1
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Schuck P, To SC, Zhao H. An automated interface for sedimentation velocity analysis in SEDFIT. PLoS Comput Biol 2023; 19:e1011454. [PMID: 37669309 PMCID: PMC10503714 DOI: 10.1371/journal.pcbi.1011454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/15/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of suitable software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Samuel C. To
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
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2
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Schuck P, To SC, Zhao H. An automated interface for sedimentation velocity analysis in SEDFIT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.14.540690. [PMID: 37425873 PMCID: PMC10327192 DOI: 10.1101/2023.05.14.540690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of available software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel C. To
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Mathieu‐Gaedke M, Böker A, Glebe U. How to Characterize the Protein Structure and Polymer Conformation in Protein‐Polymer Conjugates – a Perspective. MACROMOL CHEM PHYS 2023. [DOI: 10.1002/macp.202200353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Maria Mathieu‐Gaedke
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
| | - Alexander Böker
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
| | - Ulrich Glebe
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
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4
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Mieczkowski C, Zhang X, Lee D, Nguyen K, Lv W, Wang Y, Zhang Y, Way J, Gries JM. Blueprint for antibody biologics developability. MAbs 2023; 15:2185924. [PMID: 36880643 PMCID: PMC10012935 DOI: 10.1080/19420862.2023.2185924] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Large-molecule antibody biologics have revolutionized medicine owing to their superior target specificity, pharmacokinetic and pharmacodynamic properties, safety and toxicity profiles, and amenability to versatile engineering. In this review, we focus on preclinical antibody developability, including its definition, scope, and key activities from hit to lead optimization and selection. This includes generation, computational and in silico approaches, molecular engineering, production, analytical and biophysical characterization, stability and forced degradation studies, and process and formulation assessments. More recently, it is apparent these activities not only affect lead selection and manufacturability, but ultimately correlate with clinical progression and success. Emerging developability workflows and strategies are explored as part of a blueprint for developability success that includes an overview of the four major molecular properties that affect all developability outcomes: 1) conformational, 2) chemical, 3) colloidal, and 4) other interactions. We also examine risk assessment and mitigation strategies that increase the likelihood of success for moving the right candidate into the clinic.
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Affiliation(s)
- Carl Mieczkowski
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Xuejin Zhang
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Dana Lee
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Khanh Nguyen
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Wei Lv
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Yanling Wang
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Yue Zhang
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Jackie Way
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Jean-Michel Gries
- President, Discovery Research, Hengenix Biotech, Inc, Milpitas, CA, USA
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5
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Li D, Chu W, Sheng X, Li W. Optimization of Membrane Protein TmrA Purification Procedure Guided by Analytical Ultracentrifugation. MEMBRANES 2021; 11:membranes11100780. [PMID: 34677546 PMCID: PMC8537081 DOI: 10.3390/membranes11100780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 12/02/2022]
Abstract
Membrane proteins are involved in various cellular processes. However, purification of membrane proteins has long been a challenging task, as membrane protein stability in detergent is the bottleneck for purification and subsequent analyses. Therefore, the optimization of detergent conditions is critical for the preparation of membrane proteins. Here, we utilize analytical ultracentrifugation (AUC) to examine the effects of different detergents (OG, Triton X-100, DDM), detergent concentrations, and detergent supplementation on the behavior of membrane protein TmrA. Our results suggest that DDM is more suitable for the purification of TmrA compared with OG and TritonX-100; a high concentration of DDM yields a more homogeneous protein aggregation state; supplementing TmrA purified with a low DDM concentration with DDM maintains the protein homogeneity and aggregation state, and may serve as a practical and cost-effective strategy for membrane protein purification.
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Affiliation(s)
- Dongdong Li
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Wendan Chu
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Xinlei Sheng
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Correspondence: (X.S.); (W.L.); Tel.: +86-1062782031 (W.L.)
| | - Wenqi Li
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
- Correspondence: (X.S.); (W.L.); Tel.: +86-1062782031 (W.L.)
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6
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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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7
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Sousa AA, Schuck P, Hassan SA. Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters. NANOSCALE ADVANCES 2021; 3:2995-3027. [PMID: 34124577 PMCID: PMC8168927 DOI: 10.1039/d1na00086a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/16/2021] [Indexed: 05/03/2023]
Abstract
The use of nanoparticles (NPs) in biomedicine has made a gradual transition from proof-of-concept to clinical applications, with several NP types meeting regulatory approval or undergoing clinical trials. A new type of metallic nanostructures called ultrasmall nanoparticles (usNPs) and nanoclusters (NCs), while retaining essential properties of the larger (classical) NPs, have features common to bioactive proteins. This combination expands the potential use of usNPs and NCs to areas of diagnosis and therapy traditionally reserved for small-molecule medicine. Their distinctive physicochemical properties can lead to unique in vivo behaviors, including improved renal clearance and tumor distribution. Both the beneficial and potentially deleterious outcomes (cytotoxicity, inflammation) can, in principle, be controlled through a judicious choice of the nanocore shape and size, as well as the chemical ligands attached to the surface. At present, the ability to control the behavior of usNPs is limited, partly because advances are still needed in nanoengineering and chemical synthesis to manufacture and characterize ultrasmall nanostructures and partly because our understanding of their interactions in biological environments is incomplete. This review addresses the second limitation. We review experimental and computational methods currently available to understand molecular mechanisms, with particular attention to usNP-protein complexation, and highlight areas where further progress is needed. We discuss approaches that we find most promising to provide relevant molecular-level insight for designing usNPs with specific behaviors and pave the way to translational applications.
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Affiliation(s)
- Alioscka A Sousa
- Department of Biochemistry, Federal University of São Paulo São Paulo SP 04044 Brazil
| | - Peter Schuck
- National Institute of Biomedical Imaging and Bioengineering, NIH Bethesda MD 20892 USA
| | - Sergio A Hassan
- BCBB, National Institute of Allergy and Infectious Diseases, NIH Bethesda MD 20892 USA
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8
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A Multi-Method Approach to Assess the Self-Interaction Behavior of Infliximab. J Pharm Sci 2021; 110:1979-1988. [PMID: 33556386 DOI: 10.1016/j.xphs.2021.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/13/2021] [Accepted: 02/01/2021] [Indexed: 02/03/2023]
Abstract
Attractive self-interaction processes in antibody formulations increase the risk of aggregation and extraordinarily elevated viscosity at high protein concentrations. These challenges affect manufacturing and application. This study aimed to understand the self-interaction process of Infliximab as a model system with pronounced attractive self-interaction. The association mechanism was studied by a multi-method approach comprising analytical ultracentrifugation, dynamic light scattering, small angle X-ray scattering, self-interaction bio-layer interferometry and hydrogen-deuterium exchange mass spectrometry. Based on our results, both Fab and Fc regions of Infliximab are involved in self-interaction. We hypothesize a mechanism based on electrostatic interactions of polar and charged residues within the identified areas of the heavy and the light chain of the mAb. The combination of fast and reliable screening methods and low throughput but high resolution methods can contribute to detailed characterization and deeper understanding of specific self-interaction processes.
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9
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Correia JJ, Wright RT, Sherwood PJ, Stafford WF. Analysis of nonideality: insights from high concentration simulations of sedimentation velocity data. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:687-700. [PMID: 33159218 PMCID: PMC7701085 DOI: 10.1007/s00249-020-01474-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/22/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022]
Abstract
The Aviv fluorescence detection system (Aviv-FDS) has allowed the performance of sedimentation velocity experiments on therapeutic antibodies in highly concentrated environments like formulation buffers and serum. Methods were implemented in the software package SEDANAL for the analysis of nonideal, weakly associating AUC data acquired on therapeutic antibodies and proteins (Wright et al. Eur Biophys J 47:709–722, 2018, Anal Biochem 550:72–83, 2018). This involved fitting both hydrodynamic, ks, and thermodynamic, BM1, nonideality where concentration dependence is expressed as s = so/(1 + ksc) and D = Do(1 + 2BM1c)/(1 + ksc) and so and Do are values extrapolated to c = 0 (mg/ml). To gain insight into the consequences of these phenomenological parameters, we performed simulations with SEDANAL of a monoclonal antibody as a function of ks (0–100 ml/g) and BM1 (0–100 ml/g). This provides a visual understanding of the separate and joint impact of ks and BM1 on the shape of high-concentration sedimentation velocity boundaries and the challenge of their unique determination by finite element methods. In addition, mAbs undergo weak self- and hetero-association (Yang et al. Prot Sci 27:1334–1348, 2018) and thus we have simulated examples of nonideal weak association over a wide range of concentrations (1–120 mg/ml). Here we demonstrate these data are best analyzed by direct boundary global fitting to models that account for ks, BM1 and weak association. Because a typical clinical dose of mAb is 50–200 mg/ml, these results have relevance for biophysical understanding of concentrated therapeutic proteins.
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Affiliation(s)
- J J Correia
- Department of Cell and Molecular Biology, University of MS Medical Center, Jackson, MS, USA.
| | - R T Wright
- Biophysics Group, Janssen Biotherapeutics, Spring House, PA, USA
| | | | - W F Stafford
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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10
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Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:809-818. [PMID: 33067686 DOI: 10.1007/s00249-020-01470-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/26/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022]
Abstract
Analytical ultracentrifugation (AUC) has emerged as a robust and reliable technique for biomolecular characterization with extraordinary sensitivity. AUC is widely used to study purity, conformational changes, biomolecular interactions, and stoichiometry. Furthermore, AUC is used to determine the molecular weight of biomolecules such as proteins, carbohydrates, and DNA and RNA. Due to the multifaceted role(s) of non-coding RNAs from viruses, prokaryotes, and eukaryotes, research aimed at understanding the structure-function relationships of non-coding RNAs is rapidly increasing. However, due to their large size, flexibility, complicated secondary structures, and conformations, structural studies of non-coding RNAs are challenging. In this review, we are summarizing the application of AUC to evaluate the homogeneity, interactions, and conformational changes of non-coding RNAs from adenovirus as well as from Murray Valley, Powassan, and West Nile viruses. We also discuss the application of AUC to characterize eukaryotic long non-coding RNAs, Xist, and HOTAIR. These examples highlight the significant role AUC can play in facilitating the structural determination of non-coding RNAs and their complexes.
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11
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Pohl C, Zalar M, Bialy IE, Indrakumar S, Peters GHJ, Friess W, Golovanov AP, Streicher WW, Noergaard A, Harris P. The Effect of Point Mutations on the Biophysical Properties of an Antimicrobial Peptide: Development of a Screening Protocol for Peptide Stability Screening. Mol Pharm 2020; 17:3298-3313. [DOI: 10.1021/acs.molpharmaceut.0c00406] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christin Pohl
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Matja Zalar
- Manchester Institute of Biotechnology and Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Inas El Bialy
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5, 81377 Muenchen, Germany
| | - Sowmya Indrakumar
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Günther H. J. Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Wolfgang Friess
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5, 81377 Muenchen, Germany
| | - Alexander P. Golovanov
- Manchester Institute of Biotechnology and Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | | | | | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
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12
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Savelyev A, Gorbet GE, Henrickson A, Demeler B. Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment. PLoS Comput Biol 2020; 16:e1007942. [PMID: 32559250 PMCID: PMC7347214 DOI: 10.1371/journal.pcbi.1007942] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/09/2020] [Accepted: 05/11/2020] [Indexed: 01/19/2023] Open
Abstract
Recent advances in instrumentation have moved analytical ultracentrifugation (AUC) closer to a possible validation in a Good Manufacturing Practices (GMP) environment. In order for AUC to be validated for a GMP environment, stringent requirements need to be satisfied; analysis procedures must be evaluated for consistency and reproducibility, and GMP capable data acquisition software needs to be developed and validated. These requirements extend to multiple regulatory aspects, covering documentation of instrument hardware functionality, data handling and software for data acquisition and data analysis, process control, audit trails and automation. Here we review the requirements for GMP validation of data acquisition software and illustrate software solutions based on UltraScan that address these requirements as far as they relate to the operation and data handling in conjunction with the latest analytical ultracentrifuge, the Optima AUC by Beckman Coulter. The software targets the needs of regulatory agencies, where AUC plays a critical role in the solution-based characterization of biopolymers and macromolecular assemblies. Biopharmaceutical and regulatory agencies rely heavily on this technique for characterizations of pharmaceutical formulations, biosimilars, injectables, nanoparticles, and other soluble therapeutics. Because of its resolving power, AUC is a favorite application, despite the current lack of GMP validation. We believe that recent advances in standards, hardware, and software presented in this work manage to bridge this gap and allow AUC to be routinely used in a GMP environment. AUC has great potential to provide more detailed information, at higher resolution, and with greater confidence than other analytical techniques, and our software satisfies an urgent need for AUC operation in the GMP environment. The software, including documentation, are publicly available for free download from Github. The multi-platform software is licensed by the LGPL v.3 open source license and supports Windows, Mac and Linux platforms. Installation instructions and a mailing list are available from ultrascan.aucsolutions.com.
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Affiliation(s)
- Alexey Savelyev
- University of Montana, Dept. of Chemistry, Missoula, Montana, United States of America
| | | | - Amy Henrickson
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada
| | - Borries Demeler
- University of Montana, Dept. of Chemistry, Missoula, Montana, United States of America
- AUC Solutions, Houston, Texas, United States of America
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada
- * E-mail:
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13
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Dhankher A, Hernandez ME, Howard HC, Champion JA. Characterization and Control of Dynamic Rearrangement in a Self-Assembled Antibody Carrier. Biomacromolecules 2020; 21:1407-1416. [PMID: 32134251 DOI: 10.1021/acs.biomac.9b01712] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Thorough characterization of protein assemblies is required for the control of structure and robust performance in any given application, especially for the safety and stability of protein therapeutics. Here, we report the use of multiple, orthogonal characterization techniques to enable control over the structure of a multivalent antibody carrier for future use in drug delivery applications. The carrier, known as Hex, contains six antibody binding domains that bind the Fc region of antibodies. Using size exclusion chromatography, analytical ultracentrifugation, and dynamic light scattering, we identified the stoichiometry of assembled Hex-antibody complexes and observed changes in the stoichiometry of nanocarriers when incubated at higher temperatures over time. The characterization data informed the modification of Hex to achieve tighter control over the protein assembly structure for future therapeutic applications. This work demonstrates the importance of using orthogonal characterization techniques and observing protein assembly in different conditions over time to fully understand and control structure and dynamics.
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Affiliation(s)
- Anshul Dhankher
- School of Chemical & Biomolecular Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Manuel E Hernandez
- School of Chemical & Biomolecular Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Hannah C Howard
- School of Chemical & Biomolecular Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A Champion
- School of Chemical & Biomolecular Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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14
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Chaturvedi SK, Schuck P. A Reappraisal of Sedimentation Nonideality Coefficients for the Analysis of Weak Interactions of Therapeutic Proteins. AAPS JOURNAL 2019; 21:35. [PMID: 30815745 PMCID: PMC6394620 DOI: 10.1208/s12248-019-0307-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/11/2019] [Indexed: 11/30/2022]
Abstract
The study of weak or colloidal interactions of therapeutic proteins in different formulations allows prediction and optimization of protein stability. Various biophysical techniques have been applied to determine the second osmotic virial coefficient B2 as it reflects on the macromolecular distance distribution that governs solution behavior at high concentration. In the present work, we exploit a direct link predicted by hydrodynamic theory between B2 and the nonideality of sedimentation, commonly measured in sedimentation velocity analytical ultracentrifugation through the nonideality coefficient of sedimentation, kS. Using sedimentation equilibrium analytical ultracentrifugation for independent measurement of B2, we have examined the dependence of kS on B2 for model proteins in different buffers. The data exhibit the expected linear relationship and highlight the impact of protein shape on the magnitude of the nonideality coefficient kS. Recently, measurements of kS have been considerably simplified allowing higher throughput and simultaneous polydispersity assessment at higher protein concentrations. Thus, sedimentation velocity may offer a useful approach to compare the impact of formulation conditions on weak interactions and simultaneously on higher-order structure of therapeutic proteins.
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Affiliation(s)
- Sumit K Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bldg. 13, Rm 3N17, Bethesda, Maryland, 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bldg. 13, Rm 3N17, Bethesda, Maryland, 20892, USA.
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15
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Shi Y, Hong X, Fan H, Wu Z, Liu A. Characterizing Novel Modifications of a Therapeutic Protein Using Ultra Performance Liquid Chromatography-Tandem Mass Spectrometry, Sedimentation Velocity Analytical Ultracentrifugation, and Structural Modeling. Anal Chem 2018; 90:12870-12877. [PMID: 30295031 DOI: 10.1021/acs.analchem.8b03459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heterogeneity of biopharmaceutical products is common due to various co- and post-translational modifications and degradation events that occur during the biological production process and throughout the shelf life. Product-related variants resulting from these modifications potentially affect a product's biological activity and safety, and thus, their detailed structure characterization is of great importance for successful development of protein therapeutics. Specifically, in this study, two novel low-level product variants in a recombinant therapeutic protein were characterized via chromatographic enrichment followed by proteolytic digestion and analysis using ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). One of the variants was identified to be the therapeutic protein missing a 61-amino-acid fragment from its N-terminus. Consequently, the other variant was found to be the therapeutic protein carrying the 61-amino-acid long peptide. Furthermore, detailed structure at the modification site of the latter variant was determined as that amino group from the protein's N-terminus linked to side chain carbonyl carbon at Asp 61 residue of the peptide, based on the complementary information from collision induced dissociation and electron transfer dissociation MS/MS analysis. Results from sedimentation velocity analytical ultracentrifugation and computational structural modeling supported the hypothesis that formation of these two variants was a result of protein self-association. In dimeric state, the head-to-toe stacking conformation of two therapeutic protein molecules allowed spatial closeness between the N-terminus of one molecule and the 61st amino acid of the other molecule, resulting in a novel peptide transfer between the two protein molecules.
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Measuring macromolecular size distributions and interactions at high concentrations by sedimentation velocity. Nat Commun 2018; 9:4415. [PMID: 30356043 PMCID: PMC6200768 DOI: 10.1038/s41467-018-06902-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/14/2018] [Indexed: 12/17/2022] Open
Abstract
In concentrated macromolecular solutions, weak physical interactions control the solution behavior including particle size distribution, aggregation, liquid-liquid phase separation, or crystallization. This is central to many fields ranging from colloid chemistry to cell biology and pharmaceutical protein engineering. Unfortunately, it is very difficult to determine macromolecular assembly states and polydispersity at high concentrations in solution, since all motion is coupled through long-range hydrodynamic, electrostatic, steric, and other interactions, and scattering techniques report on the solution structure when average interparticle distances are comparable to macromolecular dimensions. Here we present a sedimentation velocity technique that, for the first time, can resolve macromolecular size distributions at high concentrations, by simultaneously accounting for average mutual hydrodynamic and thermodynamic interactions. It offers high resolution and sensitivity of protein solutions up to 50 mg/ml, extending studies of macromolecular solution state closer to the concentration range of therapeutic formulations, serum, or intracellular conditions. Many aspects of concentrated macromolecular solutions, such as encountered in cytosol or in pharmaceutical formulations, are dependent on particle size distributions and weak intermolecular interactions. Here, the authors exploit hydrodynamic separation in the centrifugal field to measure both.
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Krayukhina E, Noda M, Ishii K, Maruno T, Wakabayashi H, Tada M, Suzuki T, Ishii-Watabe A, Kato M, Uchiyama S. Analytical ultracentrifugation with fluorescence detection system reveals differences in complex formation between recombinant human TNF and different biological TNF antagonists in various environments. MAbs 2017; 9:664-679. [PMID: 28387583 PMCID: PMC5419078 DOI: 10.1080/19420862.2017.1297909] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A number of studies have attempted to elucidate the binding mechanism between tumor necrosis factor (TNF) and clinically relevant antagonists. None of these studies, however, have been conducted as close as possible to physiologic conditions, and so the relationship between the size distribution of TNF-antagonist complexes and the antagonists' biological activity or adverse effects remains elusive. Here, we characterized the binding stoichiometry and sizes of soluble TNF-antagonist complexes for adalimumab, infliximab, and etanercept that were formed in human serum and in phosphate-buffered saline (PBS). Fluorescence-detected sedimentation velocity analytical ultracentrifugation analyses revealed that adalimumab and infliximab formed a range of complexes with TNF, with the major complexes consisting of 3 molcules of the respective antagonist and one or 2 molcules of TNF. Considerably greater amounts of high-molecular-weight complexes were detected for infliximab in human serum. The emergence of peaks with higher sedimentation coefficients than the adalimumab monomer as a function of added human serum albumin (HSA) concentration in PBS suggested weak reversible interactions between HSA and immunoglobulins. Etanerept exclusively formed 1:1 complexes with TNF in PBS, and a small amount of complexes with higher stoichiometry was detected in human serum. Consistent with these biophysical characterizations, a reporter assay showed that adalimumab and infliximab, but not etanercept, exerted FcγRIIa- and FcγRIIIa-mediated cell signaling in the presence of TNF and that infliximab exhibited higher potency than adalimumab. This study shows that assessing distribution profiles in serum will contribute to a more comprehensive understanding of the in vivo behavior of therapeutic proteins.
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Affiliation(s)
- Elena Krayukhina
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan
| | - Masanori Noda
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan
| | - Kentaro Ishii
- c Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences , Higashiyama, Myodaiji, Okazaki , Aichi , Japan
| | - Takahiro Maruno
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan
| | - Hirotsugu Wakabayashi
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan
| | - Minoru Tada
- d Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kamiyoga, Setagaya-ku , Tokyo , Japan
| | - Takuo Suzuki
- d Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kamiyoga, Setagaya-ku , Tokyo , Japan
| | - Akiko Ishii-Watabe
- d Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kamiyoga, Setagaya-ku , Tokyo , Japan
| | - Masahiko Kato
- e Sysmex Corporation , Murotani, Nishi-ku, Kobe-shi , Hyogo , Japan
| | - Susumu Uchiyama
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan.,c Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences , Higashiyama, Myodaiji, Okazaki , Aichi , Japan
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Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods. Methods 2016; 118-119:146-162. [PMID: 27939506 DOI: 10.1016/j.ymeth.2016.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/01/2023] Open
Abstract
The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes.
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