic changes in the catalytic domain that directly impacted NAD+ binding which was confirmed by biolayer interferometry. Distal changes in dynamics were also detected in S2-S5 subunit interactions resulting in tighter packing of B-oligomer corresponding to increased thermal stability. Finally, antigen stimulation of human whole blood, analyzed by a previously unreported mass cytometry assay, indicated broader immunogenicity of gdPT compared to pertussis toxoid. These findings establish a direct link between the conserved structure of gdPT and its ability to generate a robust immune response.
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Affiliation(s)
- Salvador F Ausar
- Bioprocess Research and Development, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada
| | - Shaolong Zhu
- Analytical Sciences, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada.,Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada
| | - Jessica Duprez
- Analytical Sciences, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada
| | - Michael Cohen
- Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada.,Fluidigm Corporation, Markham, ON, L3R 4G5, Canada
| | - Thomas Bertrand
- Research Platform, Sanofi R&D, Vitry-sur-Seine, 94400, Paris, France
| | - Valérie Steier
- Research Platform, Sanofi R&D, Vitry-sur-Seine, 94400, Paris, France
| | - Derek J Wilson
- Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada
| | - Stephen Li
- Fluidigm Corporation, Markham, ON, L3R 4G5, Canada
| | - Anthony Sheung
- Bioprocess Research and Development, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada
| | - Roger H Brookes
- Bioprocess Research and Development, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada
| | - Artur Pedyczak
- Analytical Sciences, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada
| | - Alexey Rak
- Research Platform, Sanofi R&D, Vitry-sur-Seine, 94400, Paris, France
| | - D Andrew James
- Analytical Sciences, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada. .,Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada.
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19
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Huang RYC, Wang F, Wheeler M, Wang Y, Langish R, Chau B, Dong J, Morishige W, Bezman N, Strop P, Rajpal A, Gudmundsson O, Chen G. Integrated Approach for Characterizing Bispecific Antibody/Antigens Complexes and Mapping Binding Epitopes with SEC/MALS, Native Mass Spectrometry, and Protein Footprinting. Anal Chem 2020; 92:10709-10716. [PMID: 32639723 DOI: 10.1021/acs.analchem.0c01876] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Bispecific antibodies (BsAbs), with a unique mechanism of recognizing two different epitopes or antigens, have shown potential in various therapeutic areas. Molecular characterization of BsAbs' epitopes not only allows for detailed understanding of their mechanism of actions but also guides the design and selection of drug candidate molecules. In this study, we illustrate the practical utility of an integrated approach, including size exclusion chromatography with multiangle light scattering and native mass spectrometry (MS) for the biophysical characterization of complex formation of a BsAb with two target antigens, cluster of differentiation 3 (CD3) and B-cell maturation antigen (BCMA). MS-based protein footprinting strategies, including hydrogen/deuterium exchange MS, fast photochemical oxidation of proteins, and carboxyl group footprinting with glycine ethyl ester, were further applied to determine BsAb's binding epitopes. This combination approach provides molecular details on the binding mechanisms of BsAb to the two distinct antigens with rapid output and high resolution.
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Affiliation(s)
- Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Feng Wang
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Matthew Wheeler
- Discovery Biology, Research and Early Development, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Yun Wang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Robert Langish
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Bryant Chau
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Jia Dong
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Winse Morishige
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Natalie Bezman
- Discovery Biology, Research and Early Development, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Pavel Strop
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Arvind Rajpal
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Olafur Gudmundsson
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
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20
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Narang D, Lento C, J. Wilson D. HDX-MS: An Analytical Tool to Capture Protein Motion in Action. Biomedicines 2020; 8:biomedicines8070224. [PMID: 32709043 PMCID: PMC7399943 DOI: 10.3390/biomedicines8070224] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/07/2023] Open
Abstract
Virtually all protein functions in the cell, including pathogenic processes, require coordinated motion of atoms or domains, i.e., conformational dynamics. Understanding protein dynamics is therefore critical both for drug development and to learn about the underlying molecular causes of many diseases. Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) provides valuable information about protein dynamics, which is highly complementary to the static picture provided by conventional high-resolution structural tools (i.e., X-ray crystallography and structural NMR). The amount of protein required to carry out HDX-MS experiments is a fraction of the amount required by alternative biophysical techniques, which are also usually lower resolution. Use of HDX-MS is growing quickly both in industry and academia, and it has been successfully used in numerous drug and vaccine development efforts, with important roles in understanding allosteric effects and mapping binding sites.
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Affiliation(s)
- Dominic Narang
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
| | - Derek J. Wilson
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
- Centre for Research of Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University, Toronto, ON M3J 1P3, Canada
- Correspondence:
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21
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Zhang MM, Huang RYC, Beno BR, Deyanova EG, Li J, Chen G, Gross ML. Epitope and Paratope Mapping of PD-1/Nivolumab by Mass Spectrometry-Based Hydrogen-Deuterium Exchange, Cross-linking, and Molecular Docking. Anal Chem 2020; 92:9086-9094. [PMID: 32441507 DOI: 10.1021/acs.analchem.0c01291] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Programmed cell death-1 (PD-1), an antigen co-receptor on cell surfaces, is one of the conspicuous immune checkpoints. Nivolumab, a monoclonal antibody therapeutic approved by the FDA, binds to PD-1 and efficiently blocks its pathways. In this study, an integrated approach was developed to map the epitope/paratope of PD-1/nivolumab. The approach includes hydrogen-deuterium exchange mass spectrometry (HDX-MS) followed by electron-transfer dissociation (ETD), chemical cross-linking, and molecular docking. HDX-ETD offers some binding-site characterization with amino acid resolution. Chemical cross-linking provides complementary information on one additional epitope (i.e., the BC-loop) and a potential paratope at the N-terminus of the heavy chain. Furthermore, cross-linking identifies another loop region (i.e., the C'D-loop) that undergoes a remote conformational change. The distance restraints derived from the cross-links enable building high-confidence models of PD-1/nivolumab, evaluated with respect to a resolved crystal structure. This integrated strategy is an opportunity to characterize comprehensively other antigen-antibody interactions, to enable the understanding of binding mechanisms, and to design future antibody therapeutics.
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Affiliation(s)
- Mengru Mira Zhang
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Brett R Beno
- Molecular Structure & Design, Small Molecule Drug Discovery, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Ekaterina G Deyanova
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Jing Li
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
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22
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Huang RYC, Kuhne M, Deshpande S, Rangan V, Srinivasan M, Wang Y, Chen G. Mapping binding epitopes of monoclonal antibodies targeting major histocompatibility complex class I chain-related A (MICA) with hydrogen/deuterium exchange and electron-transfer dissociation mass spectrometry. Anal Bioanal Chem 2020; 412:1693-1700. [PMID: 31993727 DOI: 10.1007/s00216-020-02409-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/13/2019] [Accepted: 01/10/2020] [Indexed: 12/14/2022]
Abstract
Major histocompatibility complex class I chain-related A and B (MICA/B) are cell-surface proteins that act as ligands to natural killer cell receptors, NKG2D, expressed on immune cells. Prevention of proteolytic shedding of MICA/B to retain their integrity on the cell surface has become a therapeutic strategy in immuno-oncology. Given the unique mechanism of MICA/B shedding, structural characterization of MICA/B and therapeutic agent interaction is important in the drug discovery process. In this study, we describe the practical utility of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in epitope mapping studies of a cohort of four monoclonal antibodies targeting MICA in a rapid manner. HDX-MS followed by electron-transfer dissociation allows high-resolution refinement of binding epitopes. This integrated strategy offers, for the first time, molecular-level understanding of MICA's conformational dynamics in solution as well as the unique mechanism of actions of these antibodies in targeting MICA. Graphical abstract.
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Affiliation(s)
- Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, 08543, USA.
| | - Michelle Kuhne
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Redwood City, CA, 94063, USA
| | - Shrikant Deshpande
- Protein Engineering, Research and Development, Bristol-Myers Squibb Company, Redwood City, CA, 94063, USA
| | - Vangipuram Rangan
- Protein Engineering, Research and Development, Bristol-Myers Squibb Company, Redwood City, CA, 94063, USA
| | - Mohan Srinivasan
- Protein Engineering, Research and Development, Bristol-Myers Squibb Company, Redwood City, CA, 94063, USA
| | - Yun Wang
- Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, 08543, USA
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, 08543, USA.
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