1
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Hamasaki M, Takamatsu S, Nagata M, Wilson E, Suzuki H, Tanaka A, Ikebukuro K, Sode K, Asano R. Development of DNA aptamers universally bound to single-chain fragment variables and their applications in bioprocess monitoring. Biosens Bioelectron 2024; 261:116511. [PMID: 38917513 DOI: 10.1016/j.bios.2024.116511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 06/09/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
Single-chain fragment variables (scFvs), composed of variable heavy and light chains joined together by a peptide linker, can be produced using a cost-effective bacterial expression system, making them promising candidates for pharmaceutical applications. However, a versatile method for monitoring recombinant-protein production has not yet been developed. Herein, we report a novel anti-scFv aptamer-based biosensing system with high specificity and versatility. First, anti-scFv aptamers were screened using the competitive systematic evolution of ligands by exponential enrichment, focusing on a unique scFv-specific peptide linker. We selected two aptamers, P1-12 and P2-63, with KD = 2.1 μM or KD = 1.6 μM toward anti-human epidermal growth factor receptor (EGFR) scFv, respectively. These two aptamers can selectively bind to scFv but not to anti-EGFR Fv. Furthermore, the selected aptamers recognized various scFvs with different CDRs, such as anti-4-1BB and anti-hemoglobin scFv, indicating that they recognized a unique peptide linker region. An electrochemical sensor for anti-EGFR scFv was developed using anti-scFv aptamers based on square wave voltammetry. Thus, the constructed sensor could monitor anti-EGFR scFv concentrations in the range of 10-500 nM in a diluted medium for bacterial cultivation, which covered the expected concentration range for the recombinant production of scFvs. These achievements promise the realization of continuous monitoring sensors for pharmaceutical scFv, which will enable the real-time and versatile monitoring of large-scale scFv production.
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Affiliation(s)
- Mai Hamasaki
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan; Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Shouhei Takamatsu
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Madoka Nagata
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Ellie Wilson
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Hirobumi Suzuki
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Ayumi Tanaka
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
| | - Koji Sode
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA.
| | - Ryutaro Asano
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo, 183-8538, Japan.
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2
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Wang Y, Xiao J. Recent advances in the molecular understanding of immunoglobulin A. FEBS J 2024; 291:3597-3603. [PMID: 38329005 DOI: 10.1111/febs.17089] [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: 11/29/2023] [Revised: 01/11/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Immunoglobulin A (IgA) plays a crucial role in the human immune system, particularly in mucosal immunity. IgA antibodies that target the mucosal surface are made up of two to five IgA monomers linked together by the joining chain, forming polymeric molecules. These IgA polymers are transported across mucosal epithelial cells by the polymeric immunoglobulin receptor pIgR, resulting in the formation of secretory IgA (SIgA). This review aims to explore recent advancements in our molecular understanding of IgA, with a specific focus on SIgA, and the interaction between IgA and pathogen molecules.
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Affiliation(s)
- Yuxin Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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3
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Biewenga L, Vermathen R, Rosier BJ, Merkx M. A Generic Antibody-Blocking Protein That Enables pH-Switchable Activation of Antibody Activity. ACS Chem Biol 2024; 19:48-57. [PMID: 38110237 PMCID: PMC10804362 DOI: 10.1021/acschembio.3c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
Molecular strategies that allow for reversible control of antibody activity have drawn considerable interest for both therapeutic and diagnostic applications. Protein M is a generic antibody-binding protein that binds to the Fv domain of IgGs and, in doing so, blocks antigen binding. However, the dissociation of protein M is essentially irreversible, which has precluded its use as an antibody affinity reagent and molecular mask to control antibody activity. Here, we show that introduction of 8 histidine residues on the Fv binding interface of protein M results in a variant that shows pH-switchable IgG binding. This protein M-8his variant provides an attractive and universal affinity resin for the purification of IgGs, antibody fragments (Fab and single-chain variable fragments (scFv)), and antibody conjugates. Moreover, protein M-8his enables the pH-dependent blocking of therapeutic antibodies, allowing the selective targeting of cells at pH 6.0.
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Affiliation(s)
- Lieuwe Biewenga
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Robin Vermathen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Bas J.H.M. Rosier
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
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4
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Rahmati S, Bagherzadeh K, Arab SS, Torkashvand F, Amanlou M, Vaziri B. Computational designing of the ligands of Protein L affinity chromatography based on molecular docking and molecular dynamics simulations. J Biomol Struct Dyn 2023:1-11. [PMID: 37855377 DOI: 10.1080/07391102.2023.2268219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023]
Abstract
Protein L is a multidomain protein from Peptostreptococcus magnus with binding affinity to kappa light chain of human immunoglobulin (Ig) which is used for the purification of antibody fragments by affinity chromatography. The advances in protein engineering and computational biology approaches lead to the development of engineered affinity ligands with improved properties including binding affinity. In this study, molecular dynamics simulations (MDs) and Osprey software were used to design single B domains of the Protein L with higher affinity to antibody fragments. The modified B domains were then polymerized to ligand with six B domains by homology modeling methods. The results showed that single B domain mutants of MB1 (Thr865Trp) and MB2 (Thr847Met-Thr865Trp) had higher binding affinity to Fab compared to the wild single B domain. Also, MDs and molecular docking results showed that the polymerized Proteins L including the wild and mutated six B domains (6B0, 6B1, and 6B2) were stable during MDs and the two mutants of 6B1 and 6B2 showed higher binding affinity to Fab relative to the wild type.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saman Rahmati
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Kowsar Bagherzadeh
- Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Tehran, Iran
- Eye Research Center, The Five Senses Health Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrouz Vaziri
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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5
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Davies AM, Beavil RL, Barbolov M, Sandhar BS, Gould HJ, Beavil AJ, Sutton BJ, McDonnell JM. Crystal structures of the human IgD Fab reveal insights into C H1 domain diversity. Mol Immunol 2023; 159:28-37. [PMID: 37267832 DOI: 10.1016/j.molimm.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/04/2023]
Abstract
Antibodies of the IgD isotype remain the least well characterized of the mammalian immunoglobulin isotypes. Here we report three-dimensional structures for the Fab region of IgD, based on four different crystal structures, at resolutions of 1.45-2.75 Å. These IgD Fab crystals provide the first high-resolution views of the unique Cδ1 domain. Structural comparisons identify regions of conformational diversity within the Cδ1 domain, as well as among the homologous domains of Cα1, Cγ1 and Cμ1. The IgD Fab structure also possesses a unique conformation of the upper hinge region, which may contribute to the overall disposition of the very long linker sequence between the Fab and Fc regions found in human IgD. Structural similarities observed between IgD and IgG, and differences with IgA and IgM, are consistent with predicted evolutionary relationships for the mammalian antibody isotypes.
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Affiliation(s)
- Anna M Davies
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Rebecca L Beavil
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Momchil Barbolov
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Balraj S Sandhar
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Hannah J Gould
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Andrew J Beavil
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Brian J Sutton
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - James M McDonnell
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom.
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6
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Mayorga-Martinez CC, Castoralova M, Zelenka J, Ruml T, Pumera M. Swarming Magnetic Microrobots for Pathogen Isolation from Milk. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205047. [PMID: 36475385 DOI: 10.1002/smll.202205047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/01/2022] [Indexed: 06/17/2023]
Abstract
Bovine mastitis produced by Staphylococcus aureus (S. aureus) causes major problems in milk production due to the staphylococcal enterotoxins produced by this bacterium. These enterotoxins are stable and cannot be eradicated easily by common hygienic procedures once they are formed in dairy products. Here, magnetic microrobots (MagRobots) are developed based on paramagnetic hybrid microstructures loaded with IgG from rabbit serum that can bind and isolate S. aureus from milk in a concentration of 3.42 104 CFU g-1 (allowable minimum level established by the United States Food and Drug Administration, FDA). Protein A, which is present on the cell wall of S. aureus, selectively binds IgG from rabbit serum and loads the bacteria onto the surface of the MagRobots. The selective isolation of S. aureus is confirmed using a mixed suspension of S. aureus and Escherichia coli (E. coli). Moreover, this fuel-free system based on magnetic robots does not affect the natural milk microbiota or add any toxic compound resulting from fuel catalysis. This system can be used to isolate and transport efficiently S. aureus and discriminate it from nontarget bacteria for subsequent identification. Finally, this system can be scaled up for industrial use in food production.
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Affiliation(s)
- Carmen C Mayorga-Martinez
- Center for Advanced Functional Nanorobots, Department of Inorganic Chemistry, University of Chemistry and Technology Prague, Technicka 5, 166 28, Czech Republic
| | - Marketa Castoralova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Czech Republic
| | - Jaroslav Zelenka
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Czech Republic
| | - Tomas Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Czech Republic
| | - Martin Pumera
- Center for Advanced Functional Nanorobots, Department of Inorganic Chemistry, University of Chemistry and Technology Prague, Technicka 5, 166 28, Czech Republic
- Faculty of Electrical Engineering and Computer Science, VSB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava, 70800, Czech Republic
- Department of Medical Research, China Medical University Hospital, China Medical University, No. 91 Hsueh-Shih Road, Taichung, 40402, Taiwan
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
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7
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Solomon TL, Delaglio F, Giddens JP, Marino JP, Yu YB, Taraban MB, Brinson RG. Correlated analytical and functional evaluation of higher order structure perturbations from oxidation of NISTmAb. MAbs 2023; 15:2160227. [PMID: 36683157 PMCID: PMC9872951 DOI: 10.1080/19420862.2022.2160227] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The clinical efficacy and safety of protein-based drugs such as monoclonal antibodies (mAbs) rely on the integrity of the protein higher order structure (HOS) during product development, manufacturing, storage, and patient administration. As mAb-based drugs are becoming more prevalent in the treatment of many illnesses, the need to establish metrics for quality attributes of mAb therapeutics through high-resolution techniques is also becoming evident. To this end, here we used a forced degradation method, time-dependent oxidation by hydrogen peroxide, on the model biotherapeutic NISTmAb and evaluated the effects on HOS with orthogonal analytical methods and a functional assay. To monitor the oxidation process, the experimental workflow involved incubation of NISTmAb with hydrogen peroxide in a benchtop nuclear magnetic resonance spectrometer (NMR) that followed the reaction kinetics, in real-time through the water proton transverse relaxation rate R2(1H2O). Aliquots taken at defined time points were further analyzed by high-field 2D 1H-13C methyl correlation fingerprint spectra in parallel with other analytical techniques, including thermal unfolding, size-exclusion chromatography, and surface plasmon resonance, to assess changes in stability, heterogeneity, and binding affinities. The complementary measurement outputs from the different techniques demonstrate the utility of combining NMR with other analytical tools to monitor oxidation kinetics and extract the resulting structural changes in mAbs that are functionally relevant, allowing rigorous assessment of HOS attributes relevant to the efficacy and safety of mAb-based drug products.
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Affiliation(s)
- Tsega L. Solomon
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - John P. Giddens
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - John P. Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - Yihua Bruce Yu
- Bio- and Nano-Technology Center, University of Maryland School of Pharmacy, and Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States
| | - Marc B. Taraban
- Bio- and Nano-Technology Center, University of Maryland School of Pharmacy, and Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States
| | - Robert G. Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States,CONTACT Robert G. Brinson Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, 9600 Gudelsky Drive Rockville, Rockville, Maryland20850, United States
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8
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Brasino M, Wagnell E, Hamilton S, Ranganathan S, Gomes MM, Branchaud B, Messmer B, Ibsen SD. Turning antibodies off and on again using a covalently tethered blocking peptide. Commun Biol 2022; 5:1357. [PMID: 36496512 PMCID: PMC9741643 DOI: 10.1038/s42003-022-04094-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022] Open
Abstract
In their natural form, antibodies are always in an "on-state" and are capable of binding to their targets. This leads to undesirable interactions in a wide range of therapeutic, analytical, and synthetic applications. Modulating binding kinetics of antibodies to turn them from an "off-state" to an "on-state" with temporal and spatial control can address this. Here we demonstrate a method to modulate binding activity of antibodies in a predictable and reproducible way. We designed a blocking construct that uses both covalent and non-covalent interactions with the antibody. The construct consisted of a Protein L protein attached to a flexible linker ending in a blocking-peptide designed to interact with the antibody binding site. A mutant Protein L was developed to enable photo-triggered covalent crosslinking to the antibody at a specific location. The covalent bond anchored the linker and blocking peptide to the antibody light chain keeping the blocking peptide close to the antibody binding site. This effectively put the antibody into an "off-state". We demonstrate that protease-cleavable and photocleavable moieties in the tether enable controlled antibody activation to the "on-state" for anti-FLAG and cetuximab antibodies. Protein L can bind a range of antibodies used therapeutically and in research for wide applicability.
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Affiliation(s)
- Michael Brasino
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA
| | - Eli Wagnell
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA
| | - Sean Hamilton
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR 97201 USA
| | - Srivathsan Ranganathan
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA
| | - Michelle M. Gomes
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA
| | - Bruce Branchaud
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA
| | | | - Stuart D. Ibsen
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR 97201 USA
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9
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Rezvani K, WuDunn D, Hunter AK, Aspelund MT. Leveraging light chain binding avidity for control of mispaired byproducts during production of asymmetric bispecific antibodies. J Chromatogr A 2022; 1683:463533. [DOI: 10.1016/j.chroma.2022.463533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 10/31/2022]
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10
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Emerging affinity ligands and support materials for the enrichment of monoclonal antibodies. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Chouquet A, Pinto AJ, Hennicke J, Ling WL, Bally I, Schwaigerlehner L, Thielens NM, Kunert R, Reiser JB. Biophysical Characterization of the Oligomeric States of Recombinant Immunoglobulins Type-M and Their C1q-Binding Kinetics by Biolayer Interferometry. Front Bioeng Biotechnol 2022; 10:816275. [PMID: 35685087 PMCID: PMC9173649 DOI: 10.3389/fbioe.2022.816275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulins type-M (IgMs) are one of the first antibody classes mobilized during immune responses against pathogens and tumor cells. Binding to specific target antigens enables the interaction with the C1 complex which strongly activates the classical complement pathway. This biological function is the basis for the huge therapeutic potential of IgMs. But, due to their high oligomeric complexity, in vitro production, biochemical characterization, and biophysical characterization are challenging. In this study, we present recombinant production of two IgM models (IgM617 and IgM012) in pentameric and hexameric states and the evaluation of their polymer distribution using different biophysical methods (analytical ultracentrifugation, size exclusion chromatography coupled to multi-angle laser light scattering, mass photometry, and transmission electron microscopy). Each IgM construct is defined by a specific expression and purification pattern with different sample quality. Nevertheless, both purified IgMs were able to activate complement in a C1q-dependent manner. More importantly, BioLayer Interferometry (BLI) was used for characterizing the kinetics of C1q binding to recombinant IgMs. We show that recombinant IgMs possess similar C1q-binding properties as IgMs purified from human plasma.
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Affiliation(s)
- Anne Chouquet
- Institut de Biologie Structurale, UMR 5075, Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Andrea J Pinto
- Institut de Biologie Structurale, UMR 5075, Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Julia Hennicke
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Wai Li Ling
- Institut de Biologie Structurale, UMR 5075, Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Isabelle Bally
- Institut de Biologie Structurale, UMR 5075, Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Linda Schwaigerlehner
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole M Thielens
- Institut de Biologie Structurale, UMR 5075, Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Renate Kunert
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Jean-Baptiste Reiser
- Institut de Biologie Structurale, UMR 5075, Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
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12
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Engineering pan-HIV-1 neutralization potency through multispecific antibody avidity. Proc Natl Acad Sci U S A 2022; 119:2112887119. [PMID: 35064083 PMCID: PMC8795538 DOI: 10.1073/pnas.2112887119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 02/08/2023] Open
Abstract
The high genetic diversity of HIV-1 continues to be a major barrier to the development of therapeutics for prevention and treatment. Here, we describe the design of an antibody platform that allows assembly of a highly avid, multispecific molecule that targets, simultaneously, the most conserved epitopes on the HIV-1 envelope glycoprotein. The combined multivalency and multispecificity translates into extraordinary neutralization potency and pan-neutralization of HIV-1 strains, surpassing that of the most potent anti-HIV broadly neutralizing antibody cocktails. Deep mining of B cell repertoires of HIV-1–infected individuals has resulted in the isolation of dozens of HIV-1 broadly neutralizing antibodies (bNAbs). Yet, it remains uncertain whether any such bNAbs alone are sufficiently broad and potent to deploy therapeutically. Here, we engineered HIV-1 bNAbs for their combination on a single multispecific and avid molecule via direct genetic fusion of their Fab fragments to the human apoferritin light chain. The resulting molecule demonstrated a remarkable median IC50 value of 0.0009 µg/mL and 100% neutralization coverage of a broad HIV-1 pseudovirus panel (118 isolates) at a 4 µg/mL cutoff—a 32-fold enhancement in viral neutralization potency compared to a mixture of the corresponding HIV-1 bNAbs. Importantly, Fc incorporation on the molecule and engineering to modulate Fc receptor binding resulted in IgG-like bioavailability in vivo. This robust plug-and-play antibody design is relevant against indications where multispecificity and avidity are leveraged simultaneously to mediate optimal biological activity.
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13
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Abstract
Antibodies are an integral part of many biological assays and biotherapeutics. However, the sources from which antibodies are derived frequently contain other contaminants which may interfere with assays or cause adverse reactions if administered in vivo. Therefore, a means of isolating these antibodies from their source at high levels of purity is critical. Affinity chromatography is currently one of the most widely applied methods for the purification of antibodies. This method relies on specific and reversible, interactions between antibody structures, or recombinant tags fused to these structures, and ligands immobilized on solid support matrices, generally within a column. Herein, common chromatographic methods applied to antibody purification are described. These include the purification of IgG, and its recombinant forms, through protein A, protein G and immobilized metal affinity chromatography.
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Affiliation(s)
- Arabelle Cassedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland.
- Hamad Bin Khalifa University, Doha, Qatar.
- Qatar Foundation, Doha, Qatar.
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14
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Frensch M, Jäger C, Müller PF, Tadić A, Wilhelm I, Wehrum S, Diedrich B, Fischer B, Meléndez AV, Dengjel J, Eibel H, Römer W. Bacterial lectin BambL acts as a B cell superantigen. Cell Mol Life Sci 2021; 78:8165-8186. [PMID: 34731252 PMCID: PMC8629787 DOI: 10.1007/s00018-021-04009-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 10/03/2021] [Accepted: 10/21/2021] [Indexed: 11/29/2022]
Abstract
B cell superantigens crosslink conserved domains of B cell receptors (BCRs) and cause dysregulated, polyclonal B cell activation irrespective of normal BCR-antigen complementarity. The cells typically succumb to activation-induced cell death, which can impede the adaptive immune response and favor infection. In the present study, we demonstrate that the fucose-binding lectin of Burkholderia ambifaria, BambL, bears functional resemblance to B cell superantigens. By engaging surface glycans, the bacterial lectin activated human peripheral blood B cells, which manifested in the surface expression of CD69, CD54 and CD86 but became increasingly cytotoxic at higher concentrations. The effects were sensitive to BCR pathway inhibitors and excess fucose, which corroborates a glycan-driven mode of action. Interactome analyses in a model cell line suggest BambL binds directly to glycans of the BCR and regulatory coreceptors. In vitro, BambL triggered BCR signaling and induced CD19 internalization and degradation. Owing to the lectin's six binding sites, we propose a BCR activation model in which BambL functions as a clustering hub for receptor glycans, modulates normal BCR regulation, and induces cell death through exhaustive activation.
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Affiliation(s)
- Marco Frensch
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Christina Jäger
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Peter F Müller
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Annamaria Tadić
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Isabel Wilhelm
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Sarah Wehrum
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Britta Diedrich
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Dermatology, University Medical Center and University of Freiburg, Freiburg, Germany
| | - Beate Fischer
- Center for Chronic Immunodeficiency, CCI and University Medical Center Freiburg, Freiburg, Germany
| | - Ana Valeria Meléndez
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Joern Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Dermatology, University Medical Center and University of Freiburg, Freiburg, Germany
| | - Hermann Eibel
- Center for Chronic Immunodeficiency, CCI and University Medical Center Freiburg, Freiburg, Germany.
| | - Winfried Römer
- Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany.
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15
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Rahmati S, Torkashvand F, Amanlou M, Bagherzadeh K, Fard Esfahani P, Aghamirza Moghim Aliabadi H, Vaziri B. Computational Engineering of Protein L to Achieve an Optimal Affinity Chromatography Resin for Purification of Antibody Fragments. Anal Chem 2021; 93:15253-15261. [PMID: 34747593 DOI: 10.1021/acs.analchem.1c01871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein L affinity chromatography is a useful method for the purification of antibody fragments containing kappa light chains. In affinity chromatography, increasing the binding affinity leads to increased product purity, recovery, and dynamic binding capacity (DBC). In this study, molecular docking and molecular dynamics simulation techniques were used to design the engineered Protein L with higher affinity to the kappa light chain. Each engineered ligand was produced as a recombinant protein and coupled to a solid matrix. The purity, recovery, and DBC of the engineered resins were evaluated and then compared to those of a commercially available resin. The results showed important parameters for engineering more efficient Protein L ligands for affinity chromatography.
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Affiliation(s)
- Saman Rahmati
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Torkashvand
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Kowsar Bagherzadeh
- Eye Research Center, The Five Senses Institute Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran 1445613131, Iran.,Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | | | | | - Behrouz Vaziri
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
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16
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Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies). Proc Natl Acad Sci U S A 2021; 118:2115001118. [PMID: 34620716 PMCID: PMC8521671 DOI: 10.1073/pnas.2115001118] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: 1) a Fab fragment of an antibody directed against the nanobody and 2) a nanobody-binding protein A fragment fused to maltose binding protein and Fab-binding domains. The overall ensemble of ∼120 kDa, called Legobody, does not perturb the nanobody-target interaction, is easily recognizable in EM images due to its unique shape, and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23-kDa membrane protein, resulting in a map at 3.2-Å overall resolution with density sufficient for de novo model building, and for the 22-kDa receptor-binding domain (RBD) of SARS-CoV-2 spike protein, resulting in a map at 3.6-Å resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.
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17
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Borowska MT, Drees C, Yarawsky AE, Viswanathan M, Ryan SM, Bunker JJ, Herr AB, Bendelac A, Adams EJ. The molecular characterization of antibody binding to a superantigen-like protein from a commensal microbe. Proc Natl Acad Sci U S A 2021; 118:e2023898118. [PMID: 34548394 PMCID: PMC8488583 DOI: 10.1073/pnas.2023898118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2021] [Indexed: 11/18/2022] Open
Abstract
Microorganisms have coevolved diverse mechanisms to impair host defenses. A major one, superantigens, can result in devastating effects on the immune system. While all known superantigens induce vast immune cell proliferation and come from opportunistic pathogens, recently, proteins with similar broad specificity to antibody variable (V) domain families were identified in a commensal microbiota. These proteins, identified in the human commensal Ruminococcus gnavus, are called immunoglobulin-binding protein (Ibp) A and B and have been shown to activate B cells in vitro expressing either human VH3 or murine VH5/6/7. Here, we provide molecular and functional studies revealing the basis of this Ibp/immunoglobulin (Ig) interaction. The crystal structure and biochemical assays of a truncated IbpA construct in complex with mouse VH5 antigen-binding fragment (Fab) shows a binding of Ig heavy chain framework residues to the Ibp Domain D and the C-terminal heavy chain binding domain (HCBD). We used targeted mutagenesis of contact residues and affinity measurements and performed studies of the Fab-IbpA complex to determine the stoichiometry between Ibp and VH domains, suggesting Ibp may serve to cluster full-length IgA antibodies in vivo. Furthermore, in vitro stimulation experiments indicate that binding of the Ibp HCBD alone is sufficient to activate responsive murine B cell receptors. The presence of these proteins in a commensal microbe suggest that binding a broad repertoire of immunoglobulins, particularly in the gut/microbiome environment, may provide an important function in the maintenance of host/microbiome homeostasis contrasting with the pathogenic role of structurally homologous superantigens expressed by pathogens.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Christoph Drees
- Department of Pathology, University of Chicago, Chicago, IL 60637
| | - Alexander E Yarawsky
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | | | - Sean M Ryan
- Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Jeffrey J Bunker
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Andrew B Herr
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Albert Bendelac
- Department of Pathology, University of Chicago, Chicago, IL 60637;
- Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Erin J Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637;
- Committee on Immunology, University of Chicago, Chicago, IL 60637
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18
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Deacy AM, Gan SKE, Derrick JP. Superantigen Recognition and Interactions: Functions, Mechanisms and Applications. Front Immunol 2021; 12:731845. [PMID: 34616400 PMCID: PMC8488440 DOI: 10.3389/fimmu.2021.731845] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/30/2021] [Indexed: 12/27/2022] Open
Abstract
Superantigens are unconventional antigens which recognise immune receptors outside their usual recognition sites e.g. complementary determining regions (CDRs), to elicit a response within the target cell. T-cell superantigens crosslink T-cell receptors and MHC Class II molecules on antigen-presenting cells, leading to lymphocyte recruitment, induction of cytokine storms and T-cell anergy or apoptosis among many other effects. B-cell superantigens, on the other hand, bind immunoglobulins on B-cells, affecting opsonisation, IgG-mediated phagocytosis, and driving apoptosis. Here, through a review of the structural basis for recognition of immune receptors by superantigens, we show that their binding interfaces share specific physicochemical characteristics when compared with other protein-protein interaction complexes. Given that antibody-binding superantigens have been exploited extensively in industrial antibody purification, these observations could facilitate further protein engineering to optimize the use of superantigens in this and other areas of biotechnology.
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Affiliation(s)
- Anthony M. Deacy
- School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Experimental Drug Development Centre – Bioinformatics Institute (EDDC-BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore
- James Cook University, Singapore, Singapore
| | - Jeremy P. Derrick
- School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
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19
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Cockburn DW, Kibler R, Brown HA, Duvall R, Moraïs S, Bayer E, Koropatkin NM. Structure and substrate recognition by the Ruminococcus bromii amylosome pullulanases. J Struct Biol 2021; 213:107765. [PMID: 34186214 DOI: 10.1016/j.jsb.2021.107765] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/11/2021] [Accepted: 06/23/2021] [Indexed: 01/15/2023]
Abstract
Pullulanases are glycoside hydrolase family 13 (GH13) enzymes that target α1,6 glucosidic linkages within starch and aid in the degradation of the α1,4- and α1,6- linked glucans pullulan, glycogen and amylopectin. The human gut bacterium Ruminococcus bromii synthesizes two extracellular pullulanases, Amy10 and Amy12, that are incorporated into the multiprotein amylosome complex that enables the digestion of granular resistant starch from the diet. Here we provide a comparative biochemical analysis of these pullulanases and the x-ray crystal structures of the wild type and the nucleophile mutant D392A of Amy12 complexed with maltoheptaose and 63-α-D glucosyl-maltotriose. While Amy10 displays higher catalytic efficiency on pullulan and cleaves only α1,6 linkages, Amy12 has some activity on α1,4 linkages suggesting that these enzymes are not redundant within the amylosome. Our structures of Amy12 include a mucin-binding protein (MucBP) domain that follows the C-domain of the GH13 fold, an atypical feature of these enzymes. The wild type Amy12 structure with maltoheptaose captured two oligosaccharides in the active site arranged as expected following catalysis of an α1,6 branch point in amylopectin. The nucleophile mutant D392A complexed with maltoheptaose or 63-α-D glucosyl-maltotriose captured β-glucose at the reducing end in the -1 subsite, facilitated by the truncation of the active site aspartate and stabilized by stacking with Y279. The core interface between the co-crystallized ligands and Amy12 occurs within the -2 through + 1 subsites, which may allow for flexible recognition of α1,6 linkages within a variety of starch structures.
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Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Ryan Kibler
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Rebecca Duvall
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Sarah Moraïs
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Edward Bayer
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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20
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Kodali P, Schoeder CT, Schmitz S, Crowe JE, Meiler J. RosettaCM for antibodies with very long HCDR3s and low template availability. Proteins 2021; 89:1458-1472. [PMID: 34176159 PMCID: PMC8492515 DOI: 10.1002/prot.26166] [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: 04/13/2021] [Accepted: 05/26/2021] [Indexed: 11/07/2022]
Abstract
Antibody-antigen co-crystal structures are a valuable resource for the fundamental understanding of antibody-mediated immunity. Determination of structures with antibodies in complex with their antigens, however, is a laborious task without guarantee of success. Therefore, homology modeling of antibodies and docking to their respective antigens has become a very important technique to drive antibody and vaccine design. The quality of the antibody modeling process is critical for the success of these endeavors. Here, we compare different computational protocols for predicting antibody structure from sequence in the biomolecular modeling software Rosetta-all of which use multiple existing antibody structures to guide modeling. Specifically, we compare protocols developed solely to predict antibody structure (RosettaAntibody, AbPredict) with a universal homology modeling protocol (RosettaCM). Following recent advances in homology modeling with multiple templates simultaneously, we propose that the use of multiple templates over the same antibody regions may improve modeling performance. To evaluate whether multi-template comparative modeling with RosettaCM can improve the modeling accuracy of antibodies over existing methods, this study compares the performance of the three modeling algorithms when modeling human antibodies taken from antibody-antigen co-crystal structures. In these benchmarking experiments, RosettaCM outperformed other methods when modeling antibodies with long HCDR3s and few available templates.
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Affiliation(s)
- Pranav Kodali
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Clara T Schoeder
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Samuel Schmitz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Departments of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.,Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
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21
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Abstract
In the past 30 years, highly specific drugs, known as antibodies, have conquered the biopharmaceutical market. In addition to monoclonal antibodies (mAbs), antibody fragments are successfully applied. However, recombinant production faces challenges. Process analytical tools for monitoring and controlling production processes are scarce and time-intensive. In the downstream process (DSP), affinity ligands are established as the primary and most important step, while the application of other methods is challenging. The use of these affinity ligands as monitoring tools would enable a platform technology to monitor process steps in the USP and DSP. In this review, we highlight the current applications of affinity ligands (proteins A, G, and L) and discuss further applications as process analytical tools.
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22
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Chen SW, Zhang W. Current trends and challenges in the downstream purification of bispecific antibodies. Antib Ther 2021; 4:73-88. [PMID: 34056544 PMCID: PMC8155696 DOI: 10.1093/abt/tbab007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/06/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Bispecific antibodies (bsAbs) represent a highly promising class of biotherapeutic modality. The downstream processing of this class of antibodies is therefore of crucial importance in ensuring that these products can be obtained with high purity and yield. Due to the various fundamental structural similarities between bsAbs and monoclonal antibodies (mAbs), many of the current bsAb downstream purification methodologies are based on the established purification processes of mAbs, where affinity, charge, size, hydrophobicity and mixed-mode-based purification are frequently employed. Nevertheless, the downstream processing of bsAbs presents a unique set of challenges due to the presence of bsAb-specific byproducts, such as mispaired products, undesired fragments and higher levels of aggregates, that are otherwise absent or present in lower levels in mAb cell culture supernatants, thus often requiring the design of additional purification strategies in order to obtain products of high purity. Here, we outline the current major purification methods of bsAbs, highlighting the corresponding solutions that have been proposed to circumvent the unique challenges presented by this class of antibodies, including differential affinity chromatography, sequential affinity chromatography and the use of salt additives and pH gradients or multistep elutions in various modes of purification. Finally, a perspective towards future process development is offered.
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Affiliation(s)
- Serene W Chen
- Downstream Processing Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Singapore
| | - Wei Zhang
- Downstream Processing Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Singapore
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23
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Chen SW, Tan D, Yang YS, Zhang W. Investigation of the effect of salt additives in Protein L affinity chromatography for the purification of tandem single-chain variable fragment bispecific antibodies. MAbs 2021; 12:1718440. [PMID: 31983280 PMCID: PMC6999846 DOI: 10.1080/19420862.2020.1718440] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Tandem single-chain variable fragment (scFv) bispecific antibodies (bsAb) are one of the most promising bsAb formats reported thus far. Yet, because of their increased aggregation propensity, high impurity content due to low expression level, smaller size and lack of the Fc region, it is challenging to isolate these products with high yield and purity within a limited number of purification steps in a scalable fashion. A robust purification process that is able to circumvent these issues is therefore of critical importance to allow effective isolation of this group of antibodies. We investigated the addition of sodium chloride (NaCl), calcium chloride (CaCl2), and L-arginine monohydrochloride (Arg·HCl) to the elution buffer of Protein L affinity chromatography, and propose here a novel mechanism for the modification of Protein L binding avidity that can lead to enhanced high molecular weight (HMW)-monomer separation, a preferential strengthening effect of the HMW-Protein L interaction compared to the monomer-Protein L interaction. In particular, we found Arg·HCl to be the most effective salt additive in terms of purity and recovery. The mechanism we propose is different from the widely reported chaotropic effect exerted by salt additives observed in Protein A chromatography. We also demonstrate here that a final eluate containing <1% HMW species and <100 ppm host cell proteins can be obtained within a two-step process with an overall yield of 65%, highlighting the promising suitability of Protein L affinity chromatography for the purification of kappa light chain-containing tandem scFv bsAb.
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Affiliation(s)
- Serene W Chen
- Downstream Processing Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore
| | - Darryl Tan
- Downstream Processing Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore
| | - Yuan Sheng Yang
- Animal Cell Technology Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore
| | - Wei Zhang
- Downstream Processing Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore
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24
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Turner BL, Kilgour KM, Stine SJ, Daniele M, Menegatti S. Dual-Affinity Ratiometric Quenching (DARQ) Assay for the Quantification of Therapeutic Antibodies in CHO-S Cell Culture Fluids. Anal Chem 2020; 92:16274-16283. [DOI: 10.1021/acs.analchem.0c04269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Brendan L. Turner
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, North Carolina 27695, United States
| | - Katie M. Kilgour
- Department of Chemical & Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina 27695, United States
| | - Sydney J. Stine
- Department of Chemical & Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina 27695, United States
| | - Michael Daniele
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, North Carolina 27695, United States
- Department of Electrical & Computer Engineering, North Carolina State University, 890 Oval Drive, Raleigh, North Carolina 27695, United States
| | - Stefano Menegatti
- Department of Chemical & Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina 27695, United States
- Biomanufacturing Training and Education Center (BTEC), 850 Oval Drive, Raleigh, North Carolina 27606, United States
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25
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Wang Y, Chen X, Wang Y, Li Y. Impact of salt concentration in mobile phase on antibody retention in Protein A, Protein L and KappaSelect affinity chromatography. Protein Expr Purif 2020; 178:105786. [PMID: 33157199 DOI: 10.1016/j.pep.2020.105786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/12/2020] [Accepted: 10/30/2020] [Indexed: 02/04/2023]
Abstract
Protein A, Protein L and KappaSelect affinity resins have been widely used for antibody purification. Elution of antibody bound to these resins is typically achieved by acidic pH. In addition, elution can be moderately adjusted by tuning the salt concentration in mobile phase as hydrophobic interactions play a major role in binding. In this study, we assessed the impact of salt concentration in mobile phase on antibody retention in these three types of affinity chromatography. The data suggest that salt concentration has a bigger impact on retention in the two light chain-binding affinity columns (i.e., Protein L and KappaSelect) than in Protein A column. In particular, lowering salt concentration in mobile phase for Protein L and KappaSelect columns allows elution become feasible at higher pH. In addition, this finding suggests that wash in these two types of column aimed at removing weakly-bound byproducts can also be performed at increased pH by lowering salt concentration in the wash buffer. Rendering wash and elution feasible at higher pH has practical value for cases where the target antibodies are sensitive to stringent conditions.
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Affiliation(s)
- Ying Wang
- Technology and Process Development (TPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Xiujuan Chen
- Technology and Process Development (TPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Ying Wang
- Technology and Process Development (TPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Yifeng Li
- Technology and Process Development (TPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China.
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26
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Dong J, Miyake C, Yasuda T, Oyama H, Morita I, Tsukahara T, Takahashi M, Jeong HJ, Kitaguchi T, Kobayashi N, Ueda H. PM Q-probe: A fluorescent binding protein that converts many antibodies to a fluorescent biosensor. Biosens Bioelectron 2020; 165:112425. [DOI: 10.1016/j.bios.2020.112425] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 12/14/2022]
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27
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Fu X, Tao L, Wu W, Zhang X. Arming HSV-Based Oncolytic Viruses with the Ability to Redirect the Host's Innate Antiviral Immunity to Attack Tumor Cells. MOLECULAR THERAPY-ONCOLYTICS 2020; 19:33-46. [PMID: 33024817 PMCID: PMC7530262 DOI: 10.1016/j.omto.2020.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023]
Abstract
One of the major hurdles for cancer immunotherapy is the host's innate antiviral defense mechanisms. They include innate immune cells, such as natural killer (NK) cells and macrophages, which can be recruited within hours to the site of injection to clear the introduced oncolytic viruses. Here, we report a strategy to redirect these infiltrating innate immune cells to attack tumor cells instead by arming herpes simplex virus (HSV)-derived oncolytic viruses with secreted chimeric molecules that can engage these innate immune cells with tumor cells to kill the latter. These chimeric molecules have, at their N terminus, a custom-binding moiety for a tumor-associated antigen (TAA) and at their C terminus, protein L (PL) that binds to immunoglobulins (Igs). The binding of PL to Igs exposes the Fc to the Fc receptors on the surface of the innate immune cells, trigging them to attack the engaged tumor cells. In vitro and in vivo evaluation in a murine tumor model with limited permissiveness to oncolytic HSVs showed that arming the viruses with these chimeric molecules significantly boosts the killing effect and therapeutic activity. Moreover, our data also showed that the combined killing effect from the engaged innate immune cells and the oncolytic virus resulted in a more efficient stimulation of neoantigen-specific antitumor immunity than the virotherapy alone. Our data suggest that arming an oncolytic virus with this strategy represents a unique and pragmatic way of potentiating the oncolytic and immunotherapeutic effect of virotherapy.
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Affiliation(s)
- Xinping Fu
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell Signaling, University of Houston, Houston, TX, USA
| | - Lihua Tao
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell Signaling, University of Houston, Houston, TX, USA
| | - Wanfu Wu
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell Signaling, University of Houston, Houston, TX, USA
| | - Xiaoliu Zhang
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell Signaling, University of Houston, Houston, TX, USA
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Ling WL, Lua WH, Gan SKE. Sagacity in antibody humanization for therapeutics, diagnostics and research purposes: considerations of antibody elements and their roles. Antib Ther 2020; 3:71-79. [PMID: 33928226 PMCID: PMC7990220 DOI: 10.1093/abt/tbaa005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/27/2020] [Accepted: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
The humanization of antibodies for therapeutics is a critical process that can determine the success of antibody drug development. However, the science underpinning this process remains elusive with different laboratories having very different methods. Well-funded laboratories can afford automated high-throughput screening methods to derive their best binder utilizing a very expensive initial set of equipment affordable only to a few. Often within these high-throughput processes, only standard key parameters, such as production, binding and aggregation are analyzed. Given the lack of suitable animal models, it is only at clinical trials that immunogenicity and allergy adverse effects are detected through anti-human antibodies as per FDA guidelines. While some occurrences that slip through can be mitigated by additional desensitization protocols, such adverse reactions to grafted humanized antibodies can be prevented at the humanization step. Considerations such as better antibody localization, avoidance of unspecific interactions to superantigens and the tailoring of antibody dependent triggering of immune responses, the antibody persistence on cells, can all be preemptively considered through a holistic sagacious approach, allowing for better outcomes in therapy and for research and diagnostic purposes.
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Affiliation(s)
- Wei-Li Ling
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Wai-Heng Lua
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- p53 Laboratory, ASTAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
- Experimental Drug Development Center, ASTAR, 10 Biopolis Road, #05-01, Chromos, Singapore 138670
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Human IgA Monoclonal Antibodies That Neutralize Poliovirus, Produced by Hybridomas and Recombinant Expression. Antibodies (Basel) 2020; 9:antib9010005. [PMID: 32121092 PMCID: PMC7148538 DOI: 10.3390/antib9010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/01/2020] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
Poliovirus (PV)-specific intestinal IgAs are important for cessation of PV shedding in the gastrointestinal tract following an acute infection with wild type or vaccine-derived PV strains. We sought to produce IgA monoclonal antibodies (mAbs) with PV neutralizing activity. We first performed de novo IgA discovery from primary human B cells using a hybridoma method that allows assessment of mAb binding and expression on the hybridoma surface: On-Cell mAb Screening (OCMS™). Six IgA1 mAbs were cloned by this method; three potently neutralized type 3 Sabin and wt PV strains. The hybridoma mAbs were heterogeneous, expressed in monomeric, dimeric, and aberrant forms. We also used recombinant methods to convert two high-potency anti-PV IgG mAbs into dimeric IgA1 and IgA2 mAbs. Isotype switching did not substantially change their neutralization activities. To purify the recombinant mAbs, Protein L binding was used, and one of the mAbs required a single amino acid substitution in its κ LC in order to enable protein L binding. Lastly, we used OCMS to assess IgA expression on the surface of hybridomas and transiently transfected, adherent cells. These studies have generated potent anti-PV IgA mAbs, for use in animal models, as well as additional tools for the discovery and production of human IgA mAbs.
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30
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Dahal N, Nowitzke J, Eis A, Popa I. Binding-Induced Stabilization Measured on the Same Molecular Protein Substrate Using Single-Molecule Magnetic Tweezers and Heterocovalent Attachments. J Phys Chem B 2020; 124:3283-3290. [DOI: 10.1021/acs.jpcb.0c00167] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Joel Nowitzke
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
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Drikic M, Olsen S, De Buck J. Detecting total immunoglobulins in diverse animal species with a novel split enzymatic assay. BMC Vet Res 2019; 15:374. [PMID: 31660970 PMCID: PMC6816151 DOI: 10.1186/s12917-019-2126-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 10/01/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Total immunolobulin G concentration is a useful, albeit underutilized, diagnostic parameter for health assessments of non-domestic animal species, due to a lack of functional diagnostic tools. Traditional assays, including enzyme-linked immunosorbent assay or radial immunodiffusion, require development of specific reagents (e.g., polyclonal antisera and appropriate protocols) for each animal species, precluding wide and easy adoption in wildlife welfare. As an alternative, bacterial virulence factors able to bind IgGs in antigen-independent manner can be used. To further simplify the diagnostic procedure and increase the number of species recognized by an assay, in this study a recently developed Split Trehalase immunoglobulin assay (STIGA) with bIBPs as a sensing elements was used to detect antibodies in 29 species from 9 orders. Three bacterial immunoglobulin binding proteins (protein G, protein A and protein L) were incorporated into STIGA reagents to increase the number of species recognized. RESULTS IgG concentrations were detected through glucose production and produced signals were categorized in 4 categories, from not active to strong signal. Activation was detected in almost all tested animal species, apart from birds. Incorporation of Protein G, Protein A and Protein L allowed detection of IgGs in 62, 15.5 and 6.9% of species with a strong signal, respectively. Assays combining 2 bacterial immunoglobulin binding proteins as sensing element generally gave poorer performance than assays with the same bacterial immunoglobulin binding proteins fused to both trehalase fragments. CONCLUSIONS STIGA assays have potential to be further developed into an easily adoptable diagnostic test for total amount of IgGs in almost any serum sample, independent of species.
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Affiliation(s)
- Marija Drikic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Steven Olsen
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
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32
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Hannachi E, Bouratbine A, Mousli M. Enhancing the detection of Toxoplasma gondii via an anti-SAG1 scFv-alkaline phosphatase immunoconjugate. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2019; 23:e00360. [PMID: 31341791 PMCID: PMC6630058 DOI: 10.1016/j.btre.2019.e00360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/29/2019] [Accepted: 06/30/2019] [Indexed: 12/11/2022]
Abstract
The purpose of this study was to implement a fluorometric method for enhancing the detection sensitivity of Toxoplasma gondii in biological fluids. To address this challenge, we designed and produced a recombinant immunoconjugate tool based on a single-chain antibody fragment anti-T. gondii SAG1 antigen (scFvSG15) genetically fused to the bacterial alkaline phosphatase (AP) using 4-methyl-umbelliferyl-phosphate as fluorogenic substrate. The anti-SAG1 scFv-AP conjugate was fully bifunctional and was used successfully in different assays including immunoblot, fluorometric ELISA and direct immunofluorescence. The fluorometric immunoassay afforded an extremely low detection limit (1 tachyzoite/well), which was in agreement with the real-time PCR control test. The immunofluorescence imaging has provided captivating visual evidence of T. gondii detection. These results strongly suggest that the recombinant anti-SAG1-AP conjugate generated here might serve as useful and highly sensitive immunoassay probe to direct detect T. gondii in a one-step procedure, opening up new perspectives for diagnosis of toxoplasmosis.
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Affiliation(s)
| | | | - Mohamed Mousli
- Laboratoire de Parasitologie Médicale, Biotechnologies et Biomolécules, LR11-IPT06, Institut Pasteur de Tunis, Université Tunis El-Manar, 13 Place Pasteur -BP74, 1002 Tunis-Belvédère, Tunisia
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33
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Chen C, Wakabayashi T, Muraoka M, Shu F, Wei Shan C, Chor Kun C, Tim Jang C, Soehano I, Shimizu Y, Igawa T, Nezu JI. Controlled conductivity at low pH in Protein L chromatography enables separation of bispecific and other antibody formats by their binding valency. MAbs 2019; 11:632-638. [PMID: 30898021 DOI: 10.1080/19420862.2019.1583996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The complex molecular formats of recent therapeutic antibodies, including bispecific antibodies, antibody fragments, and other fusion proteins, makes the task of purifying the desired molecules in a limited number of purification steps more and more challenging. Manufacturing these complicated biologics can be substantially improved in the affinity capture stage if the simple bind-and-elute mode is accompanied by targeted removal of the impurities, such as mis-paired antibodies and oligomers or aggregates. Here, we report a method, based on the binding valency to Protein L resin, of separating proteins during the elution step by simply controlling the conductivity at low pH. We show that the method efficiently separated targeted antibodies from mis-paired and aggregated species. Notably, the number of Protein L binding sites can be built into the molecule by design to facilitate the purification. This method may be useful for purifying various antibody formats at laboratory and manufacturing scales.
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Affiliation(s)
- Chen Chen
- a Antibody Generation Group, Research Division , Chugai Pharmabody Research Pte. Ltd , Singapore
| | - Tetsuya Wakabayashi
- b Discovery Biologics Department, Research Division , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Masaru Muraoka
- a Antibody Generation Group, Research Division , Chugai Pharmabody Research Pte. Ltd , Singapore
| | - Feng Shu
- a Antibody Generation Group, Research Division , Chugai Pharmabody Research Pte. Ltd , Singapore
| | - Chia Wei Shan
- a Antibody Generation Group, Research Division , Chugai Pharmabody Research Pte. Ltd , Singapore
| | - Chong Chor Kun
- a Antibody Generation Group, Research Division , Chugai Pharmabody Research Pte. Ltd , Singapore
| | - Ching Tim Jang
- a Antibody Generation Group, Research Division , Chugai Pharmabody Research Pte. Ltd , Singapore
| | - Ishin Soehano
- a Antibody Generation Group, Research Division , Chugai Pharmabody Research Pte. Ltd , Singapore
| | - Yuichiro Shimizu
- a Antibody Generation Group, Research Division , Chugai Pharmabody Research Pte. Ltd , Singapore.,b Discovery Biologics Department, Research Division , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Tomoyuki Igawa
- b Discovery Biologics Department, Research Division , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan.,c Research Division , Chugai Pharmabody Research Pte. Ltd ., Synapse , Singapore
| | - Jun-Ichi Nezu
- d Research Division , Chugai Pharmaceutical Co., Ltd. , Kamakura , Kanagawa , Japan
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34
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Mueller GA, Min J, Foo ACY, Pomés A, Pedersen LC. Structural Analysis of Recent Allergen-Antibody Complexes and Future Directions. Curr Allergy Asthma Rep 2019; 19:17. [PMID: 30815753 DOI: 10.1007/s11882-019-0848-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
PURPOSE OF REVIEW Allergen-antibody complexes are extremely valuable in describing the detailed molecular features of epitopes. This review summarizes insights gained from recently published co-structures and what obstacles impede the acquisition of further data. RECENT FINDINGS Structural epitope data helped define the epitopes of two anti-Fel d 1 antibodies undergoing phase I clinical trials, providing a greater level of detail than was possible through hydrogen-deuterium exchange protection studies. Separately, a human camelid-like antibody structure with lysozyme described several unique features in a long variable loop that interacted with the active site cleft of Gal d 4. Finally, a co-structure conclusively demonstrated that Phl p 7 could function as a superantigen and that an antibody could simultaneously recognize two epitopes. These remarkable assertions would not have been possible without visualization of the complex. Only three new complexes have appeared in the last few years, suggesting that there are major impediments to traditional production and crystallization. The structural data was extremely valuable in describing epitopes. New techniques like cryo-EM may provide an alternative to crystallography.
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Affiliation(s)
- Geoffrey A Mueller
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA.
| | - Jungki Min
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA
| | - Alexander C Y Foo
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA
| | - Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA, USA
| | - Lars C Pedersen
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA
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35
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Structure of a patient-derived antibody in complex with allergen reveals simultaneous conventional and superantigen-like recognition. Proc Natl Acad Sci U S A 2018; 115:E8707-E8716. [PMID: 30150373 PMCID: PMC6140506 DOI: 10.1073/pnas.1806840115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibodies classically bind antigens via their complementarity-determining regions, but an alternative mode of interaction involving V-domain framework regions has been observed for some B cell "superantigens." We report the crystal structure of an antibody employing both modes of interaction simultaneously and binding two antigen molecules. This human antibody from an allergic individual binds to the grass pollen allergen Phl p 7. Not only are two allergen molecules bound to each antibody fragment (Fab) but also each allergen molecule is bound by two Fabs: One epitope is recognized classically, the other in a superantigen-like manner. A single allergen molecule thus cross-links two identical Fabs, contrary to the one-antibody-one-epitope dogma, which dictates that a dimeric allergen at least is required for this to occur. Allergens trigger immediate hypersensitivity reactions by cross-linking receptor-bound IgE molecules on effector cells. We found that monomeric Phl p 7 induced degranulation of basophils sensitized solely with this monoclonal antibody expressed as an IgE, demonstrating that the dual specificity has functional consequences. The monomeric state of Phl p 7 and two structurally related allergens was confirmed by size-exclusion chromatography and multiangle laser light scattering, and the results were supported by degranulation studies with the related allergens, a second patient-derived allergen-specific antibody lacking the nonclassical binding site, and mutagenesis of the nonclassically recognized allergen epitope. The antibody dual reactivity and cross-linking mechanism not only have implications for understanding allergenicity and allergen potency but, importantly, also have broader relevance to antigen recognition by membrane Ig and cross-linking of the B cell receptor.
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36
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Bjerregaard-Andersen K, Johannesen H, Abdel-Rahman N, Heggelund JE, Hoås HM, Abraha F, Bousquet PA, Høydahl LS, Burschowsky D, Rojas G, Oscarson S, Løset GÅ, Krengel U. Crystal structure of an L chain optimised 14F7 anti-ganglioside Fv suggests a unique tumour-specificity through an unusual H-chain CDR3 architecture. Sci Rep 2018; 8:10836. [PMID: 30022069 PMCID: PMC6052152 DOI: 10.1038/s41598-018-28918-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/28/2018] [Indexed: 12/13/2022] Open
Abstract
Targeted cancer immunotherapy offers increased efficacy concomitantly with reduced side effects. One antibody with promising clinical potential is 14F7, which specifically recognises the NeuGc GM3 ganglioside. This antigen is found in the plasma membrane of a range of tumours, but is essentially absent from healthy human cells. 14F7 can discriminate NeuGc GM3 from the very similar NeuAc GM3, a common component of cell membranes. The molecular basis for this unique specificity is poorly understood. Here we designed and expressed 14F7-derived single-chain Fvs (scFvs), which retained the specificity of the parent antibody. Detailed expression and purification protocols are described as well as the synthesis of the NeuGc GM3 trisaccharide. The most successful scFv construct, which comprises an alternative variable light chain (VLA), allowed structure determination to 2.2 Å resolution. The structure gives insights into the conformation of the important CDR H3 loop and the suspected antigen binding site. Furthermore, the presence of VLA instead of the original VL elucidates how this subdomain indirectly stabilises the CDR H3 loop. The current work may serve as a guideline for the efficient production of scFvs for structure determination.
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Affiliation(s)
| | - Hedda Johannesen
- Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway
| | - Noha Abdel-Rahman
- Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway.,Department of Biochemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Julie Elisabeth Heggelund
- Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway.,School of Biomedical Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Fana Abraha
- School of Chemistry, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Paula A Bousquet
- Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway
| | - Lene Støkken Høydahl
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, NO-0372 Oslo, Norway
| | - Daniel Burschowsky
- Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway.,Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7HB, UK
| | - Gertrudis Rojas
- Center of Molecular Immunology, Calle 216 esq 15, Atabey, Playa, La Habana, CP, 11300, Cuba
| | - Stefan Oscarson
- School of Chemistry, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Geir Åge Løset
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, NO-0372 Oslo, Norway. .,Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway. .,Nextera AS, NO-0349 Oslo, Norway.
| | - Ute Krengel
- Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway.
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Li H, Tatematsu K, Somiya M, Iijima M, Kuroda S. Development of a macrophage-targeting and phagocytosis-inducing bio-nanocapsule-based nanocarrier for drug delivery. Acta Biomater 2018; 73:412-423. [PMID: 29673839 DOI: 10.1016/j.actbio.2018.04.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 12/11/2022]
Abstract
Macrophage hyperfunction or dysfunction is tightly associated with various diseases, such as osteoporosis, inflammatory disorder, and cancers. However, nearly all conventional drug delivery system (DDS) nanocarriers utilize endocytosis for entering target cells; thus, the development of macrophage-targeting and phagocytosis-inducing DDS nanocarriers for treating these diseases is required. In this study, we developed a hepatitis B virus (HBV) envelope L particle (i.e., bio-nanocapsule (BNC)) outwardly displaying a tandem form of protein G-derived IgG Fc-binding domain and protein L-derived IgG Fab-binding domain (GL-BNC). When conjugated with the macrophage-targeting ligand, mouse IgG2a (mIgG2a), the GL-BNC itself, and the liposome-fused GL-BNC (i.e., GL-virosome) spontaneously initiated aggregation by bridging between the Fc-binding domain and Fab-binding domain with mIgG2a. The aggregates were efficiently taken up by macrophages, whereas this was inhibited by latrunculin B, a phagocytosis-specific inhibitor. The mIgG2a-GL-virosome containing doxorubicin exhibited higher cytotoxicity toward macrophages than conventional liposomes and other BNC-based virosomes. Thus, GL-BNCs and GL-virosomes may constitute promising macrophage-targeting and phagocytosis-inducing DDS nanocarriers. STATEMENT OF SIGNIFICANCE We have developed a novel macrophage-targeting and phagocytosis-inducing bio-nanocapsule (BNC)-based nanocarrier named GL-BNC, which comprises a hepatitis B virus envelope L particle outwardly displaying protein G-derived IgG Fc- and protein L-derived IgG Fab-binding domains in tandem. The GL-BNC alone or liposome-fused form (GL-virosomes) could spontaneously aggregate when conjugated with macrophage-targeting IgGs, inducing phagocytosis by the interaction between IgG Fc of aggregates and FcγR on phagocytes. Thereby these aggregates were efficiently taken up by macrophages. GL-virosomes containing doxorubicin exhibited higher cytotoxicity towards macrophages than ZZ-virosomes and liposomes. Our results suggested that GL-BNCs and GL-virosomes would serve as promising drug delivery system nanocarriers for targeting delivery to macrophages.
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Affiliation(s)
- Hao Li
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki 567-0047, Japan
| | - Kenji Tatematsu
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki 567-0047, Japan
| | - Masaharu Somiya
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki 567-0047, Japan
| | - Masumi Iijima
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki 567-0047, Japan
| | - Shun'ichi Kuroda
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki 567-0047, Japan.
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38
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Huang G, Zhong Z, Miersch S, Sidhu SS, Hou SC, Wu D. Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity. J Vis Exp 2018:57357. [PMID: 29782009 PMCID: PMC6101057 DOI: 10.3791/57357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Demand for monoclonal antibodies (mAbs) in basic research and medicine is increasing yearly. Hybridoma technology has been the dominant method for mAb development since its first report in 1975. As an alternative technology, phage display methods for mAb development are increasingly attractive since Humira, the first phage-derived antibody and one of the best-selling mAbs, was approved for clinical treatment of rheumatoid arthritis in 2002. As a non-animal based mAb development technology, phage display bypasses antigen immunogenicity, humanization, and animal maintenance that are required from traditional hybridoma technology based antibody development. In this protocol, we describe a method for construction of synthetic phage-displayed Fab libraries with diversities of 109-1010 obtainable with a single electroporation. This protocol consists of: 1) high-efficiency electro-competent cell preparation; 2) extraction of uracil-containing single-stranded DNA (dU-ssDNA); 3) Kunkel's method based oligonucleotide-directed mutagenesis; 4) electroporation and calculation of library size; 5) protein A/L-based enzyme-linked immunosorbent assay (ELISA) for folding and functional diversity evaluation; and 6) DNA sequence analysis of diversity.
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Affiliation(s)
- Ganggang Huang
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University
| | - Zhenwei Zhong
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University
| | - Shane Miersch
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto; Department of Molecular Genetics, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto
| | - Sachdev S Sidhu
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University; Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto; Department of Molecular Genetics, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto
| | - Shin-Chen Hou
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University;
| | - Donghui Wu
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University;
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39
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Nascimento A, Pinto IF, Chu V, Aires-Barros MR, Conde JP, Azevedo AM. Studies on the purification of antibody fragments. Sep Purif Technol 2018. [DOI: 10.1016/j.seppur.2017.12.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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40
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Paloni M, Cavallotti C. Molecular Modeling of the Interaction of Protein L with Antibodies. ACS OMEGA 2017; 2:6464-6472. [PMID: 31457247 PMCID: PMC6645367 DOI: 10.1021/acsomega.7b01123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/27/2017] [Indexed: 06/10/2023]
Abstract
Protein L (PpL) is a bacterial protein which is used in the affinity chromatography stage of the production of monoclonal antibodies because of its ability to form high affinity complexes with the light chains of immunoglobulins. In the present work, the binding interfaces between one domain of PpL and antigen-binding fragments (Fab) have been investigated adopting molecular dynamics with the aim of determining the binding contribution of the residues located at the Fab-PpL interface. Because it is known that PpL binds antibodies through two distinct binding sites with different affinities, simulations were performed for both sites to determine interaction free energies to assess the relative binding contribution of the two sites. Mutational studies were then performed only on the dominant binding site. The binding free energy was evaluated with the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) and umbrella sampling/weighted histogram analysis methods. Key residues for the formation of the dominant binding site complex were identified by means of alanine scanning performed both for the Fab and PpL domains. Residues of the light chain of the antibody that contribute most to binding were found to be located between SER7 and VAL13. Four residues from PpL are important for the stability of the complex: PHE839, LYS840, GLU849, and TYR853. Three residues of PpL that do not contribute to the interaction were mutated to histidine (HIS), which changes its protonation state as a function of pH, to find whether this could allow us to control the binding interaction energy. This can be useful in the elution stage of the affinity chromatography purification of antibodies if PpL is used as a ligand. These residues are GLN835, THR836, and ALA837. Molecular dynamics simulations with both protonated and unprotonated HIS were performed to mimic how changing pH may reflect on protein-ligand interaction energies. The MMPBSA approach was used to evaluate the variation of the affinity of the mutated systems with reference to the wild type. Our results show that these mutations could help in disrupting the complex under acidic conditions without impairing the affinity of PpL for the light chains at higher pHs.
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Fichtner M, Dreyling M, Binder M, Trepel M. The role of B cell antigen receptors in mantle cell lymphoma. J Hematol Oncol 2017; 10:164. [PMID: 29041946 PMCID: PMC5646121 DOI: 10.1186/s13045-017-0533-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/09/2017] [Indexed: 12/15/2022] Open
Abstract
Mantle cell lymphoma (MCL) is characterized by an aggressive clinical course and secondary resistance to currently available therapies in most cases. Therefore, despite recent advances in the treatment of this disease, it is still considered to be incurable in the majority of cases. MCL B cells retain their B cell antigen receptor (BCR) expression during and after neoplastic transformation. BCRs in MCL show distinct patterns of antigen selection and ongoing BCR signaling. However, little is known about the involved antigens and the mechanisms leading to lymphomagenesis and lymphoma progression in MCL. Recent preclinical and clinical studies have established a crucial role of the BCR and the potential of inhibiting its signaling in this disease. This has established the B cell antigen receptor signaling cascade as a very promising therapeutic target to improve outcome in MCL alone or in combination with chemo-immunotherapy in recent years.
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Affiliation(s)
- Michael Fichtner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland.,Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Martin Dreyling
- Department of Medicine III, University Hospital LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Mascha Binder
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Martin Trepel
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany. .,Department of Hematology and Oncology, Augsburg Medical Center, Stenglinstr. 2, 86156, Augsburg, Germany.
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Affiliation(s)
- Nika Kruljec
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
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Su CTT, Ling WL, Lua WH, Poh JJ, Gan SKE. The role of Antibody Vκ Framework 3 region towards Antigen binding: Effects on recombinant production and Protein L binding. Sci Rep 2017. [PMID: 28630463 PMCID: PMC5476676 DOI: 10.1038/s41598-017-02756-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Antibody research has traditionally focused on heavy chains, often neglecting the important complementary role of light chains in antibody formation and secretion. In the light chain, the complementarity-determining region 3 (VL-CDR3) is specifically implicated in disease states. By modulating VL-CDR3 exposure on the scaffold through deletions in the framework region 3 (VL-FWR3), we further investigated the effects on secretion in recombinant production and antigen binding kinetics. Our random deletions of two residues in the VL-FWR3 of a Trastuzumab model showed that the single deletions could impact recombinant production without significant effect on Her2 binding. When both the selected residues were deleted, antibody secretion was additively decreased, and so was Her2 binding kinetics. Interestingly, we also found allosteric effects on the Protein L binding site at VL-FWR1 elicited by these deletions in VL- FWR3. Together, these findings demonstrate the importance of light chain FWR3 in antigen binding, recombinant production, and antibody purification using Protein L.
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Affiliation(s)
- Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wei-Li Ling
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wai-Heng Lua
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jun-Jie Poh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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Bleymüller WM, Lämmermann N, Ebbes M, Maynard D, Geerds C, Niemann HH. MET-activating Residues in the B-repeat of the Listeria monocytogenes Invasion Protein InlB. J Biol Chem 2016; 291:25567-25577. [PMID: 27789707 DOI: 10.1074/jbc.m116.746685] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/26/2016] [Indexed: 12/20/2022] Open
Abstract
The facultative intracellular pathogen Listeria monocytogenes causes listeriosis, a rare but life-threatening disease. Host cell entry begins with activation of the human receptor tyrosine kinase MET through the bacterial invasion protein InlB, which contains an internalin domain, a B-repeat, and three GW domains. The internalin domain is known to bind MET, but no interaction partner is known for the B-repeat. Adding the B-repeat to the internalin domain potentiates MET activation and is required to stimulate Madin-Darby canine kidney (MDCK) cell scatter. Therefore, it has been hypothesized that the B-repeat may bind a co-receptor on host cells. To test this hypothesis, we mutated residues that might be important for binding an interaction partner. We identified two adjacent residues in strand β2 of the β-grasp fold whose mutation abrogated induction of MDCK cell scatter. Biophysical analysis indicated that these mutations do not alter protein structure. We then tested these mutants in human HT-29 cells that, in contrast to the MDCK cells, were responsive to the internalin domain alone. These assays revealed a dominant negative effect, reducing the activity of a construct of the internalin domain and mutated B-repeat below that of the individual internalin domain. Phosphorylation assays of MET and its downstream targets AKT and ERK confirmed the dominant negative effect. Attempts to identify a host cell receptor for the B-repeat were not successful. We conclude that there is limited support for a co-receptor hypothesis and instead suggest that the B-repeat contributes to MET activation through low affinity homodimerization.
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Affiliation(s)
- Willem M Bleymüller
- From the Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Nina Lämmermann
- From the Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Maria Ebbes
- From the Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Daniel Maynard
- From the Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Christina Geerds
- From the Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Hartmut H Niemann
- From the Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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Tatematsu K, Iijima M, Yoshimoto N, Nakai T, Okajima T, Kuroda S. Bio-nanocapsules displaying various immunoglobulins as an active targeting-based drug delivery system. Acta Biomater 2016; 35:238-47. [PMID: 26876802 DOI: 10.1016/j.actbio.2016.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/26/2016] [Accepted: 02/08/2016] [Indexed: 01/05/2023]
Abstract
The bio-nanocapsule (BNC) is an approximately 30-nm particle comprising the hepatitis B virus (HBV) envelope L protein and a lipid bilayer. The L protein harbors the HBV-derived infection machinery; therefore, BNC can encapsulate payloads such as drugs, nucleic acids, and proteins and deliver them into human hepatocytes specifically in vitro and in vivo. To diversify the possible functions of BNC, we generated ZZ-BNC by replacing the domain indispensable for the human hepatotrophic property of BNC (N-terminal region of L protein) with the tandem form of the IgG Fc-binding Z domain of Staphylococcus aureus protein A. Thus, the ZZ-BNC is an active targeting-based drug delivery system (DDS) nanocarrier that depends on the specificity of the IgGs displayed. However, the Z domain limits the animal species and subtypes of IgGs that can be displayed on ZZ-BNC. In this study, we introduced into BNC an Ig κ light chain-binding B1 domain of Finegoldia magna protein L (protein-L B1 domain) and an Ig Fc-binding C2 domain of Streptococcus species protein G (protein-G C2 domain) to produce LG-BNC. The LL-BNC was constructed in a similar way using a tandem form of the protein-L B1 domain. Both LG-BNC and LL-BNC could display rat IgGs, mouse IgG1, human IgG3, and human IgM, all of which not binding to ZZ-BNC, and accumulate in target cells in an antibody specificity-dependent manner. Thus, these BNCs could display a broad spectrum of Igs, significantly improving the prospects for BNCs as active targeting-based DDS nanocarriers. STATEMENT OF SIGNIFICANCE We previously reported that ZZ-BNC, bio-nanocapsule deploying the IgG-binding Z domain of protein A, could display cell-specific antibody in an oriented immobilization manner, and act as an active targeting-based DDS nanocarrier. Since the Z domain can only bind to limited types of Igs, we generated BNCs deploying other Ig-binding domains: LL-BNC harboring the tandem form of Ig-binding domain of protein L, and LG-BNC harboring the Ig binding domains of protein L and protein G sequentially. Both BNCs could display a broader spectrum of Igs than does the ZZ-BNC. When these BNCs displayed anti-CD11c IgG or anti-EGFR IgG, both of which cannot bind to Z domain, they could bind to and then enter their respective target cells.
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Lakhrif Z, Pugnière M, Henriquet C, di Tommaso A, Dimier-Poisson I, Billiald P, Juste MO, Aubrey N. A method to confer Protein L binding ability to any antibody fragment. MAbs 2015; 8:379-88. [PMID: 26683650 PMCID: PMC4966575 DOI: 10.1080/19420862.2015.1116657] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
Recombinant antibody single-chain variable fragments (scFv) are difficult to purify homogeneously from a protein complex mixture. The most effective, specific and fastest method of purification is an affinity chromatography on Protein L (PpL) matrix. This protein is a multi-domain bacterial surface protein that is able to interact with conformational patterns on kappa light chains. It mainly recognizes amino acid residues located at the VL FR1 and some residues in the variable and constant (CL) domain. Not all kappa chains are recognized, however, and the lack of CL can reduce the interaction. From a scFv composed of IGKV10-94 according to IMGT®, it is possible, with several mutations, to transfer the motif from the IGKV12-46 naturally recognized by the PpL, and, with the single mutation T8P, to confer PpL recognition with a higher affinity. A second mutation S24R greatly improves the affinity, in particular by modifying the dissociation rate (kd). The equilibrium dissociation constant (KD) was measured at 7.2 10(-11) M by surface plasmon resonance. It was possible to confer PpL recognition to all kappa chains. This protein interaction can be modulated according to the characteristics of scFv (e.g., stability) and their use with conjugated PpL. This work could be extrapolated to recombinant monoclonal antibodies, and offers an alternative for protein A purification and detection.
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Affiliation(s)
- Zineb Lakhrif
- a Université de Tours, UMR1282 Infectiologie et Santé Publique, 37200 Tours, France, Institut National de la Recherche Agronomique, UMR1282 Infectiologie et Santé Publique , 37380 Nouzilly , France
| | - Martine Pugnière
- b IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM, U1194, Université Montpellier, ICM Institut Régional du Cancer , Montpellier , 34090 , France
| | - Corinne Henriquet
- b IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM, U1194, Université Montpellier, ICM Institut Régional du Cancer , Montpellier , 34090 , France
| | - Anne di Tommaso
- a Université de Tours, UMR1282 Infectiologie et Santé Publique, 37200 Tours, France, Institut National de la Recherche Agronomique, UMR1282 Infectiologie et Santé Publique , 37380 Nouzilly , France
| | - Isabelle Dimier-Poisson
- a Université de Tours, UMR1282 Infectiologie et Santé Publique, 37200 Tours, France, Institut National de la Recherche Agronomique, UMR1282 Infectiologie et Santé Publique , 37380 Nouzilly , France
| | - Philippe Billiald
- c Muséum National d'Histoire Naturelle, UMR MNHN-CNRS 7245, 12 rue Buffon , Paris , 75231 , France
| | - Matthieu O Juste
- a Université de Tours, UMR1282 Infectiologie et Santé Publique, 37200 Tours, France, Institut National de la Recherche Agronomique, UMR1282 Infectiologie et Santé Publique , 37380 Nouzilly , France
| | - Nicolas Aubrey
- a Université de Tours, UMR1282 Infectiologie et Santé Publique, 37200 Tours, France, Institut National de la Recherche Agronomique, UMR1282 Infectiologie et Santé Publique , 37380 Nouzilly , France
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47
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IgG subclass specificity to C1q determined by surface plasmon resonance using Protein L capture technique. Anal Biochem 2015; 479:15-7. [DOI: 10.1016/j.ab.2015.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/04/2015] [Accepted: 03/11/2015] [Indexed: 12/17/2022]
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48
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Bailey LJ, Sheehy KM, Hoey RJ, Schaefer ZP, Ura M, Kossiakoff AA. Applications for an engineered Protein-G variant with a pH controllable affinity to antibody fragments. J Immunol Methods 2014; 415:24-30. [PMID: 25450256 DOI: 10.1016/j.jim.2014.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/09/2014] [Accepted: 10/13/2014] [Indexed: 01/28/2023]
Abstract
Immunoglobulin binding proteins (IBPs) are broadly used as reagents for the purification and detection of antibodies. Among the IBPs, the most widely used are Protein-A and Protein-G. The C2 domain of Protein-G from Streptococcus is a multi-specific protein domain; it possesses a high affinity (K(D) ~10 nM) for the Fc region of the IgG, but a much lower affinity (KD~low μM) for the constant domain of the antibody fragment (Fab), which limits some of its applications. Here, we describe the engineering of the Protein-G interface using phage display to create Protein-G-A1, a variant with 8 point mutations and an approximately 100-fold improved affinity over the parent domain for the 4D5 Fab scaffold. Protein-G-A1 is capable of robust binding to Fab fragments for numerous applications. Furthermore, we isolated a variant with pH-dependent affinity, demonstrating a 1,000-fold change in affinity from pH7 to 4. Additional rational mutagenesis endowed Protein-G with significantly enhanced stability in basic conditions relative to the parent domain while maintaining high affinity to the Fab. This property is particularly useful to regenerate Protein-G affinity columns. Lastly, the affinity-matured Protein-G-A1 variant was tethered together to produce dimers capable of providing multivalent affinity enhancement to a low affinity antibody fragment-antigen interaction. Engineered Protein-G variants should find widespread application in the use of Fab-based affinity reagents.
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Affiliation(s)
- Lucas J Bailey
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Kimberly M Sheehy
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Robert J Hoey
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Zachary P Schaefer
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Marcin Ura
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
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Kim DY, To R, Kandalaft H, Ding W, van Faassen H, Luo Y, Schrag JD, St-Amant N, Hefford M, Hirama T, Kelly JF, MacKenzie R, Tanha J. Antibody light chain variable domains and their biophysically improved versions for human immunotherapy. MAbs 2014; 6:219-35. [PMID: 24423624 PMCID: PMC3929445 DOI: 10.4161/mabs.26844] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We set out to gain deeper insight into the potential of antibody light chain variable domains (VLs) as immunotherapeutics. To this end, we generated a naïve human VL phage display library and, by using a method previously shown to select for non-aggregating antibody heavy chain variable domains (VHs), we isolated a diversity of VL domains by panning the library against B cell super-antigen protein L. Eight domains representing different germline origins were shown to be non-aggregating at concentrations as high as 450 µM, indicating VL repertoires are a rich source of non-aggregating domains. In addition, the VLs demonstrated high expression yields in E. coli, protein L binding and high reversibility of thermal unfolding. A side-by-side comparison with a set of non-aggregating human VHs revealed that the VLs had similar overall profiles with respect to melting temperature (Tm), reversibility of thermal unfolding and resistance to gastrointestinal proteases. Successful engineering of a non-canonical disulfide linkage in the core of VLs did not compromise the non-aggregation state or protein L binding properties. Furthermore, the introduced disulfide bond significantly increased their Tms, by 5.5–17.5 °C, and pepsin resistance, although it somewhat reduced expression yields and subtly changed the structure of VLs. Human VLs and engineered versions may make suitable therapeutics due to their desirable biophysical features. The disulfide linkage-engineered VLs may be the preferred therapeutic format because of their higher stability, especially for oral therapy applications that necessitate high resistance to the stomach’s acidic pH and pepsin.
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Affiliation(s)
- Dae Young Kim
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Rebecca To
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Hiba Kandalaft
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Wen Ding
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Henk van Faassen
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Yan Luo
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Joseph D Schrag
- Human Health Therapeutics; National Research Council Canada; Montréal, QC Canada
| | - Nadereh St-Amant
- Centre for Vaccine Evaluation; Biologics and Genetic Therapies Directorate;, Health Canada; Ottawa, ON Canada
| | - Mary Hefford
- Centre for Vaccine Evaluation; Biologics and Genetic Therapies Directorate;, Health Canada; Ottawa, ON Canada
| | - Tomoko Hirama
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - John F Kelly
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Roger MacKenzie
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada; School of Environmental Sciences; Ontario Agricultural College; University of Guelph; Guelph, ON Canada
| | - Jamshid Tanha
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada; School of Environmental Sciences; Ontario Agricultural College; University of Guelph; Guelph, ON Canada; Department of Biochemistry, Microbiology, and Immunology; University of Ottawa; Ottawa, ON Canada
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50
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Yang YH, Jiang YL, Zhang J, Wang L, Bai XH, Zhang SJ, Ren YM, Li N, Zhang YH, Zhang Z, Gong Q, Mei Y, Xue T, Zhang JR, Chen Y, Zhou CZ. Structural insights into SraP-mediated Staphylococcus aureus adhesion to host cells. PLoS Pathog 2014; 10:e1004169. [PMID: 24901708 PMCID: PMC4047093 DOI: 10.1371/journal.ppat.1004169] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/22/2014] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus, a Gram-positive bacterium causes a number of devastating human diseases, such as infective endocarditis, osteomyelitis, septic arthritis and sepsis. S. aureus SraP, a surface-exposed serine-rich repeat glycoprotein (SRRP), is required for the pathogenesis of human infective endocarditis via its ligand-binding region (BR) adhering to human platelets. It remains unclear how SraP interacts with human host. Here we report the 2.05 Å crystal structure of the BR of SraP, revealing an extended rod-like architecture of four discrete modules. The N-terminal legume lectin-like module specifically binds to N-acetylneuraminic acid. The second module adopts a β-grasp fold similar to Ig-binding proteins, whereas the last two tandem repetitive modules resemble eukaryotic cadherins but differ in calcium coordination pattern. Under the conditions tested, small-angle X-ray scattering and molecular dynamic simulation indicated that the three C-terminal modules function as a relatively rigid stem to extend the N-terminal lectin module outwards. Structure-guided mutagenesis analyses, in addition to a recently identified trisaccharide ligand of SraP, enabled us to elucidate that SraP binding to sialylated receptors promotes S. aureus adhesion to and invasion into host epithelial cells. Our findings have thus provided novel structural and functional insights into the SraP-mediated host-pathogen interaction of S. aureus.
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Affiliation(s)
- Yi-Hu Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Juan Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Lei Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Xiao-Hui Bai
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Shi-Jie Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Yan-Min Ren
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Na Li
- Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Yong-Hui Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Qingguo Gong
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Yide Mei
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Ting Xue
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, People's Republic of China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
- * E-mail: (YC); (CZZ)
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
- * E-mail: (YC); (CZZ)
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