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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: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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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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2
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Suzuki T, Hashii N, Tada M, Ishii-Watabe A. The influence of antibody engineering on Fc conformation and Fc receptor binding properties: Analysis of FcRn-binding engineered antibodies and an Fc fusion protein. MAbs 2021; 13:1923366. [PMID: 34030575 PMCID: PMC8158039 DOI: 10.1080/19420862.2021.1923366] [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: 11/29/2022] Open
Abstract
Therapeutic immunoglobulin G (IgG) antibodies have comparatively long half-lives because the neonatal Fc receptor (FcRn) binds to the IgG Fc at acidic pH in the endosome and protects IgG from degradation. To further prolong the half-lives, amino acid-substituted antibodies having high affinity to FcRn are being developed, and one such therapeutic antibody (ravulizumab) has been approved. In this study, we investigated the binding property to FcγR and the conformation of seven FcRn affinity-modulated adalimumab variants to clarify the impact of the amino acid substitutions on the function and conformation of IgG Fc. The amino acid substitutions in T254-P261 caused a change in deuterium uptake into some regions of Fc in HDX-MS analysis, but those at T311, M432 and N438 did not cause such a change. The conformations around F245-L255 (FLFPPKPKDTL) were particularly influenced by the amino acid substitution in M256-P261, and the conformational changes of this region were correlated with the decrease of the affinity to FcγRIIIa. Additionally, we investigated the conformational difference of Fc between a Fc fusion protein (etanercept) and a native IgG (adalimumab). Although the Fc fusion proteins were expected to have similar FcRn affinity to IgGs, the affinity of etanercept to FcRn was lower than that of adalimumab, and its half-life was shorter than those of the IgG antibodies. Differences in deuterium uptakes were observed in the two regions where they were also detected in the adalimumab variants, and the conformational differences appeared to be an important factor for the low FcRn affinity of etanercept.
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Affiliation(s)
- Takuo Suzuki
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kanagawa, Japan
| | - Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kanagawa, Japan
| | - Minoru Tada
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kanagawa, Japan
| | - Akiko Ishii-Watabe
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kanagawa, Japan
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3
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Hageman TS, Wrigley MS, Weis DD. Statistical Equivalence Testing of Higher-Order Protein Structures with Differential Hydrogen Exchange-Mass Spectrometry (HX-MS). Anal Chem 2021; 93:6980-6988. [PMID: 33913686 DOI: 10.1021/acs.analchem.0c05279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen exchange-mass spectrometry (HX-MS) is widely recognized for its potential utility for establishing the equivalence of the higher-order structures of proteins, particularly in comparability and similarity contexts. However, recent progress in the statistical analysis of HX-MS data has instead placed an emphasis on significance testing to identify regions of proteins where there are significant differences in HX between two or more protein states. In the cases involving assessment of similarity or equivalence of the higher-order structure of different protein samples (e.g., biosimilars), significance testing of HX-MS data is unsuitable. To meet this need, we have adapted the univariate two one-sided test (TOST) equivalence testing method for HX-MS data. Equivalence acceptance criteria were determined using maximum deviations from randomized resampling of truly equivalent samples to define hybrid equivalence criteria (maximum deviation of true equivalents, MDTE). Application of the TOST-MDTE test on differential HX-MS measurements of wild-type and mutated maltose-binding proteins demonstrates that the equivalence testing method was fit-for-purpose. Three infliximab biosimilars (Remsima, Renflexis, and Inflectra) were found to be equivalent to their Remicade reference product based on differential HX-MS measurements, while 5% deglycosylated NIST mAb was not statistically equivalent to the unmodified NIST mAb reference.
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Affiliation(s)
- Tyler S Hageman
- Department of Chemistry, The University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Michael S Wrigley
- Department of Chemistry, The University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - David D Weis
- Department of Chemistry, The University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
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4
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Wang W, Ohtake S. Science and art of protein formulation development. Int J Pharm 2019; 568:118505. [PMID: 31306712 DOI: 10.1016/j.ijpharm.2019.118505] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 02/07/2023]
Abstract
Protein pharmaceuticals have become a significant class of marketed drug products and are expected to grow steadily over the next decade. Development of a commercial protein product is, however, a rather complex process. A critical step in this process is formulation development, enabling the final product configuration. A number of challenges still exist in the formulation development process. This review is intended to discuss these challenges, to illustrate the basic formulation development processes, and to compare the options and strategies in practical formulation development.
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Affiliation(s)
- Wei Wang
- Biological Development, Bayer USA, LLC, 800 Dwight Way, Berkeley, CA 94710, United States.
| | - Satoshi Ohtake
- Pharmaceutical Research and Development, Pfizer Biotherapeutics Pharmaceutical Sciences, Chesterfield, MO 63017, United States
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5
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Hageman TS, Weis DD. Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach. Anal Chem 2019; 91:8008-8016. [DOI: 10.1021/acs.analchem.9b01325] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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6
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Hageman TS, Weis DD. A Structural Variant Approach for Establishing a Detection Limit in Differential Hydrogen Exchange-Mass Spectrometry Measurements. Anal Chem 2019; 91:8017-8024. [DOI: 10.1021/acs.analchem.9b01326] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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7
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Le Quellec S, Dane A, Enjolras N, McIntosh J, Rosales C, Negrier C, Nathwani A. Potential limits of AAV-based gene therapy with the use of new transgenes expressing factor IX fusion proteins. Haemophilia 2018; 25:e11-e18. [PMID: 30520547 DOI: 10.1111/hae.13651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 11/28/2022]
Abstract
INTRODUCTION The variety of treatment for haemophilia B (HB) has recently improved with the emergence of both AAV-based gene therapy and bioengineered human factor IX (hFIX) molecules with prolonged half-life due to fusion to either albumin (Alb) or immunoglobulin Fc fragment (Fc). AIM Adeno-associated viral vectors (AAV) mediating expression of hFIX-Alb and hFIX-Fc fusion proteins was investigated for gene therapy of HB to explore if their extended half-life translates to higher plasma levels of FIX. METHODS Single-stranded cross-packaged AAV2/8 vectors expressing hFIX-Alb, hFIX-Fc and hFIX were evaluated in vitro, and in mice. RESULTS Both hFIX-Alb and hFIX-Fc fusion proteins were synthesized and expressed as single chains of expected size following AAV-mediated gene transfer in vitro and in vivo. The procoagulant properties of these hFIX-fusion proteins were comparable to wild-type hFIX. However, their expression levels were threefold lower than wild-type hFIX in vivo most likely due to inefficient secretion. CONCLUSION This, the first, evaluation of hFIX-fusion proteins in the context of AAV gene transfer suggests that the hFIX-fusion proteins are secreted inefficiently from the liver, thus preventing their optimal use in gene therapy approaches.
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Affiliation(s)
- Sandra Le Quellec
- EA 4609-Hémostase et Cancer, Université Claude Bernard Lyon I, Lyon, France.,Laboratoire D'hématologie, Hospices Civils de Lyon, Lyon, France
| | - Allison Dane
- Research Department of Haematology, University of London Cancer Institute, London, UK
| | - Nathalie Enjolras
- EA 4609-Hémostase et Cancer, Université Claude Bernard Lyon I, Lyon, France.,Laboratoire D'hématologie, Hospices Civils de Lyon, Lyon, France
| | - Jenny McIntosh
- Research Department of Haematology, University of London Cancer Institute, London, UK
| | - Cecilia Rosales
- Research Department of Haematology, University of London Cancer Institute, London, UK
| | - Claude Negrier
- EA 4609-Hémostase et Cancer, Université Claude Bernard Lyon I, Lyon, France.,Laboratoire D'hématologie, Hospices Civils de Lyon, Lyon, France
| | - Amit Nathwani
- Research Department of Haematology, University of London Cancer Institute, London, UK
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Trabjerg E, Nazari ZE, Rand KD. Conformational analysis of complex protein states by hydrogen/deuterium exchange mass spectrometry (HDX-MS): Challenges and emerging solutions. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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9
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MS-based conformation analysis of recombinant proteins in design, optimization and development of biopharmaceuticals. Methods 2018; 144:134-151. [PMID: 29678586 DOI: 10.1016/j.ymeth.2018.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/10/2018] [Accepted: 04/12/2018] [Indexed: 01/18/2023] Open
Abstract
Mass spectrometry (MS)-based methods for analyzing protein higher order structures have gained increasing application in the field of biopharmaceutical development. The predominant methods used in this area include native MS, hydrogen deuterium exchange-MS, covalent labeling, cross-linking and limited proteolysis. These MS-based methods will be briefly described in this article, followed by a discussion on how these methods contribute at different stages of discovery and development of protein therapeutics.
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Karageorgos I, Gallagher ES, Galvin C, Gallagher DT, Hudgens JW. Biophysical characterization and structure of the Fab fragment from the NIST reference antibody, RM 8671. Biologicals 2017; 50:27-34. [PMID: 28965821 DOI: 10.1016/j.biologicals.2017.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022] Open
Abstract
Monoclonal antibody pharmaceuticals are the fastest-growing class of therapeutics, with a wide range of clinical applications. To assure their safety, these protein drugs must demonstrate highly consistent purity and stability. Key to these objectives is higher order structure measurements validated by calibration to reference materials. We describe preparation, characterization, and crystal structure of the Fab fragment prepared from the NIST Reference Antibody RM 8671 (NISTmAb). NISTmAb is a humanized IgG1κ antibody, produced in murine cell culture and purified by standard biopharmaceutical production methods, developed at the National Institute of Standards and Technology (NIST) to serve as a reference material. The Fab fragment was derived from NISTmAb through papain cleavage followed by protein A based purification. The purified Fab fragment was characterized by SDS-PAGE, capillary gel electrophoresis, multi-angle light scattering, size exclusion chromatography, mass spectrometry, and x-ray crystallography. The crystal structure at 0.2 nm resolution includes four independent Fab molecules with complete light chains and heavy chains through Cys 223, enabling assessment of conformational variability and providing a well-characterized reference structure for research and engineering applications. This nonproprietary, publically available reference material of known higher-order structure can support metrology in biopharmaceutical applications, and it is a suitable platform for validation of molecular modeling studies.
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Affiliation(s)
- Ioannis Karageorgos
- Biomolecular Measurement Division, National Institute of Standards & Technology, Rockville, MD 20850, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
| | - Elyssia S Gallagher
- Biomolecular Measurement Division, National Institute of Standards & Technology, Rockville, MD 20850, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
| | - Connor Galvin
- Biomolecular Measurement Division, National Institute of Standards & Technology, Rockville, MD 20850, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - D Travis Gallagher
- Biomolecular Measurement Division, National Institute of Standards & Technology, Rockville, MD 20850, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
| | - Jeffrey W Hudgens
- Biomolecular Measurement Division, National Institute of Standards & Technology, Rockville, MD 20850, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
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11
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Hydrogen deuterium exchange mass spectrometry in biopharmaceutical discovery and development – A review. Anal Chim Acta 2016; 940:8-20. [DOI: 10.1016/j.aca.2016.08.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/25/2016] [Accepted: 08/07/2016] [Indexed: 01/14/2023]
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12
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Affiliation(s)
- Gregory
F. Pirrone
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - Roxana E. Iacob
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - John R. Engen
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
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13
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Phillips AS, Gomes AF, Kalapothakis JMD, Gillam JE, Gasparavicius J, Gozzo FC, Kunath T, MacPhee C, Barran PE. Conformational dynamics of α-synuclein: insights from mass spectrometry. Analyst 2015; 140:3070-81. [DOI: 10.1039/c4an02306d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Different mass spectrometry approaches are combined to investigate the conformational flexibility of α-synuclein.
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Affiliation(s)
- Ashley S. Phillips
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Alexandre F. Gomes
- Dalton Mass Spectrometry Laboratory
- University of Campinas – UNICAMP
- Brazil
| | | | - Jay E. Gillam
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh
- UK
| | | | - Fabio C. Gozzo
- Dalton Mass Spectrometry Laboratory
- University of Campinas – UNICAMP
- Brazil
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine
- University of Edinburgh
- Edinburgh
- UK
| | - Cait MacPhee
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh
- UK
| | - Perdita E. Barran
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
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14
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Mannucci PM. Half-life extension technologies for haemostatic agents. Thromb Haemost 2014; 113:165-76. [PMID: 25274414 DOI: 10.1160/th14-04-0332] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 08/27/2014] [Indexed: 12/18/2022]
Abstract
The use of plasma-derived and recombinant coagulation factors for the treatment of haemophilia A and B is well established and permits patients to live a relatively normal life. In order to improve treatment options, several products are in development, which have a prolonged duration of action, thus enabling less frequent prophylactic dosing and aiming to reduce the burden of treatment. Several innovative approaches are being pursued to extend the half-life of factor VIIa, factor VIII and factor IX, utilising technologies such as Fc fusion, recombinant albumin fusion and addition of polyethyleneglycol (PEG) (PEGylation). These methods prolong the time in the circulation by reducing degradation and elimination. This review summarises the technologies and products in development and their stages of development, and also discusses their pros and cons.
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Affiliation(s)
- Pier Mannuccio Mannucci
- Pier Mannuccio Mannucci, Scientific Director, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, IRCCS Cà Grande Maggiore Policlinico Hospital Foundation, Milan, Italy, Tel.: +39 02 55038377, Fax: +39 02 50320723, E-mail:
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15
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Wei H, Mo J, Tao L, Russell RJ, Tymiak AA, Chen G, Iacob RE, Engen JR. Hydrogen/deuterium exchange mass spectrometry for probing higher order structure of protein therapeutics: methodology and applications. Drug Discov Today 2013; 19:95-102. [PMID: 23928097 DOI: 10.1016/j.drudis.2013.07.019] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 07/19/2013] [Accepted: 07/29/2013] [Indexed: 10/26/2022]
Abstract
The higher order structure of protein therapeutics can be interrogated with hydrogen/deuterium exchange mass spectrometry (HDX-MS). HDX-MS is now a widely used tool in the structural characterization of protein therapeutics. In this review, HDX-MS based workflows designed for protein therapeutic discovery and development processes are presented, focusing on the specific applications of epitope mapping for protein/drug interactions and biopharmaceutical comparability studies. Future trends in the application of HDX-MS in protein therapeutics characterization are also described.
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Affiliation(s)
- Hui Wei
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Jingjie Mo
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Li Tao
- Biologics Manufacturing and Process Development, Global Manufacturing and Supply, Bristol-Myers Squibb, Hopewell, NJ, USA
| | - Reb J Russell
- Biologics Manufacturing and Process Development, Global Manufacturing and Supply, Bristol-Myers Squibb, Bloomsbury, NJ, USA
| | - Adrienne A Tymiak
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Princeton, NJ, USA.
| | - Roxana E Iacob
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, USA
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, USA.
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Hamasaki-Katagiri N, Salari R, Wu A, Qi Y, Schiller T, Filiberto AC, Schisterman EF, Komar AA, Przytycka TM, Kimchi-Sarfaty C. A gene-specific method for predicting hemophilia-causing point mutations. J Mol Biol 2013; 425:4023-33. [PMID: 23920358 DOI: 10.1016/j.jmb.2013.07.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/16/2013] [Accepted: 07/22/2013] [Indexed: 01/21/2023]
Abstract
A fundamental goal of medical genetics is the accurate prediction of genotype-phenotype correlations. As an approach to develop more accurate in silico tools for prediction of disease-causing mutations of structural proteins, we present a gene- and disease-specific prediction tool based on a large systematic analysis of missense mutations from hemophilia A (HA) patients. Our HA-specific prediction tool, HApredictor, showed disease prediction accuracy comparable to other publicly available prediction software. In contrast to those methods, its performance is not limited to non-synonymous mutations. Given the role of synonymous mutations in disease and drug codon optimization, we propose that utilizing a gene- and disease-specific method can be highly useful to make functional predictions possible even for synonymous mutations. Incorporating computational metrics at both nucleotide and amino acid levels along with multiple protein sequence/structure alignment significantly improved the predictive performance of our tool. HApredictor is freely available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/HA_Predict/index.htm.
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Affiliation(s)
- Nobuko Hamasaki-Katagiri
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA
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