1
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Barlow KA, Battles MB, Brown ME, Canfield K, Lu X, Lynaugh H, Morrill M, Rappazzo CG, Reyes SP, Sandberg C, Sharkey B, Strong C, Zhao J, Sivasubramanian A. Design of orthogonal constant domain interfaces to aid proper heavy/light chain pairing of bispecific antibodies. MAbs 2025; 17:2479531. [PMID: 40126074 PMCID: PMC11934185 DOI: 10.1080/19420862.2025.2479531] [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: 12/13/2024] [Revised: 03/06/2025] [Accepted: 03/10/2025] [Indexed: 03/25/2025] Open
Abstract
The correct pairing of cognate heavy and light chains is critical to the efficient manufacturing of IgG-like bispecific antibodies (bsAbs) from a single host cell. We present a general solution for the elimination of heavy chain (HC):light chain (LC) mispairs in bsAbs with κ LCs via the use of two orthogonal constant domain (CH1:Cκ ) interfaces comprising computationally designed amino acid substitutions. Substitutions were designed by Rosetta to introduce novel hydrogen bond (H-bond) networks at the CH1:Cκ interface, followed by Rosetta energy calculations to identify designs with enhanced pairing specificity and interface stability. Our final design, featuring a total of 11 amino acid substitutions across two Fab constant regions, was tested on a set of six IgG-like bsAbs featuring a diverse set of unmodified human antibody variable domains. Purity assessments showed near-complete elimination of LC mispairs, including in cases with high baseline mispairing with wild-type constant domains. The engineered bsAbs broadly recapitulated the antigen-binding and biophysical developability properties of their monospecific counterparts and no adverse immunogenicity signal was identified by an in vitro assay. Fab crystal structures containing engineered constant domain interfaces revealed no major perturbations relative to the wild-type coordinates and validated the presence of the designed hydrogen bond interactions. Our work enables the facile assembly of independently discovered IgG-like bispecific antibodies in a single-cell host and demonstrates a streamlined and generalizable computational and experimental workflow for redesigning conserved protein:protein interfaces.
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Affiliation(s)
| | | | | | | | - Xiaojun Lu
- Protein Analytics, Adimab, Lebanon, NH, USA
| | | | | | | | | | | | - Beth Sharkey
- High-Throughput Expression, Adimab, Lebanon, NH, USA
| | | | | | - Arvind Sivasubramanian
- Computational Biology, Adimab, Mountain View, CA, USA
- Platform Technologies, Adimab, Lebanon, NH, USA
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2
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Rogers GL, Huang C, Mathur A, Huang X, Chen HY, Stanten K, Morales H, Chang CH, Kezirian EJ, Cannon PM. Reprogramming human B cells with custom heavy-chain antibodies. Nat Biomed Eng 2024; 8:1700-1714. [PMID: 39039240 DOI: 10.1038/s41551-024-01240-4] [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: 06/07/2024] [Accepted: 06/22/2024] [Indexed: 07/24/2024]
Abstract
The immunoglobulin locus of B cells can be reprogrammed by genome editing to produce custom or non-natural antibodies that are not induced by immunization. However, current strategies for antibody reprogramming require complex expression cassettes and do not allow for customization of the constant region of the antibody. Here we show that human B cells can be edited at the immunoglobulin heavy-chain locus to express heavy-chain-only antibodies that support alterations to both the fragment crystallizable domain and the antigen-binding domain, which can be based on both antibody and non-antibody components. Using the envelope protein (Env) from the human immunodeficiency virus as a model antigen, we show that B cells edited to express heavy-chain antibodies to Env support the regulated expression of B cell receptors and antibodies through alternative splicing and that the cells respond to the Env antigen in a tonsil organoid model of immunization. This strategy allows for the reprogramming of human B cells to retain the potential for in vivo amplification while producing molecules with flexibility of composition beyond that of standard antibodies.
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Affiliation(s)
- Geoffrey L Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Chun Huang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Atishay Mathur
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Xiaoli Huang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Hsu-Yu Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Kalya Stanten
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Heidy Morales
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Chan-Hua Chang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Eric J Kezirian
- Department of Otolaryngology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Paula M Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
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3
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Madsen AV, Pedersen LE, Kristensen P, Goletz S. Design and engineering of bispecific antibodies: insights and practical considerations. Front Bioeng Biotechnol 2024; 12:1352014. [PMID: 38333084 PMCID: PMC10850309 DOI: 10.3389/fbioe.2024.1352014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
Bispecific antibodies (bsAbs) have attracted significant attention due to their dual binding activity, which permits simultaneous targeting of antigens and synergistic binding effects beyond what can be obtained even with combinations of conventional monospecific antibodies. Despite the tremendous therapeutic potential, the design and construction of bsAbs are often hampered by practical issues arising from the increased structural complexity as compared to conventional monospecific antibodies. The issues are diverse in nature, spanning from decreased biophysical stability from fusion of exogenous antigen-binding domains to antibody chain mispairing leading to formation of antibody-related impurities that are very difficult to remove. The added complexity requires judicious design considerations as well as extensive molecular engineering to ensure formation of high quality bsAbs with the intended mode of action and favorable drug-like qualities. In this review, we highlight and summarize some of the key considerations in design of bsAbs as well as state-of-the-art engineering principles that can be applied in efficient construction of bsAbs with diverse molecular formats.
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Affiliation(s)
- Andreas V. Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lasse E. Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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4
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Koga H, Kuroi H, Hirano R, Hirayama H, Nabuchi Y, Kuramochi T. Rapid Generation of Murine Bispecific Antibodies Using FAST-Ig TM for Preclinical Screening of HER2/CD3 T-Cell Engagers. Antibodies (Basel) 2024; 13:3. [PMID: 38247567 PMCID: PMC10801562 DOI: 10.3390/antib13010003] [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: 10/25/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Bispecific antibodies (BsAbs) can bind to two different antigens, enabling therapeutic concepts that cannot be achieved with monoclonal antibodies. Immuno-competent mice are essential for validating drug discovery concepts, necessitating the development of surrogate mouse BsAbs. In this study, we explored the potential of FAST-IgTM, a previously reported BsAb technology, for mouse BsAb production. We investigated charge-based orthogonal Fab mutations to facilitate the correct assembly of heavy and light chains of mouse antibodies and employed knobs-into-holes mutations to facilitate the heterodimerization of heavy chains. We combined five anti-CD3 and two anti-HER2 antibodies in mouse IgG1 and IgG2a subclasses. These 20 BsAbs were analyzed using mass spectrometry or ion exchange chromatography to calculate the percentages of BsAbs with correct chain pairing (BsAb yields). Using FAST-Ig, 19 out of the 20 BsAbs demonstrated BsAb yields of 90% or higher after simple protein A purification from transiently expressed antibodies in Expi293F cells. Importantly, the mouse BsAbs maintained their fundamental physicochemical properties and affinity against each antigen. A Jurkat NFAT-luciferase reporter cell assay demonstrated the combined effects of epitope, affinity, and subclasses. Our findings highlight the potential of FAST-Ig technology for efficiently generating mouse BsAbs for preclinical studies.
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Affiliation(s)
- Hikaru Koga
- Chugai Pharmaceutical Co., Ltd., Yokohama 244-8602, Japan
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5
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Amash A, Volkers G, Farber P, Griffin D, Davison KS, Goodman A, Tonikian R, Yamniuk A, Barnhart B, Jacobs T. Developability considerations for bispecific and multispecific antibodies. MAbs 2024; 16:2394229. [PMID: 39189686 DOI: 10.1080/19420862.2024.2394229] [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: 06/13/2024] [Revised: 08/08/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024] Open
Abstract
Bispecific antibodies (bsAb) and multispecific antibodies (msAb) encompass a diverse variety of formats that can concurrently bind multiple epitopes, unlocking mechanisms to address previously difficult-to-treat or incurable diseases. Early assessment of candidate developability enables demotion of antibodies with low potential and promotion of the most promising candidates for further development. Protein-based therapies have a stringent set of developability requirements in order to be competitive (e.g. high-concentration formulation, and long half-life) and their assessment requires a robust toolkit of methods, few of which are validated for interrogating bsAbs/msAbs. Important considerations when assessing the developability of bsAbs/msAbs include their molecular format, likelihood for immunogenicity, specificity, stability, and potential for high-volume production. Here, we summarize the critical aspects of developability assessment, and provide guidance on how to develop a comprehensive plan tailored to a given bsAb/msAb.
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Affiliation(s)
- Alaa Amash
- AbCellera Biologics Inc, Vancouver, BC, Canada
| | | | | | | | | | | | | | | | | | - Tim Jacobs
- AbCellera Biologics Inc, Vancouver, BC, Canada
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6
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Fawcett C, Tickle JR, Coles CH. Facilitating high throughput bispecific antibody production and potential applications within biopharmaceutical discovery workflows. MAbs 2024; 16:2311992. [PMID: 39674918 DOI: 10.1080/19420862.2024.2311992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 12/17/2024] Open
Abstract
A major driver for the recent investment surge in bispecific antibody (bsAb) platforms and products is the multitude of distinct mechanisms of action that bsAbs offer compared to a combination of two monoclonal antibodies. Four bsAb products were granted first regulatory approvals in the US or EU during 2023 and the biopharmaceutical industry pipeline is brimming with bsAb candidates across a broad range of therapeutic applications. In previously reported bsAb discovery campaigns, following a hypothesis-based choice of two specific target proteins, selections and screening activities have often been performed in mono-specific formats. The conversion to bispecific modalities has usually been positioned toward the end of the discovery process and has involved small numbers of lead molecules, largely due to challenges in expressing, purifying, and analyzing large numbers of bsAbs. In this review, we discuss emerging strategies to facilitate the production of expanded bsAb panels, focusing particularly upon combinatorial methods to generate bsAb matrices. Such technologies will enable screening in. bispecific formats at earlier stages of discovery campaigns, not only widening the accessible protein space to maximize chances of success, but also advancing empirical bi-target validation activities to assess initial target selection hypotheses.
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Affiliation(s)
- Caitlin Fawcett
- Large Molecule Discovery, GSK, GSK Medicines Research Centre, Stevenage, UK
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Joseph R Tickle
- Large Molecule Discovery, GSK, GSK Medicines Research Centre, Stevenage, UK
| | - Charlotte H Coles
- Large Molecule Discovery, GSK, GSK Medicines Research Centre, Stevenage, UK
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7
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Keri D, Walker M, Singh I, Nishikawa K, Garces F. Next generation of multispecific antibody engineering. Antib Ther 2024; 7:37-52. [PMID: 38235376 PMCID: PMC10791046 DOI: 10.1093/abt/tbad027] [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: 07/31/2023] [Revised: 10/16/2023] [Accepted: 11/15/2023] [Indexed: 01/19/2024] Open
Abstract
Multispecific antibodies recognize two or more epitopes located on the same or distinct targets. This added capability through protein design allows these man-made molecules to address unmet medical needs that are no longer possible with single targeting such as with monoclonal antibodies or cytokines alone. However, the approach to the development of these multispecific molecules has been met with numerous road bumps, which suggests that a new workflow for multispecific molecules is required. The investigation of the molecular basis that mediates the successful assembly of the building blocks into non-native quaternary structures will lead to the writing of a playbook for multispecifics. This is a must do if we are to design workflows that we can control and in turn predict success. Here, we reflect on the current state-of-the-art of therapeutic biologics and look at the building blocks, in terms of proteins, and tools that can be used to build the foundations of such a next-generation workflow.
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Affiliation(s)
- Daniel Keri
- Department of Protein Therapeutics, Research, Gilead Research, 324 Lakeside Dr, Foster City, CA 94404, USA
| | - Matt Walker
- Department of Protein Therapeutics, Research, Gilead Research, 324 Lakeside Dr, Foster City, CA 94404, USA
| | - Isha Singh
- Department of Protein Therapeutics, Research, Gilead Research, 324 Lakeside Dr, Foster City, CA 94404, USA
| | - Kyle Nishikawa
- Department of Protein Therapeutics, Research, Gilead Research, 324 Lakeside Dr, Foster City, CA 94404, USA
| | - Fernando Garces
- Department of Protein Therapeutics, Research, Gilead Research, 324 Lakeside Dr, Foster City, CA 94404, USA
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8
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Yoshikawa M, Nakamura H, Oda-Ueda N, Ohkuri T. Analysis of thermostability for seven Phe to Ala and six Pro to Gly mutants in the Fab constant region of adalimumab. J Biochem 2023; 174:345-353. [PMID: 37390406 DOI: 10.1093/jb/mvad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
To identify amino acids that play important roles in the structural stability of Fab, seven phenylalanine residues in the Fab constant region of the therapeutic antibody adalimumab were subjected to alanine mutagenesis. Six Fab mutants, H:F130A, H:F154A, H:F174A, L:F118A, L:F139A and L:F209A, showed decreased thermostability compared with wild-type Fab. In contrast, the Tm for the L:F116A mutant was 1.7°C higher than that of wild-type Fab, indicating that the F116 residue was unfavorable for Fab thermostability. Six proline mutants, H:P131G, H:P155G, H:P175G, L:P119G, L:P120G and L:P141G, were also prepared to investigate the effect of proline residues adjacent to mutated phenylalanine residues. The thermostability of the H:P155G and L:P141G mutants in particular was significantly reduced, with decreases in Tm of 5.0 and 3.0°C, respectively, compared with wild-type Fab. The H:P155 and L:P141 residues have a cis conformation, whereas the other mutated proline residues have a trans conformation. H:P155 and L:P141 had stacking interactions with the H:F154 and L:Y140, respectively, at the interface between the variable and constant regions. It is suggested that the interactions of the aromatic ring with a cis-form proline at the interface between the variable and constant regions is important for stability of Fab.
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Affiliation(s)
- Moeka Yoshikawa
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Hitomi Nakamura
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Naoko Oda-Ueda
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Takatoshi Ohkuri
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
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9
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Phung W, Bakalarski CE, Hinkle TB, Sandoval W, Marty MT. UniDec Processing Pipeline for Rapid Analysis of Biotherapeutic Mass Spectrometry Data. Anal Chem 2023; 95:11491-11498. [PMID: 37478487 DOI: 10.1021/acs.analchem.3c02010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Recent advances in native mass spectrometry (MS) and denatured intact protein MS have made these techniques essential for biotherapeutic characterization. As MS analysis has increased in throughput and scale, new data analysis workflows are needed to provide rapid quantitation from large datasets. Here, we describe the UniDec processing pipeline (UPP) for the analysis of batched biotherapeutic intact MS data. UPP is built into the UniDec software package, which provides fast processing, deconvolution, and peak detection. The user and programming interfaces for UPP read a spreadsheet that contains the data file names, deconvolution parameters, and quantitation settings. After iterating through the spreadsheet and analyzing each file, it returns a spreadsheet of results and HTML reports. We demonstrate the use of UPP to measure the correct pairing percentage on a set of bispecific antibody data and to measure drug-to-antibody ratios from antibody-drug conjugates. Moreover, because the software is free and open-source, users can easily build on this platform to create customized workflows and calculations. Thus, UPP provides a flexible workflow that can be deployed in diverse settings and for a wide range of biotherapeutic applications.
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Affiliation(s)
- Wilson Phung
- Microchemistry, Proteomics, and Lipidomics Department, Genentech, Inc., South San Francisco, California 94080, United States
| | - Corey E Bakalarski
- Microchemistry, Proteomics, and Lipidomics Department, Genentech, Inc., South San Francisco, California 94080, United States
| | - Trent B Hinkle
- Microchemistry, Proteomics, and Lipidomics Department, Genentech, Inc., South San Francisco, California 94080, United States
| | - Wendy Sandoval
- Microchemistry, Proteomics, and Lipidomics Department, Genentech, Inc., South San Francisco, California 94080, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry and the Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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10
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Pomarici ND, Waibl F, Quoika PK, Bujotzek A, Georges G, Fernández-Quintero ML, Liedl KR. Structural mechanism of Fab domain dissociation as a measure of interface stability. J Comput Aided Mol Des 2023; 37:201-215. [PMID: 36918473 PMCID: PMC10049950 DOI: 10.1007/s10822-023-00501-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/23/2023] [Indexed: 03/16/2023]
Abstract
Therapeutic antibodies should not only recognize antigens specifically, but also need to be free from developability issues, such as poor stability. Thus, the mechanistic understanding and characterization of stability are critical determinants for rational antibody design. In this study, we use molecular dynamics simulations to investigate the melting process of 16 antigen binding fragments (Fabs). We describe the Fab dissociation mechanisms, showing a separation in the VH-VL and in the CH1-CL domains. We found that the depths of the minima in the free energy curve, corresponding to the bound states, correlate with the experimentally determined melting temperatures. Additionally, we provide a detailed structural description of the dissociation mechanism and identify key interactions in the CDR loops and in the CH1-CL interface that contribute to stabilization. The dissociation of the VH-VL or CH1-CL domains can be represented by conformational changes in the bend angles between the domains. Our findings elucidate the melting process of antigen binding fragments and highlight critical residues in both the variable and constant domains, which are also strongly germline dependent. Thus, our proposed mechanisms have broad implications in the development and design of new and more stable antigen binding fragments.
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Affiliation(s)
- Nancy D Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Patrick K Quoika
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
- Center for Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, 82377, Penzberg, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, 82377, Penzberg, Germany
| | - Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria.
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria.
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11
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Tang H, Gao Y, Han J. Application Progress of the Single Domain Antibody in Medicine. Int J Mol Sci 2023; 24:ijms24044176. [PMID: 36835588 PMCID: PMC9967291 DOI: 10.3390/ijms24044176] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The camelid-derived single chain antibody (sdAb), also termed VHH or nanobody, is a unique, functional heavy (H)-chain antibody (HCAb). In contrast to conventional antibodies, sdAb is a unique antibody fragment consisting of a heavy-chain variable domain. It lacks light chains and a first constant domain (CH1). With a small molecular weight of only 12~15 kDa, sdAb has a similar antigen-binding affinity to conventional Abs but a higher solubility, which exerts unique advantages for the recognition and binding of functional, versatile, target-specific antigen fragments. In recent decades, with their unique structural and functional features, nanobodies have been considered promising agents and alternatives to traditional monoclonal antibodies. As a new generation of nano-biological tools, natural and synthetic nanobodies have been used in many fields of biomedicine, including biomolecular materials, biological research, medical diagnosis and immune therapies. This article briefly overviews the biomolecular structure, biochemical properties, immune acquisition and phage library construction of nanobodies and comprehensively reviews their applications in medical research. It is expected that this review will provide a reference for the further exploration and unveiling of nanobody properties and function, as well as a bright future for the development of drugs and therapeutic methods based on nanobodies.
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Affiliation(s)
- Huaping Tang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuan Gao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
- Correspondence:
| | - Jiangyuan Han
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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12
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Pance K, Gramespacher JA, Byrnes JR, Salangsang F, Serrano JAC, Cotton AD, Steri V, Wells JA. Modular cytokine receptor-targeting chimeras for targeted degradation of cell surface and extracellular proteins. Nat Biotechnol 2023; 41:273-281. [PMID: 36138170 PMCID: PMC9931583 DOI: 10.1038/s41587-022-01456-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/01/2022] [Indexed: 12/20/2022]
Abstract
Targeted degradation of cell surface and extracellular proteins via lysosomal delivery is an important means to modulate extracellular biology. However, these approaches have limitations due to lack of modularity, ease of development, restricted tissue targeting and applicability to both cell surface and extracellular proteins. We describe a lysosomal degradation strategy, termed cytokine receptor-targeting chimeras (KineTACs), that addresses these limitations. KineTACs are fully genetically encoded bispecific antibodies consisting of a cytokine arm, which binds its cognate cytokine receptor, and a target-binding arm for the protein of interest. We show that KineTACs containing the cytokine CXCL12 can use the decoy recycling receptor, CXCR7, to target a variety of target proteins to the lysosome for degradation. Additional KineTACs were designed to harness other CXCR7-targeting cytokines, CXCL11 and vMIPII, and the interleukin-2 (IL-2) receptor-targeting cytokine IL-2. Thus, KineTACs represent a general, modular, selective and simple genetically encoded strategy for inducing lysosomal delivery of extracellular and cell surface targets with broad or tissue-specific distribution.
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Affiliation(s)
- Katarina Pance
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,EpiBiologics, Inc., San Carlos, CA, USA
| | - Josef A Gramespacher
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,EpiBiologics, Inc., San Carlos, CA, USA
| | - James R Byrnes
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Fernando Salangsang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Preclinical Therapeutics Core, University of California San Francisco, San Francisco, CA, USA
| | - Juan-Antonio C Serrano
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Preclinical Therapeutics Core, University of California San Francisco, San Francisco, CA, USA
| | - Adam D Cotton
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Preclinical Therapeutics Core, University of California San Francisco, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
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13
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Koga H, Yamano T, Betancur J, Nagatomo S, Ikeda Y, Yamaguchi K, Nabuchi Y, Sato K, Teranishi-Ikawa Y, Sato M, Hirayama H, Hayasaka A, Torizawa T, Haraya K, Sampei Z, Shiraiwa H, Kitazawa T, Igawa T, Kuramochi T. Efficient production of bispecific antibody by FAST-Ig TM and its application to NXT007 for the treatment of hemophilia A. MAbs 2023; 15:2222441. [PMID: 37339067 PMCID: PMC10283433 DOI: 10.1080/19420862.2023.2222441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/22/2023] Open
Abstract
Efficient production of bispecific antibodies (BsAbs) in single mammalian cells is essential for basic research and industrial manufacturing. However, preventing unwanted pairing of heavy chains (HCs) and light chains (LCs) is a challenging task. To address this, we created an engineering technology for preferential cognate HC/LC and HC/HC paring called FAST-Ig (Four-chain Assembly by electrostatic Steering Technology - Immunoglobulin), and applied it to NXT007, a BsAb for the treatment of hemophilia A. We introduced charged amino-acid substitutions at the HC/LC interface to facilitate the proper assembly for manufacturing a standard IgG-type BsAb. We generated CH1/CL interface-engineered antibody variants that achieved > 95% correct HC/LC pairing efficiency with favorable pharmacological properties and developability. Among these, we selected a design (C3) that allowed us to separate the mis-paired species with an unintended pharmacological profile using ion-exchange chromatography. Crystal structure analysis demonstrated that the C3 design did not affect the overall structure of both Fabs. To determine the final design for HCs-heterodimerization, we compared the stability of charge-based and knobs into hole-based Fc formats in acidic conditions and selected the more stable charge-based format. FAST-Ig was also applicable to stable CHO cell lines for industrial production and demonstrated robust chain pairing with different subclasses of parent BsAbs. Thus, it can be applied to a wide variety of BsAbs both preclinically and clinically.
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Affiliation(s)
- Hikaru Koga
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Takashi Yamano
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Juan Betancur
- API Process Development Department, Chugai Pharmaceutical Co., Ltd, Ukima, Tokyo, Japan
| | - Satoko Nagatomo
- Analytical Development Department, Chugai Pharmaceutical Co, Ltd, Ukima, Tokyo, Japan
| | - Yousuke Ikeda
- Analytical Development Department, Chugai Pharmaceutical Co, Ltd, Ukima, Tokyo, Japan
| | - Kazuki Yamaguchi
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Yoshiaki Nabuchi
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Kazuki Sato
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | | | - Motohiko Sato
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Hiroyuki Hirayama
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Akira Hayasaka
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Takuya Torizawa
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Kenta Haraya
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Zenjiro Sampei
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Hirotake Shiraiwa
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Takehisa Kitazawa
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
| | - Tomoyuki Igawa
- Translational Research Division, Chugai Pharmaceutical Co., Ltd, Chuo-Ku, Tokyo, Japan
| | - Taichi Kuramochi
- Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan
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14
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Bagert JD, Oganesyan V, Chiang CI, Iannotti M, Lin J, Yang C, Payne S, McMahon W, Edwards S, Dippel A, Hutchinson M, Huang F, Aleti V, Niu C, Qian C, Denham J, Ferreira S, Pradhan P, Penney M, Wang C, Liu W, Walseng E, Mazor Y. Robust production of monovalent bispecific IgG antibodies through novel electrostatic steering mutations at the C H1-C λ interface. MAbs 2023; 15:2273449. [PMID: 37930310 PMCID: PMC10629431 DOI: 10.1080/19420862.2023.2273449] [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: 08/17/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023] Open
Abstract
Bispecific antibodies represent an increasingly large fraction of biologics in therapeutic development due to their expanded scope in functional capabilities. Asymmetric monovalent bispecific IgGs (bsIgGs) have the additional advantage of maintaining a native antibody-like structure, which can provide favorable pharmacology and pharmacokinetic profiles. The production of correctly assembled asymmetric monovalent bsIgGs, however, is a complex engineering endeavor due to the propensity for non-cognate heavy and light chains to mis-pair. Previously, we introduced the DuetMab platform as a general solution for the production of bsIgGs, which utilizes an engineered interchain disulfide bond in one of the CH1-CL domains to promote orthogonal chain pairing between heavy and light chains. While highly effective in promoting cognate heavy and light chain pairing, residual chain mispairing could be detected for specific combinations of Fv pairs. Here, we present enhancements to the DuetMab design that improve chain pairing and production through the introduction of novel electrostatic steering mutations at the CH1-CL interface with lambda light chains (CH1-Cλ). These mutations work together with previously established charge-pair mutations at the CH1-CL interface with kappa light chains (CH1-Cκ) and Fab disulfide engineering to promote cognate heavy and light chain pairing and enable the reliable production of bsIgGs. Importantly, these enhanced DuetMabs do not require engineering of the variable domains and are robust when applied to a panel of bsIgGs with diverse Fv sequences. We present a comprehensive biochemical, biophysical, and functional characterization of the resulting DuetMabs to demonstrate compatibility with industrial production benchmarks. Overall, this enhanced DuetMab platform substantially streamlines process development of these disruptive biotherapeutics.
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Affiliation(s)
- John D. Bagert
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | | | - Chi-I Chiang
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Mike Iannotti
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Jia Lin
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Chunning Yang
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Sterling Payne
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Will McMahon
- Process and Analytical Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Samuel Edwards
- Process and Analytical Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Andrew Dippel
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | | | - Fengying Huang
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Vineela Aleti
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Chendi Niu
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Chen Qian
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Jessica Denham
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Sofia Ferreira
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Pallab Pradhan
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Mark Penney
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Chunlei Wang
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Wenhai Liu
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Even Walseng
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
| | - Yariv Mazor
- Biologics Engineering, AstraZeneca, Gaithersburg, MD, USA
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15
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Campuzano IDG, Pelegri-O'Day EM, Srinivasan N, Lippens JL, Egea P, Umeda A, Aral J, Zhang T, Laganowsky A, Netirojjanakul C. High-Throughput Mass Spectrometry for Biopharma: A Universal Modality and Target Independent Analytical Method for Accurate Biomolecule Characterization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2191-2198. [PMID: 36206542 DOI: 10.1021/jasms.2c00138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Reversed-phase liquid chromatographic mass spectrometry (rpLC-MS) is a universal, platformed, and essential analytical technique within pharmaceutical and biopharmaceutical research. Typical rpLC method gradient times can range from 5 to 20 min. As monoclonal antibody (mAb) therapies continue to evolve and bispecific antibodies (BsAbs) become more established, research stage engineering panels will clearly evolve in size. Therefore, high-throughput (HT) MS and automated deconvolution methods are key for success. Additionally, newer therapeutics such as bispecific T-cell engagers and nucleic acid-based modalities will also require MS characterization. Herein, we present a modality and target agnostic HT solid-phase extraction (SPE) MS method that affords the analysis of a 96-well plate in 41.4 min, compared to the traditional rpLC-MS method that would typically take 14.4 h. The described method can accurately determine the molecular weights for monodispersed and highly polydispersed biotherapeutic species and membrane proteins; determine levels of glycosylation, glycation, and formylation; detect levels of chain mispairing; and determine accurate drug-to-antibody ratio values.
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Affiliation(s)
- Iain D G Campuzano
- Amgen Research, Molecular Analytics, Biologics Therapeutic Discovery, 1 Amgen Center Drive, Thousand Oaks, California91320, United States
| | - Emma M Pelegri-O'Day
- Amgen Research, Molecular Analytics, Biologics Therapeutic Discovery, 1 Amgen Center Drive, Thousand Oaks, California91320, United States
| | - Nithya Srinivasan
- Amgen Research, Molecular Analytics, Biologics Therapeutic Discovery, 1 Amgen Center Drive, Thousand Oaks, California91320, United States
| | - Jennifer L Lippens
- Pivotal Attribute Sciences, Process Development, 1 Amgen Center Drive, Thousand Oaks, California91320, United States
| | - Pascal Egea
- Department of Biological Chemistry, University of California─Los Angeles, Los Angeles, California90095, United States
| | - Aiko Umeda
- Amgen Research, Platform Engineering, Biologics Therapeutic Discovery, 1 Amgen Center Drive, Thousand Oaks, California91320, United States
| | - Jennifer Aral
- Amgen Research, Platform Engineering, Biologics Therapeutic Discovery, 1 Amgen Center Drive, Thousand Oaks, California91320, United States
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, Texas77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas77843, United States
| | - Chawita Netirojjanakul
- Amgen Research, Platform Engineering, Biologics Therapeutic Discovery, 1 Amgen Center Drive, Thousand Oaks, California91320, United States
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16
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Vukovic N, Halabi S, Russo-Cabrera JS, Blokhuis B, Berraondo P, Redegeld FAM, Zaiss DMW. A human IgE bispecific antibody shows potent cytotoxic capacity mediated by monocytes. J Biol Chem 2022; 298:102153. [PMID: 35718062 PMCID: PMC9293656 DOI: 10.1016/j.jbc.2022.102153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
The generation of bispecific antibodies (bsAbs) targeting two different antigens opens a new level of specificity and, compared to mAbs, improved clinical efficacy in cancer therapy. Currently, the different strategies for development of bsAbs primarily focus on IgG isotypes. Nevertheless, in comparison to IgG isotypes, IgE has been shown to offer superior tumor control in preclinical models. Therefore, in order to combine the promising potential of IgE molecules with increased target selectivity of bsAbs, we developed dual tumor-associated antigen-targeting bispecific human IgE antibodies. As proof of principle, we used two different pairing approaches - knobs-into-holes and leucine zipper-mediated pairing. Our data show that both strategies were highly efficient in driving bispecific IgE formation, with no undesired pairings observed. Bispecific IgE antibodies also showed a dose-dependent binding to their target antigens, and cell bridging experiments demonstrated simultaneous binding of two different antigens. As antibodies mediate a major part of their effector functions through interaction with Fc receptors (FcRs) expressed on immune cells, we confirmed FcεR binding by inducing in vitro mast cell degranulation and demonstrating in vitro and in vivo monocyte-mediated cytotoxicity against target antigen-expressing Chinese hamster ovary cells. Moreover, we demonstrated that the IgE bsAb construct was significantly more efficient in mediating antibody-dependent cell toxicity than its IgG1 counterpart. In conclusion, we describe the successful development of first bispecific IgE antibodies with superior antibody-dependent cell toxicity-mediated cell killing in comparison to IgG bispecific antibodies. These findings highlight the relevance of IgE-based bispecific antibodies for clinical application.
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Affiliation(s)
- Natasa Vukovic
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Samer Halabi
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Joan Salvador Russo-Cabrera
- Program of Immunology and Immunotherapy, CIMA, Universidad de Navarra, Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - Bart Blokhuis
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Pedro Berraondo
- Program of Immunology and Immunotherapy, CIMA, Universidad de Navarra, Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain; Spanish Center for Biomedical Research Network in Oncology (CIBERONC), Madrid, Spain
| | - Frank A M Redegeld
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.
| | - Dietmar M W Zaiss
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK; Department of Immune Medicine, University Regensburg, Regensburg, Germany; Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany; Institute of Pathology, University Regensburg, Regensburg, Germany.
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17
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Fernández-Quintero ML, Kroell KB, Grunewald LJ, Fischer ALM, Riccabona JR, Liedl KR. CDR loop interactions can determine heavy and light chain pairing preferences in bispecific antibodies. MAbs 2022; 14:2024118. [PMID: 35090383 PMCID: PMC8803122 DOI: 10.1080/19420862.2021.2024118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/27/2021] [Indexed: 11/02/2022] Open
Abstract
As the current biotherapeutic market is dominated by antibodies, the design of different antibody formats, like bispecific antibodies, is critical to the advancement of the field. In contrast to monovalent antibodies, which consist of two identical antigen-binding sites, bispecific antibodies can target two different epitopes by containing two different antigen-binding sites. Thus, the rise of new formats as successful therapeutics has reignited the interest in advancing and facilitating the efficient production of bispecific antibodies. Here, we investigate the influence of point mutations in the antigen-binding site, the paratope, on heavy and light chain pairing preferences by using molecular dynamics simulations. In agreement with experiments, we find that specific residues in the antibody variable domain (Fv), i.e., the complementarity-determining region (CDR) L3 and H3 loops, determine heavy and light chain pairing preferences. Excitingly, we observe substantial population shifts in CDR-H3 and CDR-L3 loop conformations in solution accompanied by a decrease in bispecific IgG yield. These conformational changes in the CDR3 loops induced by point mutations also influence all other CDR loop conformations and consequentially result in different CDR loop states in solution. However, besides their effect on the obtained CDR loop ensembles, point mutations also lead to distinct interaction patterns in the VH-VL interface. By comparing the interaction patterns among all investigated variants, we observe specific contacts in the interface that drive heavy and light chain pairing. Thus, these findings have broad implications in the field of antibody engineering and design because they provide a mechanistic understanding of antibody interfaces, by identifying critical factors driving the pairing preferences, and thus can help to advance the design of bispecific antibodies.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Katharina B. Kroell
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Lukas J. Grunewald
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Anna-Lena M. Fischer
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Jakob R. Riccabona
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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18
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Campuzano IDG, Sandoval W. Denaturing and Native Mass Spectrometric Analytics for Biotherapeutic Drug Discovery Research: Historical, Current, and Future Personal Perspectives. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1861-1885. [PMID: 33886297 DOI: 10.1021/jasms.1c00036] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Mass spectrometry (MS) plays a key role throughout all stages of drug development and is now as ubiquitous as other analytical techniques such as surface plasmon resonance, nuclear magnetic resonance, and supercritical fluid chromatography, among others. Herein, we aim to discuss the history of MS, both electrospray and matrix-assisted laser desorption ionization, specifically for the analysis of antibodies, evolving through to denaturing and native-MS analysis of newer biologic moieties such as antibody-drug conjugates, multispecific antibodies, and interfering nucleic acid-based therapies. We discuss challenging therapeutic target characterization such as membrane protein receptors. Importantly, we compare and contrast the MS and hyphenated analytical chromatographic methods used to characterize these therapeutic modalities and targets within biopharmaceutical research and highlight the importance of appropriate MS deconvolution software and its essential contribution to project progression. Finally, we describe emerging applications and MS technologies that are still predominantly within either a development or academic stage of use but are poised to have significant impact on future drug development within the biopharmaceutic industry once matured. The views reflected herein are personal and are not meant to be an exhaustive list of all relevant MS performed within biopharmaceutical research but are what we feel have been historically, are currently, and will be in the future the most impactful for the drug development process.
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MESH Headings
- Antibodies, Monoclonal/analysis
- Automation, Laboratory
- Biopharmaceutics/methods
- Chromatography, Liquid
- Drug Discovery/methods
- Drug Industry/history
- History, 20th Century
- History, 21st Century
- Humans
- Immunoconjugates/analysis
- Immunoconjugates/chemistry
- Protein Denaturation
- Protein Processing, Post-Translational
- Proteins/analysis
- Spectrometry, Mass, Electrospray Ionization/history
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/history
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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Affiliation(s)
- Iain D G Campuzano
- Discovery Attribute Sciences, Amgen Research, 1 Amgen Center Drive, Thousand Oaks, California 92130, United States
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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19
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Guo C, Chen F, Xiao Q, Catterall HB, Robinson JH, Wang Z, Mock M, Hubert R. Expression liabilities in a four-chain bispecific molecule. Biotechnol Bioeng 2021; 118:3744-3759. [PMID: 34110008 DOI: 10.1002/bit.27850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/07/2021] [Accepted: 06/01/2021] [Indexed: 12/18/2022]
Abstract
Multispecific antibodies, often composed of three to five polypeptide chains, have become increasingly relevant in the development of biotherapeutics. These molecules have mechanisms of action that include redirecting T cells to tumors and blocking multiple pathogenic mediators simultaneously. One of the major challenges for asymmetric multispecific antibodies is generating a high proportion of the correctly paired antibody during production. To understand the causes and effects of chain mispairing impurities in a difficult to express multispecific hetero-IgG, we investigated consequences of individual and pairwise chain expression in mammalian transient expression hosts. We found that one of the two light chains (LC) was not secretion competent when transfected individually or cotransfected with the noncognate heavy chain (HC). Overexpression of this secretion impaired LC reduced cell growth while inducing endoplasmic reticulum stress and CCAAT/enhancer-binding protein homologous protein (CHOP) expression. The majority of this LC was observed as monomer with incomplete intrachain disulfide bonds when expressed individually. Russell bodies (RB) were induced when this LC was co-expressed with the cognate HC. Moreover, one HC paired promiscuously with noncognate LC. These results identify the causes for the low product quality observed from stable cell lines expressing this heteroIgG and suggest mitigation strategies to improve overall process productivity of the correctly paired multispecific antibody. The approach described here provides a general strategy for identifying the molecular and cellular liabilities associated with difficult to express multispecific antibodies.
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Affiliation(s)
- Cai Guo
- Department of Therapeutic Discovery, Amgen Research, Amgen Inc., Thousand Oaks, California, USA
| | - Fuyi Chen
- Department of Therapeutic Discovery, Amgen Research, Amgen Inc., Thousand Oaks, California, USA
| | - Qiang Xiao
- Department of Therapeutic Discovery, Amgen Research, Amgen Inc., Thousand Oaks, California, USA
| | - Hannah B Catterall
- Department of Therapeutic Discovery, Amgen Research, Amgen Inc., Thousand Oaks, California, USA
| | - John H Robinson
- Department of Therapeutic Discovery, Amgen Research, Amgen Inc., Thousand Oaks, California, USA
| | - Zhulun Wang
- Department of Therapeutic Discovery, Amgen Research, Amgen Inc., San Francisco, California, USA
| | - Marissa Mock
- Department of Therapeutic Discovery, Amgen Research, Amgen Inc., Thousand Oaks, California, USA
| | - René Hubert
- Department of Therapeutic Discovery, Amgen Research, Amgen Inc., Thousand Oaks, California, USA
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20
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Lim SA, Gramespacher JA, Pance K, Rettko NJ, Solomon P, Jin J, Lui I, Elledge SK, Liu J, Bracken CJ, Simmons G, Zhou XX, Leung KK, Wells JA. Bispecific VH/Fab antibodies targeting neutralizing and non-neutralizing Spike epitopes demonstrate enhanced potency against SARS-CoV-2. MAbs 2021; 13:1893426. [PMID: 33666135 PMCID: PMC7939556 DOI: 10.1080/19420862.2021.1893426] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/10/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous neutralizing antibodies that target SARS-CoV-2 have been reported, and most directly block binding of the viral Spike receptor-binding domain (RBD) to angiotensin-converting enzyme II (ACE2). Here, we deliberately exploit non-neutralizing RBD antibodies, showing they can dramatically assist in neutralization when linked to neutralizing binders. We identified antigen-binding fragments (Fabs) by phage display that bind RBD, but do not block ACE2 or neutralize virus as IgGs. When these non-neutralizing Fabs were assembled into bispecific VH/Fab IgGs with a neutralizing VH domain, we observed a ~ 25-fold potency improvement in neutralizing SARS-CoV-2 compared to the mono-specific bi-valent VH-Fc alone or the cocktail of the VH-Fc and IgG. This effect was epitope-dependent, reflecting the unique geometry of the bispecific antibody toward Spike. Our results show that a bispecific antibody that combines both neutralizing and non-neutralizing epitopes on Spike-RBD is a promising and rapid engineering strategy to improve the potency of SARS-CoV-2 antibodies.
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MESH Headings
- Antibodies, Bispecific/genetics
- Antibodies, Bispecific/immunology
- Antibodies, Bispecific/therapeutic use
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- COVID-19/genetics
- COVID-19/immunology
- Epitopes/genetics
- Epitopes/immunology
- HEK293 Cells
- Humans
- Immunoglobulin Fab Fragments/genetics
- Immunoglobulin Fab Fragments/immunology
- Immunoglobulin Fab Fragments/therapeutic use
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- COVID-19 Drug Treatment
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Affiliation(s)
- Shion A. Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Josef A. Gramespacher
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Katarina Pance
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Nicholas J. Rettko
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Paige Solomon
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Jing Jin
- Vitalant Research Institute and Department of Laboratory Medicine, University of California San Francisco, University of California San Francisco, California, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Susanna K. Elledge
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Jia Liu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Colton J. Bracken
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Graham Simmons
- Vitalant Research Institute and Department of Laboratory Medicine, University of California San Francisco, University of California San Francisco, California, USA
| | - Xin X. Zhou
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Kevin K. Leung
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - James A. Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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Surowka M, Schaefer W, Klein C. Ten years in the making: application of CrossMab technology for the development of therapeutic bispecific antibodies and antibody fusion proteins. MAbs 2021; 13:1967714. [PMID: 34491877 PMCID: PMC8425689 DOI: 10.1080/19420862.2021.1967714] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
Bispecific antibodies have recently attracted intense interest. CrossMab technology was described in 2011 as novel approach enabling correct antibody light-chain association with their respective heavy chain in bispecific antibodies, together with methods enabling correct heavy-chain association using existing pairs of antibodies. Since the original description, CrossMab technology has evolved in the past decade into one of the most mature, versatile, and broadly applied technologies in the field, and nearly 20 bispecific antibodies based on CrossMab technology developed by Roche and others have entered clinical trials. The most advanced of these are the Ang-2/VEGF bispecific antibody faricimab, currently undergoing regulatory review, and the CD20/CD3 T cell bispecific antibody glofitamab, currently in pivotal Phase 3 trials. In this review, we introduce the principles of CrossMab technology, including its application for the generation of bi-/multispecific antibodies with different geometries and mechanisms of action, and provide an overview of CrossMab-based therapeutics in clinical trials.
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Sawant MS, Streu CN, Wu L, Tessier PM. Toward Drug-Like Multispecific Antibodies by Design. Int J Mol Sci 2020; 21:E7496. [PMID: 33053650 PMCID: PMC7589779 DOI: 10.3390/ijms21207496] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
The success of antibody therapeutics is strongly influenced by their multifunctional nature that couples antigen recognition mediated by their variable regions with effector functions and half-life extension mediated by a subset of their constant regions. Nevertheless, the monospecific IgG format is not optimal for many therapeutic applications, and this has led to the design of a vast number of unique multispecific antibody formats that enable targeting of multiple antigens or multiple epitopes on the same antigen. Despite the diversity of these formats, a common challenge in generating multispecific antibodies is that they display suboptimal physical and chemical properties relative to conventional IgGs and are more difficult to develop into therapeutics. Here we review advances in the design and engineering of multispecific antibodies with drug-like properties, including favorable stability, solubility, viscosity, specificity and pharmacokinetic properties. We also highlight emerging experimental and computational methods for improving the next generation of multispecific antibodies, as well as their constituent antibody fragments, with natural IgG-like properties. Finally, we identify several outstanding challenges that need to be addressed to increase the success of multispecific antibodies in the clinic.
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Affiliation(s)
- Manali S. Sawant
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Craig N. Streu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemistry, Albion College, Albion, MI 49224, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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