1
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Eisinger M, Rahn H, Chen Y, Fernandes M, Lin Z, Hentze N, Tavella D, Moussa EM. Elucidation of the Reversible Self-Association Interface of a Diabody-Interleukin Fusion Protein Using Hydrogen-Exchange Mass Spectrometry and In Silico Modeling. Mol Pharm 2024. [PMID: 38922328 DOI: 10.1021/acs.molpharmaceut.4c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Reversible self-association (RSA) of therapeutic proteins presents major challenges in the development of high-concentration formulations, especially those intended for subcutaneous administration. Understanding self-association mechanisms is therefore critical to the design and selection of candidates with acceptable developability to advance to clinical trials. The combination of experiments and in silico modeling presents a powerful tool to elucidate the interface of self-association. RSA of monoclonal antibodies has been studied extensively under different solution conditions and have been shown to involve interactions for both the antigen-binding fragment and the crystallizable fragment. Novel modalities such as bispecific antibodies, antigen-binding fragments, single-chain-variable fragments, and diabodies constitute a fast-growing class of antibody-based therapeutics that have unique physiochemical properties compared to monoclonal antibodies. In this study, the RSA interface of a diabody-interleukin 22 fusion protein (FP-1) was studied using hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) in combination with in silico modeling. Taken together, the results show that a complex solution behavior underlies the self-association of FP-1 and that the interface thereof can be attributed to a specific segment in the variable light chain of the diabody. These findings also demonstrate that the combination of HDX-MS with in silico modeling is a powerful tool to guide the design and candidate selection of novel biotherapeutic modalities.
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Affiliation(s)
- Martin Eisinger
- Biologics Analytical Research and Development, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen 67061, Germany
| | - Harri Rahn
- Biologics Analytical Research and Development, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen 67061, Germany
| | - Yong Chen
- Biologics Analytical Research and Development, AbbVie Inc., North Chicago, Illinois 60061, United States
| | - Melissa Fernandes
- Biologics Drug Product Development, AbbVie Inc., North Chicago, Illinois 60061, United States
| | - Zhiyi Lin
- Biologics Drug Product Development, AbbVie Inc., North Chicago, Illinois 60061, United States
| | - Nikolai Hentze
- Biologics Analytical Research and Development, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen 67061, Germany
| | - Davide Tavella
- Biotherapeutics and Genetic Medicine, AbbVie Inc., Worcester, Massachusetts 01604, United States
| | - Ehab M Moussa
- Biologics Drug Product Development, AbbVie Inc., North Chicago, Illinois 60061, United States
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2
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Sinha I, Garde S, Cramer SM. Comparative Analysis of Protein Surface Hydrophobicity Maps Determined by Sparse Sampling INDUS and Spatial Aggregation Propensity. J Phys Chem B 2023; 127:10304-10314. [PMID: 37993107 DOI: 10.1021/acs.jpcb.3c04902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Protein surface hydrophobicity plays a central role in various biological processes such as protein folding and aggregation, as well as in the design and manufacturing of biotherapeutics. While the hydrophobicity of protein surface patches has been linked to their constituent residue hydropathies, recent research has shown that protein surface hydrophobicity is more complex and characterized by the response of water to these surfaces. In this work, we employ water density perturbations to map the surface hydrophobicity of a set of model proteins using sparse indirect umbrella sampling simulations (SSI). This technique is used to identify hydrophobic surface patches for the set of model proteins, and the results are compared to those obtained from the widely adopted spatial aggregation propensity (SAP) technique. While SAP-based calculations show agreement with SSI in some cases, there are several examples of disagreement. We identify four general classes of difference in behavior and study factors that contribute to these differences. We find that the SAP method can sometimes mask the effect of weakly nonpolar or isolated nonpolar residues that can lead to strong hydrophobic patches on the protein surface. In addition, hydrophobic patches identified by SAP can exhibit shifts in both position and strength on the SSI map. Our results demonstrate that the combination of topography and chemical context controls the hydrophobicity of a given patch above and beyond the intrinsic polarity of the residues present on the patch surface. The availability of more accurate protein hydrophobicity maps in concert with new classes of hydrophobic molecular descriptors may create significant opportunities for in silico prediction of protein behavior for a range of applications, such as protein design, biomanufacturability, and downstream bioprocessing.
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Affiliation(s)
- Imee Sinha
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States of America
| | - Shekhar Garde
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States of America
| | - Steven M Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States of America
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3
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Tao Y, Chen Y, Howard W, Ibrahim M, Patel SM, McMahon WP, Kim YJ, Delmar JA, Davis D. Mechanism of Insoluble Aggregate Formation in a Reconstituted Solution of Spray-Dried Protein Powder. Pharm Res 2023; 40:2355-2370. [PMID: 37131104 PMCID: PMC10661820 DOI: 10.1007/s11095-023-03524-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/13/2023] [Indexed: 05/04/2023]
Abstract
BACKGROUND Spray-drying is considered a promising alternative drying method to lyophilization (freeze-drying) for therapeutic proteins. Particle counts in reconstituted solutions of dried solid dosage forms of biologic drug products are closely monitored to ensure product quality. We found that high levels of particles formed after reconstitution of protein powders that had been spray-dried under suboptimal conditions. METHODS Visible and subvisible particles were evaluated. Soluble proteins in solution before spray-drying and in the reconstituted solution of spray-dried powder were analyzed for their monomer content levels and melting temperatures. Insoluble particles were collected and analyzed by Fourier transform infrared microscopy (FTIR), and further analyzed with hydrogen-deuterium exchange (HDX). RESULTS Particles observed after reconstitution were shown not to be undissolved excipients. FTIR confirmed their identity as proteinaceous in nature. These particles were therefore considered to be insoluble protein aggregates, and HDX was applied to investigate the mechanism underlying aggregate formation. Heavy-chain complementarity-determining region 1 (CDR-1) in the aggregates showed significant protection by HDX, suggesting CDR-1 was critical for aggregate formation. In contrast, various regions became more conformationally dynamic globally, suggesting the aggregates have lost protein structural integrity and partially unfolded after spray-drying. DISCUSSION The spray-drying process could have disrupted the higher-order structure of proteins and exposed the hydrophobic residues in CDR-1 of the heavy chain, contributing to the formation of aggregate through hydrophobic interactions upon reconstitution of spray-dried powder. These results can contribute to efforts to design spray-dry resilient protein constructs and improve the robustness of the spray-drying process.
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Affiliation(s)
- Yeqing Tao
- Process and Analytical Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20787, USA.
| | - Yuan Chen
- Dosage Form Design & Development, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Wesley Howard
- Process and Analytical Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20787, USA
| | - Mariam Ibrahim
- Dosage Form Design & Development, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Sajal M Patel
- Dosage Form Design & Development, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - William P McMahon
- Process and Analytical Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20787, USA
| | - Yoen Joo Kim
- Process and Analytical Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20787, USA
| | - Jared A Delmar
- Process and Analytical Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20787, USA
| | - Darryl Davis
- Process and Analytical Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20787, USA
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4
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Chen G, Tao L, Li Z. Recent advancements in mass spectrometry for higher order structure characterization of protein therapeutics. Drug Discov Today 2021; 27:196-206. [PMID: 34571276 DOI: 10.1016/j.drudis.2021.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 01/15/2023]
Abstract
Molecular characterization of higher order structure (HOS) in protein therapeutics is crucial to the selection of candidate molecules, understanding of structure-function relationships, formulation development, stability assessment, and comparability studies. Recent advances in mass spectrometry (MS), including native MS, hydrogen/deuterium exchange (HDX)-MS, and fast photochemical oxidation of proteins (FPOP) coupled with MS, have provided orthogonal ways to characterize HOS of protein therapeutics. In this review, we present the utility of native MS, HDX-MS and FPOP-MS in protein therapeutics discovery and development, with a focus on epitope mapping, aggregation assessment, and comparability studies. We also discuss future trends in the application of these MS methods to HOS characterization.
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Affiliation(s)
- Guodong Chen
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, NJ, USA.
| | - Li Tao
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Zhengjian Li
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, NJ, USA
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5
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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
![]()
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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6
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Barton C, Li XS, Li SP, Flaherty B, Sison L, Lu Q, Yeung B, Wu SL. Impact of Glycosylation on the Comparability of the Higher-Order Structures in Idursulfase by Hydrogen-Deuterium Exchange Mass Spectrometry. Anal Chem 2020; 92:8306-8314. [PMID: 32420732 DOI: 10.1021/acs.analchem.0c00661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Characterization of the higher-order structures in idursulfase (iduronate-2-sulfatase, I2S) has been accomplished through the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS). The method has over 97% sequence coverage, including seven of the eight glycosylation sites, and has been used to study the impact of glycosylation on backbone proton exchange. In addition, the method adapted a well-used biophysical spectra comparison method (similarity scoring) to define quantitative acceptance criteria for analytical comparability of different batches of drug substance as well as samples with modulated glycans. Differences in the HDX profile were induced by enzymatic removal of terminal sialic and phosphate groups on negatively charged glycans. These differences were mapped to the crystal structure and demonstrated synergistic HDX changes focused around the N221 and N255 glycosylation sites, which contain mannose-6-phosphate motifs important for I2S uptake into cells.
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Affiliation(s)
| | | | - Siyang Peter Li
- BioAnalytix, Inc., 790 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | | | | | | | | | - Shiaw-Lin Wu
- BioAnalytix, Inc., 790 Memorial Drive, Cambridge, Massachusetts 02139, United States
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7
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Makarov AA, Iacob RE, Pirrone GF, Rodriguez-Granillo A, Joyce L, Mangion I, Moore JC, Sherer EC, Engen JR. Combination of HDX-MS and in silico modeling to study enzymatic reactivity and stereo-selectivity at different solvent conditions. J Pharm Biomed Anal 2020; 182:113141. [PMID: 32036298 DOI: 10.1016/j.jpba.2020.113141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/16/2022]
Abstract
The higher-order structure of a protein defines its function, and protein structural dynamics are often essential for protein binding and enzyme catalysis. Methods for protein characterization in solution are continuously being developed to understand and explore protein conformational changes with regards to function and activity. The goal of this study was to survey the use of combining HDX-MS global conformational screening with in silico modeling and continuous labeling peptide-level HDX-MS as an approach to highlight regions of interest within an enzyme required for biocatalytic processes. We surveyed in silico modeling correlated with peptide level HDX-MS experiments to characterize and localize transaminase enzyme structural dynamics at different conditions. This approach was orthogonally correlated with a global Size-Exclusion-HDX (SEC-HDX) screen for global conformational comparison and global alpha-helical content measurements by circular dichroism. Enzymatic activity and stereo-selectivity of transaminases were compared at different reaction-solution conditions that forced protein conformational changes by increasing acetonitrile concentration. The experimental peptide-level HDX-MS results demonstrated similar trends to the modeling data showing that certain regions remained folded in transaminases ATA-036 and ATA-303 with increasing acetonitrile concentration, which is also associated with shifting stereoselectivity. HDX modeling, SEC-HDX and CD experimental data showed that transaminase ATA-234 had the highest level of global unfolding with increasing acetonitrile concentration compared to the other two enzymes, which correlated with drastically reduced product conversion in transamination reaction. The combined HDX modeling/experimental workflow, based on enzymatic reactions studied at different conditions to induce changes in enzyme conformation, could be used as a tool to guide directed evolution efforts by identifying and focusing on the regions of an enzyme required for reaction product conversion and stereoselectivity.
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Affiliation(s)
- Alexey A Makarov
- Merck & Co., Inc., Process Research & Development, Rahway, NJ 07065, USA.
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Gregory F Pirrone
- Merck & Co., Inc., Process Research & Development, Rahway, NJ 07065, USA
| | | | - Leo Joyce
- Merck & Co., Inc., Process Research & Development, Rahway, NJ 07065, USA
| | - Ian Mangion
- Merck & Co., Inc., Process Research & Development, Rahway, NJ 07065, USA
| | - Jeffrey C Moore
- Merck & Co., Inc., Process Research & Development, Rahway, NJ 07065, USA
| | - Edward C Sherer
- Merck & Co., Inc., Computational and Structural Chemistry, Rahway, NJ 07065, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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8
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Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Filliben JJ, Huang RYC, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. Interlaboratory Comparison of Hydrogen-Deuterium Exchange Mass Spectrometry Measurements of the Fab Fragment of NISTmAb. Anal Chem 2019; 91:7336-7345. [PMID: 31045344 DOI: 10.1021/acs.analchem.9b01100] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an established, powerful tool for investigating protein-ligand interactions, protein folding, and protein dynamics. However, HDX-MS is still an emergent tool for quality control of biopharmaceuticals and for establishing dynamic similarity between a biosimilar and an innovator therapeutic. Because industry will conduct quality control and similarity measurements over a product lifetime and in multiple locations, an understanding of HDX-MS reproducibility is critical. To determine the reproducibility of continuous-labeling, bottom-up HDX-MS measurements, the present interlaboratory comparison project evaluated deuterium uptake data from the Fab fragment of NISTmAb reference material (PDB: 5K8A ) from 15 laboratories. Laboratories reported ∼89 800 centroid measurements for 430 proteolytic peptide sequences of the Fab fragment (∼78 900 centroids), giving ∼100% coverage, and ∼10 900 centroid measurements for 77 peptide sequences of the Fc fragment. Nearly half of peptide sequences are unique to the reporting laboratory, and only two sequences are reported by all laboratories. The majority of the laboratories (87%) exhibited centroid mass laboratory repeatability precisions of ⟨ sLab⟩ ≤ (0.15 ± 0.01) Da (1σx̅). All laboratories achieved ⟨sLab⟩ ≤ 0.4 Da. For immersions of protein at THDX = (3.6 to 25) °C and for D2O exchange times of tHDX = (30 s to 4 h) the reproducibility of back-exchange corrected, deuterium uptake measurements for the 15 laboratories is σreproducibility15 Laboratories( tHDX) = (9.0 ± 0.9) % (1σ). A nine laboratory cohort that immersed samples at THDX = 25 °C exhibited reproducibility of σreproducibility25C cohort( tHDX) = (6.5 ± 0.6) % for back-exchange corrected, deuterium uptake measurements.
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Affiliation(s)
- Jeffrey W Hudgens
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Elyssia S Gallagher
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Ioannis Karageorgos
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Kyle W Anderson
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - James J Filliben
- Statistical Engineering Division , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - George M Bou-Assaf
- Analytical Development , Biogen Inc. , 225 Binney Street , Cambridge , Massachusetts 02142 , United States
| | - Alfonso Espada
- Centro de Investigación Lilly S.A. , 28108 Alcobendas , Spain
| | - Michael J Chalmers
- Lilly Research Laboratories , Eli Lilly and Company , Indianapolis , Indiana 46285 , United States
| | | | - Hui-Min Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Benjamin T Walters
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jennifer Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - John Venable
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States.,Joint Center for Structural Genomics , La Jolla , California 92037 , United States
| | - Inhee Park
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Xiaojun Lu
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Ratnesh Pandey
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Arun Chandramohan
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Ganesh Srinivasan Anand
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Sasidhar N Nirudodhi
- Vaccine R&D , Pfizer Inc. , 401 N Middletown Rd , Pearl River, New York 10965 , United States
| | - Justin B Sperry
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Jason C Rouse
- Analytical R&D , Pfizer Inc. , 1 Burtt Road , Andover , Massachusetts 01810 , United States
| | - James A Carroll
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Kasper D Rand
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Ulrike Leurs
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - David D Weis
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Mohammed A Al-Naqshabandi
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States.,Department of General Science , Soran University , Kawa Street , Soran , Kurdistan Region, Iraq
| | - Tyler S Hageman
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Daniel Deredge
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Malvina Papanastasiou
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - John D Lambris
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - Sheng Li
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Sarah Urata
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
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9
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Cao X, Flagg SC, Li X, Chennamsetty N, Balakrishnan G, Das TK. Quadrupole Dalton-Based Controlled Proteolysis Method for Characterization of Higher Order Protein Structure. Anal Chem 2019; 91:5339-5345. [DOI: 10.1021/acs.analchem.9b00306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Xiang Cao
- Biologics Methods and Analytical Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Shannon C. Flagg
- Biologics Methods and Analytical Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Xue Li
- Biologics Methods and Analytical Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Naresh Chennamsetty
- Biologics Methods and Analytical Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Gurusamy Balakrishnan
- Biologics Methods and Analytical Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Tapan K. Das
- Biologics Methods and Analytical Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
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10
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Benhaim M, Lee KK, Guttman M. Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry. Protein Pept Lett 2019; 26:16-26. [PMID: 30543159 PMCID: PMC6386625 DOI: 10.2174/0929866526666181212165037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 11/17/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Structural biology has provided a fundamental understanding of protein structure and mechanistic insight into their function. However, high-resolution structures alone are insufficient for a complete understanding of protein behavior. Higher energy conformations, conformational changes, and subtle structural fluctuations that underlie the proper function of proteins are often difficult to probe using traditional structural approaches. Hydrogen/Deuterium Exchange with Mass Spectrometry (HDX-MS) provides a way to probe the accessibility of backbone amide protons under native conditions, which reports on local structural dynamics of solution protein structure that can be used to track complex structural rearrangements that occur in the course of a protein's function. CONCLUSION In the last 20 years the advances in labeling techniques, sample preparation, instrumentation, and data analysis have enabled HDX to gain insights into very complex biological systems. Analysis of challenging targets such as membrane protein complexes is now feasible and the field is paving the way to the analysis of more and more complex systems.
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Affiliation(s)
- Mark Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
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11
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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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12
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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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13
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Zhang J, Woods C, He F, Han M, Treuheit MJ, Volkin DB. Structural Changes and Aggregation Mechanisms of Two Different Dimers of an IgG2 Monoclonal Antibody. Biochemistry 2018; 57:5466-5479. [DOI: 10.1021/acs.biochem.8b00575] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun Zhang
- Process Development, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Christopher Woods
- Process Development, Amgen Inc., Thousand Oaks, California 91320, United States
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66049, United States
| | - Feng He
- Process Development, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Mei Han
- Pharmacokinetics & Drug Metabolism, Amgen Inc., South San Francisco, California 94080, United States
| | - Michael J. Treuheit
- Process Development, Amgen Inc., Thousand Oaks, California 91320, United States
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66049, United States
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14
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Oganesyan I, Lento C, Wilson DJ. Contemporary hydrogen deuterium exchange mass spectrometry. Methods 2018; 144:27-42. [DOI: 10.1016/j.ymeth.2018.04.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/16/2018] [Accepted: 04/21/2018] [Indexed: 02/07/2023] Open
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15
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Huang RYC, O'Neil SR, Lipovšek D, Chen G. Conformational Assessment of Adnectin and Adnectin-Drug Conjugate by Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1524-1531. [PMID: 29736601 DOI: 10.1007/s13361-018-1966-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 06/08/2023]
Abstract
Higher-order structure (HOS) characterization of therapeutic protein-drug conjugates for comprehensive assessment of conjugation-induced protein conformational changes is an important consideration in the biopharmaceutical industry to ensure proper behavior of protein therapeutics. In this study, conformational dynamics of a small therapeutic protein, adnectin 1, together with its drug conjugate were characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) with different spatial resolutions. Top-down HDX allows detailed assessment of the residue-level deuterium content in the payload conjugation region. HDX-MS dataset revealed the ability of peptide-based payload/linker to retain deuterium in HDX experiments. Combined results from intact, top-down, and bottom-up HDX indicated no significant conformational changes of adnectin 1 upon payload conjugation. Graphical Abstract ᅟ.
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Affiliation(s)
- Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA.
| | - Steven R O'Neil
- Molecular Discovery Technologies, Research and Development, Bristol-Myers Squibb Company, Waltham, MA, USA
| | - Daša Lipovšek
- Molecular Discovery Technologies, Research and Development, Bristol-Myers Squibb Company, Waltham, MA, USA
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA.
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16
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Rathore D, Faustino A, Schiel J, Pang E, Boyne M, Rogstad S. The role of mass spectrometry in the characterization of biologic protein products. Expert Rev Proteomics 2018; 15:431-449. [DOI: 10.1080/14789450.2018.1469982] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Deepali Rathore
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anneliese Faustino
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - John Schiel
- Biomolecular Measurement Division, National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Eric Pang
- Office of Lifecycle Drug Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Michael Boyne
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
- COUR Pharmaceuticals Development Company, Northbrook, IL, USA
| | - Sarah Rogstad
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
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17
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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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18
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Toth RT, Pace SE, Mills BJ, Joshi SB, Esfandiary R, Middaugh CR, Weis DD, Volkin DB. Evaluation of Hydrogen Exchange Mass Spectrometry as a Stability-Indicating Method for Formulation Excipient Screening for an IgG4 Monoclonal Antibody. J Pharm Sci 2018; 107:1009-1019. [DOI: 10.1016/j.xphs.2017.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/25/2017] [Accepted: 12/06/2017] [Indexed: 12/23/2022]
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19
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Huang RYC, Iacob RE, Sankaranarayanan S, Yang L, Ahlijanian M, Tao L, Tymiak AA, Chen G. Probing Conformational Dynamics of Tau Protein by Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:174-182. [PMID: 28971440 DOI: 10.1007/s13361-017-1815-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 06/07/2023]
Abstract
Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization. HDX-MS studies including anti-tau antibody epitope mapping experiments provided molecular level details of the full-length tau's conformational dynamics and its regional solvent accessibility upon soluble aggregates formation. The results demonstrate that R3 region in the full-length tau's microtubule binding repeat region (MTBR) is stabilized in the aggregation process, leaving both N and C terminal regions to be solvent exposed in the soluble aggregates and fibrils. The findings also illustrate the practical utility of orthogonal analytical methodologies for the characterization of protein higher order structure. Graphical Abstract ᅟ.
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Affiliation(s)
- Richard Y-C Huang
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Sethu Sankaranarayanan
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Ling Yang
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Michael Ahlijanian
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Li Tao
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Hopewell, NJ, USA
| | - Adrienne A Tymiak
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA.
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20
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High Throughput Prediction Approach for Monoclonal Antibody Aggregation at High Concentration. Pharm Res 2017; 34:1831-1839. [DOI: 10.1007/s11095-017-2191-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/23/2017] [Indexed: 02/05/2023]
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