1
|
Imamura H, Honda S. Cue to Acid-Induced Long-Range Conformational Changes in an Antibody Preceding Aggregation: The Structural Origins of the Subpeaks in Kratky Plots of Small-Angle X-ray Scattering. Int J Mol Sci 2023; 24:12042. [PMID: 37569415 PMCID: PMC10418478 DOI: 10.3390/ijms241512042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Antibody aggregation, followed by acid denaturation and neutralization of pH, is one of the reasons why the production of therapeutic monoclonal antibodies (mAbs) is expensive. Determining the structural details of acid-denatured antibodies is important for understanding their aggregation mechanism and for antibody engineering. Recent research has shown that monoclonal antibodies of human/humanized immunoglobulin G1 (IgG1) become smaller globules at pH 2 compared to their native structure at pH 7. This acid-denatured species is unstable at pH 7 and prone to aggregation by neutralization of pH. Small-angle X-ray scattering (SAXS) data have revealed an acid-induced reduction in the subpeaks in Kratky plot, indicating conformational changes that can lead to aggregation. The subpeaks are well resolved at pH > 3 but less pronounced at pH ≤ 2. One of the weakened subpeaks indicates loosely organized inter-region (Fab-Fab and Fab-Fc) correlations due to acid denaturation. However, the structural origin of the other subpeak (called q3 peak in this study) has not been established because its q region could represent the various inter-region, inter-domain, and intra-domain correlations in IgG1. In this study, we aimed to untangle the effects of domain-domain correlations on Kratky's q3 peak based on the computed SAXS of the crystal structure of IgG1. The q3 peak appeared in the static structure and was more prominent in the Fc region than in the Fab or isolated domains. Further brute-force analysis indicated that longer domain-domain correlations, including the inter-region, also positively contribute to Kratky's q3 peak. Thus, the distortion of the Fc region and a longer inter-region correlation initiate acid denaturation and aggregation.
Collapse
Affiliation(s)
- Hiroshi Imamura
- Department of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama 526-0829, Japan
| | - Shinya Honda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
| |
Collapse
|
2
|
Imamura H, Ooishi A, Honda S. Getting Smaller by Denaturation: Acid-Induced Compaction of Antibodies. J Phys Chem Lett 2023; 14:3898-3906. [PMID: 37093025 PMCID: PMC10150727 DOI: 10.1021/acs.jpclett.3c00258] [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: 01/29/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
Protein denaturation is a ubiquitous process that occurs both in vitro and in vivo. While our molecular understanding of the denatured structures of proteins is limited, it is commonly accepted that the loss of unique intramolecular contacts makes proteins larger. Herein, we report compaction of the immunoglobulin G1 (IgG1) protein upon acid denaturation. Small-angle X-ray scattering coupled with size exclusion chromatography revealed that IgG1 radii of gyration at pH 2 were ∼75% of those at a neutral pH. Scattering profiles showed a compact globular shape, supported by analytical ultracentrifugation. The acid denaturation of proteins with a decrease in size is energetically costly, and acid-induced compaction requires an attractive force for domain reorientation. Such intramolecular aggregation may be widespread in immunoglobulin proteins as noncanonical structures. Herein, we discuss the potential biological significance of these noncanonical structures of antibodies.
Collapse
Affiliation(s)
- Hiroshi Imamura
- Biomedical
Research Institute, National Institute of
Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Department
of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
- Department
of Bio-Science, Nagahama Institute of Bio-Science
and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Ayako Ooishi
- Biomedical
Research Institute, National Institute of
Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shinya Honda
- Biomedical
Research Institute, National Institute of
Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| |
Collapse
|
3
|
Arakawa T, Tomioka Y, Nakagawa M, Sakuma C, Kurosawa Y, Ejima D, Tsumoto K, Akuta T. Non-Affinity Purification of Antibodies. Antibodies (Basel) 2023; 12:antib12010015. [PMID: 36810520 PMCID: PMC9944463 DOI: 10.3390/antib12010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Currently, purification of antibodies is mainly carried out using a platform technology composed primarily of Protein A chromatography as a capture step, regardless of the scale. However, Protein A chromatography has a number of drawbacks, which are summarized in this review. As an alternative, we propose a simple small-scale purification protocol without Protein A that uses novel agarose native gel electrophoresis and protein extraction. For large-scale antibody purification, we suggest mixed-mode chromatography that can in part mimic the properties of Protein A resin, focusing on 4-Mercapto-ethyl-pyridine (MEP) column chromatography.
Collapse
Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, San Diego, CA 92130, USA
- Correspondence:
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Tahahagi 318-0004, Japan
| | - Masataka Nakagawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Tahahagi 318-0004, Japan
| | - Chiaki Sakuma
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Tahahagi 318-0004, Japan
| | - Yasunori Kurosawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Tahahagi 318-0004, Japan
| | - Daisuke Ejima
- Bio-Diagnostic Reagent Technology Center, Sysmex Corporation, Sayama 350-1332, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Tahahagi 318-0004, Japan
| |
Collapse
|
4
|
Nakayama T, Kobayashi K, Kameda T, Hase M, Hirano A. Protein's Protein Corona: Nanoscale Size Evolution of Human Immunoglobulin G Aggregates Induced by Serum Albumin. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32937-32947. [PMID: 35822632 DOI: 10.1021/acsami.2c08271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanoparticles are readily coated by proteins in biological systems. The protein layers on the nanoparticles, which are called the protein corona, influence the biological impacts of the nanoparticles, including internalization into cells and cytotoxicity. This study expands the scope of the nanoparticle's protein corona for exogenous artificial nanoparticles to that for exogenous proteinaceous nanoparticles. Specifically, this study addresses the formation of protein coronas on nanoscale human antibody aggregates with a radius of approximately 20-40 nm, where the antibody aggregates were induced by a pH shift from low to neutral pH. The size of the human immunoglobulin G (hIgG) aggregates grew to approximately 25 times the original size in the presence of human serum albumin (HSA). This size evolution was ascribed to the association of the hIgG aggregates, which was triggered by the formation of the hIgG aggregate's protein corona, i.e., protein's protein corona, consisting of the adsorbed HSA molecules. Because hIgG aggregate association was significantly reduced by the addition of 30-150 mM NaCl, it was attributed to electrostatic attraction, which was supported by molecular dynamics (MD) simulations. Currently, the use of antibodies as biopharmaceuticals is concerning because of undesired immune responses caused by antibody aggregates that are typically generated by a pH shift during the antibody purification process. The present findings suggest that nanoscale antibody aggregates form protein coronas induced by HSA and the resulting nanoscale antibody-HSA complexes are stable in blood containing approximately 150 mM salt ions, at least in terms of the size evolution. Mechanistic insights into protein corona formation on nanoscale antibody aggregates are useful for understanding the unintentional biological impacts of antibody drugs.
Collapse
Affiliation(s)
- Tomohito Nakayama
- Department of Applied Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Kaito Kobayashi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo135-0064, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo135-0064, Japan
| | - Muneaki Hase
- Department of Applied Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| |
Collapse
|
5
|
Senga Y, Doi M, Onitsuka M, Honda S. Live-cell imaging to analyze intracellular aggregation of recombinant IgG in CHO cells. Cell Chem Biol 2021; 29:120-132.e4. [PMID: 34739851 DOI: 10.1016/j.chembiol.2021.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 07/05/2021] [Accepted: 08/20/2021] [Indexed: 12/16/2022]
Abstract
Recombinant immunoglobulin G (IgG) aggregates are formed during their production. However, the process underlying intracellular/extracellular aggregation in cell culture conditions is not well understood, and no effective method exists to assess IgG aggregates. Here, we establish an approach to detect intracellular aggregates using AF.2A1, a small artificial protein that binds to non-native IgG conformers and aggregates. Fluorescent-labeled AF.2A1 is prepared via conjugation and transfected into antibody-producing Chinese hamster ovary (CHO) cells. Micrographic images show intracellular IgG aggregates in CHO cells. The relative amount of intracellular aggregates (versus total intracellular IgG) differed depending on the type of additives used during cell culture. Interestingly, the relative amount of intracellular aggregates moderately correlates with that of in vitro extracellular IgG aggregates, suggesting they are secreted. This method will allow the investigation of antibody aggregation in cells, and may guide the production of therapeutic antibodies with high yield/quality.
Collapse
Affiliation(s)
- Yukako Senga
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Motomichi Doi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Masayoshi Onitsuka
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima, Tokushima, Tokushima 770-8513, Japan
| | - Shinya Honda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| |
Collapse
|
6
|
Nano-Microscopy of Therapeutic Antibody Aggregates in Solution. Methods Mol Biol 2021. [PMID: 34478141 DOI: 10.1007/978-1-0716-1450-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Scanning electron-assisted dielectric microscopy (SE-ADM) is a new microscope technology developed to observe the fine structure of biological samples in aqueous solution. One main advantage of SE-ADM is that it does not require sample pretreatment, including dehydration, drying, and staining, which is indispensable in conventional scanning electron microscopy (SEM) and can cause sample deformation. In addition, the sample is not directly irradiated with an electron beam in SE-ADM, further avoiding damage. The resolution of SE-ADM is higher than that of an optical microscope, which is typically used for observing biological samples in a solution, allowing for the observation of the detailed structure of samples. Considering these advantages, we applied SE-ADM to observe aggregates of therapeutic immunoglobulin G (IgG) of various sizes and shapes in an aqueous solution. In this chapter, we outline the step-by-step procedure for observing aggregates of monoclonal antibodies using SE-ADM and the subsequent analysis of the particle distribution and calculation of the fractal dimension using SE-ADM image data. The proposed method for particle analysis is highly reliable with respect to size measurement and can determine the diameter of a sample with an accuracy of ±20%, a precision of ±10%, and a lower limit of quantification of ≤50 nm. Further, by calculating the fractal dimension of the image, it is possible to classify the shape of the aggregates and determine the mechanism of aggregation.
Collapse
|
7
|
Stanevich V, Pachalla A, Nunez B, McInnes M, Nieder C, Schreffler J. Improving viral filtration capacity in biomanufacturing processes using aggregate binding properties of polyamide-6,6. Biotechnol Bioeng 2020; 118:1105-1115. [PMID: 33241852 DOI: 10.1002/bit.27634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/10/2022]
Abstract
Virus retention filtration is a common step in modern biopharmaceutical manufacturing as it enables efficient removal of potential adventitious and endogenous viruses via size exclusion. Modern parvovirus retention filters have significantly improved fluxes and parvovirus retention in comparison to earlier versions of these filters. However, these filters may be more susceptible to premature fouling and require more effort for process optimization. Here, we demonstrate that polyamide-6,6 (nylon-6,6) membranes when used as prefilters can increase the capacity of these Parvovirus retentive filters that are less susceptible to premature fouling. We found that the mechanism of polyamide-mediated filtration improvement can be explained by the binding of monoclonal antibody (mAb) aggregates with a diameter of 20-100 nm, and we show that this mechanism is shared by other types of adsorptive prefilters. Finally, by the combination of mobile phase screening, additive spiking, and molecular dynamics simulations, we show that polyamide-6,6 removes mAb aggregates through hydrophobic interactions making its design space potentially complementary to other available prefilters. Our studies support the aggregate-mediated mechanism of flux decay during viral filtration and suggest that polyamide-6,6 could be considered as an alternative cost-effective option to extend the capacity of viral filters.
Collapse
Affiliation(s)
- Vitali Stanevich
- Janssen Pharmaceutical Companies of Johnson and Johnson, Malvern, Pennsylvania, USA
| | - Abhishek Pachalla
- Janssen Pharmaceutical Companies of Johnson and Johnson, Malvern, Pennsylvania, USA
| | - Briana Nunez
- Janssen Pharmaceutical Companies of Johnson and Johnson, Malvern, Pennsylvania, USA
| | | | | | - John Schreffler
- Janssen Pharmaceutical Companies of Johnson and Johnson, Malvern, Pennsylvania, USA
| |
Collapse
|