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Tscheliessnig R, Silva GL, Plewka J, Jakob LA, Lichtenegger H, Jungbauer A, Dias-Cabral AC. Antibody-ligand interactions on a high-capacity staphylococcal protein A resin. J Chromatogr A 2024; 1730:465102. [PMID: 38941799 DOI: 10.1016/j.chroma.2024.465102] [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: 04/16/2024] [Revised: 06/14/2024] [Accepted: 06/16/2024] [Indexed: 06/30/2024]
Abstract
Staphylococcal protein-A affinity chromatography has been optimized for antibody purification, achieving a current capacity of up to 90 mg/ml in packed bed. The morphology of the particles, the number of antibodies bound per ligand and the spatial arrangement of the ligands were assessed by in-situ Small-angle X-ray scattering (SAXS) and scanning electron microscopy (SEM) combined with measurement of adsorption isotherms. We employed SAXS measurements to probe the nanoscale structure of the chromatographic resin. From scanning electron microcopy, the morphology and area of the beads were obtained. The adsorption isotherm revealed a bi-Langmuirian behavior where the association constant varied with the critical bulk concentration, indicating multilayer adsorption. Determining the antibody-ligand stoichiometry was crucial for understanding the adsorption mechanism, which was estimated to be 4 at lower concentrations and 4.5 at higher concentrations, suggestive of reversible protein-protein interactions. The same results were reached from the in-situ small angle X-ray scattering measurements. A stoichiometry of 6 cannot be achieved since the two protein A monomers are anchored to the stationary phase and thus sterically hindered. Normalization through ellipsoids facilitated SAXS analysis, enabling the determination of distances between ligands and antibody-ligand complexes. Density fluctuations were examined by subtracting the elliptical fit, providing insights into ligand density distribution. The dense ligand packing of TOYOPEARL® AF-rProtein A HC was confirmed, making further increases in ligand density impractical. Additionally, SAXS analysis revealed structural rearrangements of the antibody-ligand complex with increasing antibody surface load, suggesting reversible association of antibodies.
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Affiliation(s)
- Rupert Tscheliessnig
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna 1190, Austria; Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna 1190, Austria; Department of Theoretical Chemistry, University of Vienna, Vienna, Austria; Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Goncalo L Silva
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna 1190, Austria
| | - Jacek Plewka
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna 1190, Austria; Department of Material Science and Process Engineering, University of Natural Resources and Life Sciences, Peter-Jordan Strasse 82, Vienna 1190, Austria
| | - Leo A Jakob
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna 1190, Austria; Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna 1190, Austria
| | - Helga Lichtenegger
- Department of Material Science and Process Engineering, University of Natural Resources and Life Sciences, Peter-Jordan Strasse 82, Vienna 1190, Austria
| | - Alois Jungbauer
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna 1190, Austria; Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna 1190, Austria.
| | - Ana C Dias-Cabral
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, Covilhã 6201-506, Portugal; Department of Chemistry, University of Beira Interior, R. Marquês d'Ávila e Bolama, Covilhã 6201-001, Portugal
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2
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Zimmermann I, Kaveh-Baghbaderani Y, Eilts F, Kohn N, Fraga-García P, Berensmeier S. Direct Affinity Ligand Immobilization onto Bare Iron Oxide Nanoparticles Enables Efficient Magnetic Separation of Antibodies. ACS APPLIED BIO MATERIALS 2024; 7:3942-3952. [PMID: 38740514 PMCID: PMC11190986 DOI: 10.1021/acsabm.4c00280] [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: 02/28/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024]
Abstract
Magnetic separation is a promising alternative to chromatography for enhancing the downstream processing (DSP) of monoclonal antibodies (mAbs). However, there is a lack of efficient magnetic particles for successful application. Aiming to fill this gap, we demonstrate the suitability of bare iron oxide nanoparticles (BION) with physical site-directed immobilization of an engineered Protein A affinity ligand (rSpA) as an innovative magnetic material. The rSpA ligand contains a short peptide tag that enables the direct and stable immobilization onto the uncoated BION surface without commonly required laborious particle activation. The resulting BION@rSpA have beneficial characteristics outperforming conventional Protein A-functionalized magnetic particles: a simple, fast, low-cost synthesis, a particle size in the nanometer range with a large effective specific surface area enabling large immunoglobulin G (IgG) binding capacity, and a high magnetophoretic velocity advantageous for fast processing. We further show rapid interactions of IgG with the easily accessible rSpA ligands. The binding of IgG to BION@rSpA is thereby highly selective and not impeded by impurity molecules in perfusion cell culture supernatant. Regarding the subsequent acidic IgG elution from BION@rSpA@IgG, we observed a hampering pH increase caused by the protonation of large iron oxide surfaces after concentrating the particles in 100 mM sodium acetate buffer. However, the pH can be stabilized by adding 50 mM glycine to the elution buffer, resulting in recoveries above 85% even at high particle concentrations. Our work shows that BION@rSpA enable efficient magnetic mAb separation and could help to overcome emerging bottlenecks in DSP.
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Affiliation(s)
- Ines Zimmermann
- Chair
of Bioseparation Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748 Garching, Germany
| | - Yasmin Kaveh-Baghbaderani
- Chair
of Bioseparation Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748 Garching, Germany
| | - Friederike Eilts
- Chair
of Bioseparation Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748 Garching, Germany
| | - Nadja Kohn
- Chair
of Bioseparation Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748 Garching, Germany
| | - Paula Fraga-García
- Chair
of Bioseparation Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748 Garching, Germany
| | - Sonja Berensmeier
- Chair
of Bioseparation Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748 Garching, Germany
- Munich
Institute of Integrated Materials, Energy and Process Engineering, Technical University of Munich, Lichtenbergstraße 4a, 85748 Garching, Germany
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3
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Bhoyar S, Foster M, Oh YH, Xu X, Traylor SJ, Guo J, Ghose S, Lenhoff AM. Engineering protein A ligands to mitigate antibody loss during high-pH washes in protein A chromatography. J Chromatogr A 2023; 1696:463962. [PMID: 37043977 DOI: 10.1016/j.chroma.2023.463962] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/05/2023]
Abstract
Protein A chromatography is a workhorse in monoclonal antibody (mAb) manufacture since it provides effective separation of mAbs from impurities such as host-cell proteins (HCPs) in a single capture step. HCP clearance can be aided by the inclusion of a wash step prior to low-pH elution. Although high-pH washes can be effective in removing additional HCPs from the loaded column, they may also contribute to a reduced mAb yield. In this work we show that this yield loss is reflected in a pH-dependent variation of the equilibrium binding capacity of the protein A resin, which is also observed for the capacity of the Fc fragments alone and therefore not a result of steric interactions involving the Fab fragments in the intact mAbs. We therefore hypothesized that the high-pH wash loss was due to protonation or deprotonation of ionizable residues on the protein A ligand. To evaluate this, we applied a rational protein engineering approach to the Z domain (the Fc-binding component of most commercial protein A ligands) and expressed engineered mutants in E. coli. Biolayer interferometry and affinity chromatography experiments showed that some of the Z domain mutants were able to mitigate wash loss at high pH while maintaining similar binding characteristics at neutral pH. These experiments enabled elucidation of the roles of specific interactions in the Z domain - Fc complex, but more importantly offer a route to ameliorating the disadvantages of high-pH washes in protein A chromatography.
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4
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Nosrati M, Housaindokht MR. New insights into the effect of mutations on affibody-Fc interaction, a molecular dynamics simulation approach. J Struct Biol 2023; 215:107925. [PMID: 36470559 DOI: 10.1016/j.jsb.2022.107925] [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: 08/01/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Staphylococcal protein A (SpA) domain B (the basis of affibody) has been widely used in affinity chromatography and found therapeutic applications against inflammatory diseases through targeting the Fc part of immunoglobulin G (IgG). We have performed extensive molecular dynamics simulation of 41 SpA mutants and compared their dynamics and conformations to wild type. The simulations revealed the molecular details of structural and dynamics changes that occurred due to introducing point mutations and helped to explain the SPR results. It was observed in some variants a point mutation caused extensive structural changes far from the mutation site, while an effect of some other mutations was limited to the site of the mutated residue. Also, the pattern of hydrogen bond networks and hydrophobic core arrangements were investigated. We figured out mutations that occurred at positions 128, 136, 150 and 153, affected two hydrophobic cores at the interface as well as mutations introduced at positions 129 and 154 interrupted two hydrogen bond networks of the interface, SPR data showed all of these mutations reduced binding affinity significantly. Overall, by scanning the SpA-Fc interface through the large numbers of introduced mutations, the new insights have been gained which would help to design high- affinity ligands of IgG.
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Affiliation(s)
- Masoumeh Nosrati
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Department of Cell and Molecular Biology, Uppsala University, BMC, Uppsala, Sweden.
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5
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Lali N, Satzer P, Jungbauer A. Residence Time Distribution in Counter-Current Protein A Affinity Chromatography Using an Inert Tracer. J Chromatogr A 2022; 1683:463530. [DOI: 10.1016/j.chroma.2022.463530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/24/2022]
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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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7
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Chu W, Prodromou R, Day KN, Schneible JD, Bacon KB, Bowen JD, Kilgore RE, Catella CM, Moore BD, Mabe MD, Alashoor K, Xu Y, Xiao Y, Menegatti S. Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics. J Chromatogr A 2020; 1635:461632. [PMID: 33333349 DOI: 10.1016/j.chroma.2020.461632] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.
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Affiliation(s)
- Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kevin N Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Schneible
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kaitlyn B Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Carly M Catella
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Matthew D Mabe
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kawthar Alashoor
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Yiman Xu
- College of Material Science and Engineering, Donghua University, 201620 Shanghai, People's Republic of China
| | - Yuanxin Xiao
- College of Textile, Donghua University, Songjiang District, Shanghai, 201620, People's Republic of China
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606.
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8
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Li M, Zhang Q, Lin D, Yao S. Development and application of hydrophobic charge-induction chromatography for bioseparation. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1134-1135:121850. [DOI: 10.1016/j.jchromb.2019.121850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/18/2019] [Accepted: 10/25/2019] [Indexed: 12/14/2022]
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9
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Antibody Binding Heterogeneity of Protein A Resins. Biotechnol J 2019; 14:e1800632. [DOI: 10.1002/biot.201800632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/08/2019] [Indexed: 01/25/2023]
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10
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Kangwa M, Yelemane V, Ponnurangam A, Fernández-Lahore M. An engineered Staphylococcal Protein A based ligand: Production, characterization and potential application for the capture of Immunoglobulin and Fc-fusion proteins. Protein Expr Purif 2018; 155:27-34. [PMID: 30445097 DOI: 10.1016/j.pep.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 12/28/2022]
Abstract
In antibody purification processes, affinity chromatography has been used with Staphylococcus aureus protein A (SpA) as the main ligand. In this work, we present a novel Staphylococcal Protein A (AviPure thereafter), a synthetic ligand analogue based on native SpA B domain, with a molecular weight of approximately 14 kDa. The binding affinity of mAbs to AviPure was evaluated using Surface Plasmon Resonance (SPR) and affinity chromatography methods. The equilibrium dissociation constant (KD) between the AviPure and mAbs was systematically measured using 1:1 (Langmuir) model and found to be 4.7 × 10-8 M, with constant of dissociation at kd ≤ 1.0 × 10-3 s-1 and ka being 3.1 × 104 M-1 s-1. When immobilized on Sepharose, the AviPure ligand density was 429 nmol/g moist weight resin and was able to effectively bind immunoglobulin and Fc fragment samples with higher affinity and the most effective flow rate when using ligand - Sepharose beads was at 75 cm/h giving the dynamic binding capacity of 53 mg/mL and 91% recovery of IgG. Suitable ligands used in affinity purification should have a KD ≤ 10-6 M and a dissociation rate (ka) averaging 10-3 M-1 s-1 with the kd ranging between 103 - 108 M-1. Therefore, the AviPure ligand can be used as an alternative to the standard protein A ligand in the purification of mAbs and Fc-fused proteins.
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Affiliation(s)
- Martin Kangwa
- Downstream Bioprocessing Laboratory, Department of Life Sciences & Chemistry, Jacobs University, Campus Ring 1, D-28759, Bremen, Germany.
| | - Vikas Yelemane
- Downstream Bioprocessing Laboratory, Department of Life Sciences & Chemistry, Jacobs University, Campus Ring 1, D-28759, Bremen, Germany
| | - Adilah Ponnurangam
- Downstream Bioprocessing Laboratory, Department of Life Sciences & Chemistry, Jacobs University, Campus Ring 1, D-28759, Bremen, Germany
| | - Marcelo Fernández-Lahore
- Downstream Bioprocessing Laboratory, Department of Life Sciences & Chemistry, Jacobs University, Campus Ring 1, D-28759, Bremen, Germany.
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11
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L Silva G, Plewka J, Lichtenegger H, Dias-Cabral AC, Jungbauer A, Tscheließnig R. The pearl necklace model in protein A chromatography: Molecular mechanisms at the resin interface. Biotechnol Bioeng 2018; 116:76-86. [PMID: 30252938 PMCID: PMC6587469 DOI: 10.1002/bit.26843] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/17/2018] [Accepted: 09/21/2018] [Indexed: 01/08/2023]
Abstract
Staphylococcal protein A chromatography is an established core technology for monoclonal antibody purification and capture in the downstream processing. MabSelect SuRe involves a tetrameric chain of a recombinant form of the B domain of staphylococcal protein A, called the Z-domain. Little is known about the stoichiometry, binding orientation, or preferred binding. We analyzed small-angle X-ray scattering data of the antibody-protein A complex immobilized in an industrial highly relevant chromatographic resin at different antibody concentrations. From scattering data, we computed the normalized radial density distributions. We designed three-dimensional (3D) models with protein data bank crystallographic structures of an IgG1 (the isoform of trastuzumab, used here; Protein Data Bank: 1HZH) and the staphylococcal protein A B domain (the native form of the recombinant structure contained in MabSelect SuRe resin; Protein Data Bank: 1BDD). We computed different binding conformations for different antibody to protein A stoichiometries (1:1, 2:1, and 3:1) and compared the normalized radial density distributions computed from 3D models with those obtained from the experimental data. In the linear range of the isotherm we favor a 1:1 ratio, with the antibody binding to the outer domains in the protein A chain at very low and high concentrations. In the saturation region, a 2:1 ratio is more likely to occur. A 3:1 stoichiometry is excluded because of steric effects.
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Affiliation(s)
- Goncalo L Silva
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal.,Department of Chemistry, University of Beira Interior, Covilhã, Portugal.,Department of Biotechnology, Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Jacek Plewka
- Department of Biotechnology, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Material Science and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Helga Lichtenegger
- Department of Biotechnology, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Material Science and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ana C Dias-Cabral
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal.,Department of Chemistry, University of Beira Interior, Covilhã, Portugal
| | - Alois Jungbauer
- Department of Biotechnology, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Rupert Tscheließnig
- Department of Biotechnology, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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12
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Fang YM, Lin DQ, Yao SJ. Review on biomimetic affinity chromatography with short peptide ligands and its application to protein purification. J Chromatogr A 2018; 1571:1-15. [DOI: 10.1016/j.chroma.2018.07.082] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/12/2018] [Accepted: 07/29/2018] [Indexed: 10/28/2022]
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13
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A novel rProtein A chromatographic media for enhancing cleaning-in-place performance. J Immunol Methods 2018; 460:45-50. [DOI: 10.1016/j.jim.2018.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/19/2018] [Accepted: 06/06/2018] [Indexed: 12/21/2022]
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14
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Identification and Characterization of Novel Fc-Binding Heptapeptides from Experiments and Simulations. Polymers (Basel) 2018; 10:polym10070778. [PMID: 30960703 PMCID: PMC6404062 DOI: 10.3390/polym10070778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 01/17/2023] Open
Abstract
Purification of biologically-derived therapeutics is a major cost contributor to the production of this rapidly growing class of pharmaceuticals. Monoclonal antibodies comprise a large percentage of these products, therefore new antibody purification tools are needed. Small peptides, as opposed to traditional antibody affinity ligands such as Protein A, may have advantages in stability and production costs. Multiple heptapeptides that demonstrate Fc binding behavior that have been identified from a combinatorial peptide library using M13 phage display are presented herein. Seven unique peptide sequences of diverse hydrophobicity and charge were identified. All seven peptides showed strong binding to the four major human IgG isotypes, human IgM, as well as binding to canine, rat, and mouse IgG. These seven peptides were also shown to bind human IgG4 from DMEM cell culture media with 5% FCS and 5 g/L ovalbumin present. These peptides may be useful as surface ligands for antibody detection and purification purposes. Molecular docking and classical molecular dynamics (MD) simulations were conducted to elucidate the mechanisms and energetics for the binding of these peptides to the Fc region. The binding site was found to be located between the two glycan chains inside the Fc fragment. Both hydrogen bonding and hydrophobic interactions were found to be crucial for the binding interactions. Excellent agreement for the binding strength was obtained between experimental results and simulations.
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15
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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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16
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Geuijen KPM, van Wijk-Basten DEJW, Egging DF, Schasfoort RBM, Eppink MH. Rapid Buffer and Ligand Screening for Affinity Chromatography by Multiplexed Surface Plasmon Resonance Imaging. Biotechnol J 2017; 12. [PMID: 28731574 DOI: 10.1002/biot.201700154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/09/2017] [Indexed: 11/11/2022]
Abstract
Protein purifications are often based on the principle of affinity chromatography, where the protein of interest selectively binds to an immobilized ligand. The development of affinity purification requires selecting proper wash and elution conditions. In recent years, miniaturization of the purification process is applied to speed up the development (e.g., microtiterplates, robocolumns). The application of surface plasmon resonance imaging (SPRi) as a tool to simultaneously screen many buffer conditions for wash and elution steps in an affinity-based purification process is studied. Additionally, the protein A ligand stability after exposure to harsh cleaning conditions often limits the reuse of resins and is determined at lab scale. The SPRi technology to screen ligand life-time with respect to alkali stability is used. It is also demonstrated that SPRi can successfully be applied in screening experiments for process developments in a miniaturized approach. The amount of resin, protein and buffer in these studies is reduced 30-300-fold compared to 1 mL column scale, and approximately 10-1000-fold compared to filter plate experiments. The overall development time can be decreased from several months towards days. The multiplexed SPRi can be applied in screening affinity chromatography conditions in early stage development for ligand development and recombinant protein production.
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Affiliation(s)
- Karin P M Geuijen
- Downstream Processing, Synthon Biopharmaceuticals BV, PO Box 7071, 6503 GN, Nijmegen, The Netherlands.,Bioprocess Engineering, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | | | - David F Egging
- Preclinical Department, Synthon Biopharmaceuticals BV, PO Box 7071, 6503 GN, Nijmegen, The Netherlands
| | - Richard B M Schasfoort
- Medical Cell Biophysics Group, MIRA institute, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE, Enschede, The Netherlands
| | - Michel H Eppink
- Downstream Processing, Synthon Biopharmaceuticals BV, PO Box 7071, 6503 GN, Nijmegen, The Netherlands.,Bioprocess Engineering, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
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Tong HF, Cavallotti C, Yao SJ, Lin DQ. Molecular insight into protein binding orientations and interaction modes on hydrophobic charge-induction resin. J Chromatogr A 2017; 1512:34-42. [DOI: 10.1016/j.chroma.2017.06.071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/15/2017] [Accepted: 06/29/2017] [Indexed: 11/28/2022]
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18
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Dai L, Li W, Sun F, Li B, Li H, Zhang H, Zheng Q, Liang C. A strategy of designing the ligand of antibody affinity chromatography based on molecular dynamics simulation. J Chromatogr A 2016; 1463:81-9. [DOI: 10.1016/j.chroma.2016.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/30/2016] [Accepted: 08/02/2016] [Indexed: 10/21/2022]
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19
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Xue A, Zhao WW, Liu X(M, Sun Y. Affinity chromatography of human IgG with octapeptide ligands identified from eleven peptide-ligand candidates. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.11.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Lin CP, Boysen RI, Campi EM, Saito K, Hearn MTW. Studies on the binding sites of IgG2 monoclonal antibodies recognized by terpyridine-based affinity ligands. J Mol Recognit 2016; 29:334-42. [PMID: 26842829 DOI: 10.1002/jmr.2535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 12/16/2015] [Indexed: 11/09/2022]
Abstract
This investigation has examined the origin of the molecular recognition associated with the interaction of monoclonal IgG2's with terpyridine-based ligands immobilized onto agarose-derived chromatographic adsorbents. Isothermal titration calorimetric (ITC) methods have been employed to acquire thermodynamic data associated with the IgG2-ligand binding. These ITC investigations have documented that different enthalpic and entropic processes are involved depending on the nature of the chemical substituents in the core structure of the terpyridinyl moiety. In addition, molecular docking studies have been carried out with IgG2 structures with the objective to identify possible ligand binding sites and key interacting amino acid residues. These molecular docking experiments with the different terpyridine-based ligands have shown that all of the examined ligands can potentially undergo favorable interactions with a site located within the Fab region of the IgG2. However, another favorable binding site was also identified from the docking poses to exist within the Fc region of the IgG2 for some, but not all, of the ligands studied. These investigations have provided a basis to elucidate the unique binding properties and chromatographic behaviors shown by several substituted terpyridine ligands in their interaction with IgGs of different isotype. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Chih-Pei Lin
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Reinhard I Boysen
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Eva M Campi
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Kei Saito
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Milton T W Hearn
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
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21
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Mazzer AR, Perraud X, Halley J, O'Hara J, Bracewell DG. Protein A chromatography increases monoclonal antibody aggregation rate during subsequent low pH virus inactivation hold. J Chromatogr A 2015; 1415:83-90. [PMID: 26346187 PMCID: PMC4582070 DOI: 10.1016/j.chroma.2015.08.068] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/07/2015] [Accepted: 08/14/2015] [Indexed: 01/01/2023]
Abstract
Protein A chromatography is a near-ubiquitous method of mAb capture in bioprocesses. The use of low pH buffer for elution from protein A is known to contribute to product aggregation. Yet, a more limited set of evidence suggests that low pH may not be the sole cause of aggregation in protein A chromatography, rather, other facets of the process may contribute significantly. This paper presents a well-defined method for investigating this problem. An IgG4 was incubated in elution buffer after protein A chromatography (typical of the viral inactivation hold) and the quantity of monomer in neutralised samples was determined by size exclusion chromatography; elution buffers of different pH values predetermined to induce aggregation of the IgG4 were used. Rate constants for monomer decay over time were determined by fitting exponential decay functions to the data. Similar experiments were implemented in the absence of a chromatography step, i.e. IgG4 aggregation at low pH. Rate constants for aggregation after protein A chromatography were considerably higher than those from low pH exposure alone; a distinct shift in aggregation rates was apparent across the pH range tested.
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Affiliation(s)
- Alice R Mazzer
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gordon Street, London WC1H 0AH, United Kingdom
| | - Xavier Perraud
- UCB Celltech, 216 Bath Road, Slough SL13WE, United Kingdom
| | | | - John O'Hara
- UCB Celltech, 216 Bath Road, Slough SL13WE, United Kingdom
| | - Daniel G Bracewell
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gordon Street, London WC1H 0AH, United Kingdom.
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22
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Salvalaglio M, Paloni M, Guelat B, Morbidelli M, Cavallotti C. A two level hierarchical model of protein retention in ion exchange chromatography. J Chromatogr A 2015; 1411:50-62. [DOI: 10.1016/j.chroma.2015.07.101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/23/2015] [Accepted: 07/27/2015] [Indexed: 10/23/2022]
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Abstract
INTRODUCTION The molecular mechanics energies combined with the Poisson-Boltzmann or generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods are popular approaches to estimate the free energy of the binding of small ligands to biological macromolecules. They are typically based on molecular dynamics simulations of the receptor-ligand complex and are therefore intermediate in both accuracy and computational effort between empirical scoring and strict alchemical perturbation methods. They have been applied to a large number of systems with varying success. AREAS COVERED The authors review the use of MM/PBSA and MM/GBSA methods to calculate ligand-binding affinities, with an emphasis on calibration, testing and validation, as well as attempts to improve the methods, rather than on specific applications. EXPERT OPINION MM/PBSA and MM/GBSA are attractive approaches owing to their modular nature and that they do not require calculations on a training set. They have been used successfully to reproduce and rationalize experimental findings and to improve the results of virtual screening and docking. However, they contain several crude and questionable approximations, for example, the lack of conformational entropy and information about the number and free energy of water molecules in the binding site. Moreover, there are many variants of the method and their performance varies strongly with the tested system. Likewise, most attempts to ameliorate the methods with more accurate approaches, for example, quantum-mechanical calculations, polarizable force fields or improved solvation have deteriorated the results.
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Affiliation(s)
- Samuel Genheden
- University of Southampton, School of Chemistry, Highfield, SO17 1BJ, Southampton, UK
| | - Ulf Ryde
- Lund University, Chemical Centre, Department of Theoretical Chemistry, P. O. Box 124, SE-221 00 Lund, Sweden+46 46 2224502; +46 46 2228648;
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Paloni M, Cavallotti C. Molecular modeling of the affinity chromatography of monoclonal antibodies. Methods Mol Biol 2015; 1286:321-335. [PMID: 25749965 DOI: 10.1007/978-1-4939-2447-9_25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular modeling is a methodology that offers the possibility of studying complex systems such as protein-ligand complexes from an atomistic point of view, making available information that can be difficultly obtained from experimental studies. Here, a protocol for the construction of molecular models of the interaction between antibodies and ligands that can be used for an affinity chromatography process is presented. The outlined methodology focuses mostly on the description of a procedure that may be adopted to determine the structure and free energy of interaction between the antibody and the affinity ligand. A procedure to extend the proposed methodology to include the effect of the environment (buffer solution, spacer, support matrix) is also briefly outlined.
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Affiliation(s)
- Matteo Paloni
- Department of Chimica Materiali e Ingegneria Chimica, G. Natta, Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
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25
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Insaidoo FK, Rauscher MA, Smithline SJ, Kaarsholm NC, Feuston BP, Ortigosa AD, Linden TO, Roush DJ. Targeted purification development enabled by computational biophysical modeling. Biotechnol Prog 2014; 31:154-64. [DOI: 10.1002/btpr.2023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/02/2014] [Indexed: 01/12/2023]
Affiliation(s)
| | | | | | - Niels C. Kaarsholm
- Merck Research Laboratories, Merck & Co., Inc; Whitehouse Station NJ 08889
| | - Bradley P. Feuston
- Merck Research Laboratories, Merck & Co., Inc; Whitehouse Station NJ 08889
| | | | - Thomas O. Linden
- Merck Research Laboratories, Merck & Co., Inc; Whitehouse Station NJ 08889
| | - David J. Roush
- Merck Research Laboratories, Merck & Co., Inc; Whitehouse Station NJ 08889
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26
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Tsukamoto M, Watanabe H, Ooishi A, Honda S. Engineered protein A ligands, derived from a histidine-scanning library, facilitate the affinity purification of IgG under mild acidic conditions. J Biol Eng 2014; 8:15. [PMID: 25057290 PMCID: PMC4107488 DOI: 10.1186/1754-1611-8-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 06/21/2014] [Indexed: 11/18/2022] Open
Abstract
Background In antibody purification processes, the acidic buffer commonly used to elute the bound antibodies during conventional affinity chromatograph, can damage the antibody. Herein we describe the development of several types of affinity ligands which enable the purification of antibodies under much milder conditions. Results Staphylococcal protein A variants were engineered by using both structure-based design and combinatorial screening methods. The frequency of amino acid residue substitutions was statistically analyzed using the sequences isolated from a histidine-scanning library screening. The positions where the frequency of occurrence of a histidine residue was more than 70% were thought to be effective histidine-mutation sites. Consequently, we identified PAB variants with a D36H mutation whose binding of IgG was highly sensitive to pH change. Conclusion The affinity column elution chromatograms demonstrated that antibodies could be eluted at a higher pH (∆pH**≧2.0) than ever reported (∆pH = 1.4) when the Staphylococcal protein A variants developed in this study were used as affinity ligands. The interactions between Staphylococcal protein A and IgG-Fab were shown to be important for the behavior of IgG bound on a SpA affinity column, and alterations in the affinity of the ligands for IgG-Fab clearly affected the conditions for eluting the bound IgG. Thus, a histidine-scanning library combined with a structure-based design was shown to be effective in engineering novel pH-sensitive proteins.
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Affiliation(s)
- Masayuki Tsukamoto
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan ; Manufacturing Technology Association of Biologics, Chuo-ku, Kobe, Japan
| | - Hideki Watanabe
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Ayako Ooishi
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shinya Honda
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan ; Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki 305-8566, Japan ; Manufacturing Technology Association of Biologics, Chuo-ku, Kobe, Japan
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27
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Tong HF, Lin DQ, Zhang QL, Wang RZ, Yao SJ. Molecular recognition of Fc-specific ligands binding onto the consensus binding site of IgG: insights from molecular simulation. J Mol Recognit 2014; 27:501-9. [DOI: 10.1002/jmr.2373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 03/11/2014] [Accepted: 03/15/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Hong-Fei Tong
- State Key Laboratory of Chemical Engineering, Department of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Dong-Qiang Lin
- State Key Laboratory of Chemical Engineering, Department of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Qi-Lei Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Rong-Zhu Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Shan-Jing Yao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
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28
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Wang RZ, Lin DQ, Tong HF, Yao SJ. Molecular insights into the binding selectivity of a synthetic ligand DAAG to Fc fragment of IgG. J Mol Recognit 2014; 27:250-9. [DOI: 10.1002/jmr.2356] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 12/23/2013] [Accepted: 12/26/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Rong-Zhu Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Dong-Qiang Lin
- State Key Laboratory of Chemical Engineering; Zhejiang University; Hangzhou 310027 China
| | - Hong-Fei Tong
- State Key Laboratory of Chemical Engineering; Zhejiang University; Hangzhou 310027 China
| | - Shan-Jing Yao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
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29
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Barroso T, Branco RJF, Aguiar-Ricardo A, Roque ACA. Structural evaluation of an alternative Protein A biomimetic ligand for antibody purification. J Comput Aided Mol Des 2014; 28:25-34. [DOI: 10.1007/s10822-013-9703-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/23/2013] [Indexed: 11/29/2022]
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30
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Chang CC, Chuang TL, Wang DS, Wang CH, Lin CW. Comparative Assessment of Oriented Antibody Immobilization on Surface Plasmon Resonance Biosensing. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201300116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Lin DQ, Tong HF, Wang HY, Shao S, Yao SJ. Molecular mechanism of hydrophobic charge-induction chromatography: Interactions between the immobilized 4-mercaptoethyl-pyridine ligand and IgG. J Chromatogr A 2012; 1260:143-53. [DOI: 10.1016/j.chroma.2012.08.080] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 07/27/2012] [Accepted: 08/21/2012] [Indexed: 10/27/2022]
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Branco RJF, Dias AMGC, Roque ACA. Understanding the molecular recognition between antibody fragments and protein A biomimetic ligand. J Chromatogr A 2012; 1244:106-15. [PMID: 22621885 DOI: 10.1016/j.chroma.2012.04.071] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/23/2012] [Accepted: 04/26/2012] [Indexed: 10/28/2022]
Abstract
Affinity chromatography with protein A from Staphylococcus aureus (SpA) is the most widespread and accepted methodology for antibody capture during the downstream process of antibody manufacturing. A triazine based ligand (ligand 22/8) was previously developed as an inexpensive and robust alternative to SpA chromatography (Li et al. and Teng et al.). Despite the experimental success, there is no structural information on the binding modes of ligand 22/8 to antibodies, namely to Immunoglobulin G (IgG) molecules and fragments. In this work, we addressed this issue by a molecular docking approach allied to molecular dynamics simulations. Theoretical results confirmed the preference of the synthetic ligand to bind IgG through the binding site found in the crystallographic structure of the natural complex between SpA and the Fc fragment of IgG. Our studies also suggested other unknown "hot-spots" for specific binding of the affinity ligand at the hinge between V(H) and C(H)1 domains of Fab fragment. The best docking poses were further analysed by molecular dynamics studies at three different protonation states (pH 3, 7 and 11). The main interactions between ligand 22/8 and the IgG fragments found at pH 7 were weaker at pH 3 and pH 11 and in these conditions the ligand start losing tight contact with the binding site, corroborating the experimental evidence for protein elution from the chromatographic adsorbents at these pH conditions.
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Affiliation(s)
- Ricardo J F Branco
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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33
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Lin DQ, Tong HF, Wang HY, Yao SJ. Molecular Insight into the Ligand–IgG Interactions for 4-Mercaptoethyl-pyridine Based Hydrophobic Charge-Induction Chromatography. J Phys Chem B 2012; 116:1393-400. [DOI: 10.1021/jp206817b] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dong-Qiang Lin
- State Key Laboratory
of Chemical Engineering, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hong-Fei Tong
- State Key Laboratory
of Chemical Engineering, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hong-Yin Wang
- State Key Laboratory
of Chemical Engineering, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Shan-Jing Yao
- State Key Laboratory
of Chemical Engineering, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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34
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Mikulskis P, Genheden S, Rydberg P, Sandberg L, Olsen L, Ryde U. Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods. J Comput Aided Mol Des 2011; 26:527-41. [PMID: 22198518 DOI: 10.1007/s10822-011-9524-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/08/2011] [Indexed: 11/28/2022]
Abstract
We have estimated affinities for the binding of 34 ligands to trypsin and nine guest molecules to three different hosts in the SAMPL3 blind challenge, using the MM/PBSA, MM/GBSA, LIE, continuum LIE, and Glide score methods. For the trypsin challenge, none of the methods were able to accurately predict the experimental results. For the MM/GB(PB)SA and LIE methods, the rankings were essentially random and the mean absolute deviations were much worse than a null hypothesis giving the same affinity to all ligand. Glide scoring gave a Kendall's τ index better than random, but the ranking is still only mediocre, τ = 0.2. However, the range of affinities is small and most of the pairs of ligands have an experimental affinity difference that is not statistically significant. Removing those pairs improves the ranking metric to 0.4-1.0 for all methods except CLIE. Half of the trypsin ligands were non-binders according to the binding assay. The LIE methods could not separate the inactive ligands from the active ones better than a random guess, whereas MM/GBSA and MM/PBSA were slightly better than random (area under the receiver-operating-characteristic curve, AUC = 0.65-0.68), and Glide scoring was even better (AUC = 0.79). For the first host, MM/GBSA and MM/PBSA reproduce the experimental ranking fairly good, with τ = 0.6 and 0.5, respectively, whereas the Glide scoring was considerably worse, with a τ = 0.4, highlighting that the success of the methods is system-dependent.
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Affiliation(s)
- Paulius Mikulskis
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, 221 00 Lund, Sweden
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35
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Huang B, Liu FF, Dong XY, Sun Y. Molecular mechanism of the effects of salt and pH on the affinity between protein A and human immunoglobulin G1 revealed by molecular simulations. J Phys Chem B 2011; 116:424-33. [PMID: 22136061 DOI: 10.1021/jp205770p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein A from the bacterium Staphylococcus aureus (SpA) has been widely used as an affinity ligand for purification of immunoglobulin G (IgG). The affinity between SpA and IgG is affected differently by salt and pH, but their molecular mechanisms still remain unclear. In this work, molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area analysis were performed to investigate the salt (NaCl) and pH effects on the affinity between SpA and human IgG1 (hIgG1). It is found that salt and pH affect the interactions of the hot spots of SpA by different mechanisms. In the salt solution, the compensations between helices I and II of SpA as well as between the nonpolar and electrostatic energies make the binding free energy independent of salt concentration. At pH 3.0, the unfavorable electrostatic interactions increase greatly and become the driving force for dissociation of the SpA-hIgG1 complex. They mainly come from the strong electrostatic repulsions between positively charged residues (H137, R146, and K154) of SpA and the positively charged residues of hIgG1. It is considered to be the molecular basis for hIgG1 elution from SpA-based affinity adsorbents at pH 3.0. The dissociation mechanism is then used to refine the binding model of SpA to hIgG1. The model is expected to help design high-affinity peptide ligands of IgG.
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Affiliation(s)
- Bo Huang
- Department of Biological Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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36
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Salvalaglio M, Cavallotti C. Molecular modeling to rationalize ligand-support interactions in affinity chromatography. J Sep Sci 2011; 35:7-19. [DOI: 10.1002/jssc.201100595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/26/2011] [Accepted: 09/30/2011] [Indexed: 11/09/2022]
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37
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Genheden S, Ryde U. Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies. J Chem Theory Comput 2011; 7:3768-78. [DOI: 10.1021/ct200163c] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Samuel Genheden
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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38
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Huang B, Liu FF, Dong XY, Sun Y. Molecular Mechanism of the Affinity Interactions between Protein A and Human Immunoglobulin G1 Revealed by Molecular Simulations. J Phys Chem B 2011; 115:4168-76. [DOI: 10.1021/jp111216g] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bo Huang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Fu-Feng Liu
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiao-Yan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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Moiani D, Salvalaglio M, Cavallotti C, Bujacz A, Redzynia I, Bujacz G, Dinon F, Pengo P, Fassina G. Structural Characterization of a Protein A Mimetic Peptide Dendrimer Bound to Human IgG. J Phys Chem B 2009; 113:16268-75. [DOI: 10.1021/jp909405b] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. Moiani
- Department of Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, 20131 Milano, Italy, Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, Lodz, Poland, and Xeptagen S.p.A., VEGA Science Park-Building Auriga Via delle Industrie 9, I-30175 Marghera (VE), Italy
| | - M. Salvalaglio
- Department of Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, 20131 Milano, Italy, Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, Lodz, Poland, and Xeptagen S.p.A., VEGA Science Park-Building Auriga Via delle Industrie 9, I-30175 Marghera (VE), Italy
| | - C. Cavallotti
- Department of Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, 20131 Milano, Italy, Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, Lodz, Poland, and Xeptagen S.p.A., VEGA Science Park-Building Auriga Via delle Industrie 9, I-30175 Marghera (VE), Italy
| | - A. Bujacz
- Department of Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, 20131 Milano, Italy, Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, Lodz, Poland, and Xeptagen S.p.A., VEGA Science Park-Building Auriga Via delle Industrie 9, I-30175 Marghera (VE), Italy
| | - I. Redzynia
- Department of Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, 20131 Milano, Italy, Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, Lodz, Poland, and Xeptagen S.p.A., VEGA Science Park-Building Auriga Via delle Industrie 9, I-30175 Marghera (VE), Italy
| | - G. Bujacz
- Department of Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, 20131 Milano, Italy, Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, Lodz, Poland, and Xeptagen S.p.A., VEGA Science Park-Building Auriga Via delle Industrie 9, I-30175 Marghera (VE), Italy
| | - F. Dinon
- Department of Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, 20131 Milano, Italy, Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, Lodz, Poland, and Xeptagen S.p.A., VEGA Science Park-Building Auriga Via delle Industrie 9, I-30175 Marghera (VE), Italy
| | - P. Pengo
- Department of Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, 20131 Milano, Italy, Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, Lodz, Poland, and Xeptagen S.p.A., VEGA Science Park-Building Auriga Via delle Industrie 9, I-30175 Marghera (VE), Italy
| | - G. Fassina
- Department of Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, 20131 Milano, Italy, Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, Lodz, Poland, and Xeptagen S.p.A., VEGA Science Park-Building Auriga Via delle Industrie 9, I-30175 Marghera (VE), Italy
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