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Asano R, Takeuchi M, Nakakido M, Ito S, Aikawa C, Yokoyama T, Senoo A, Ueno G, Nagatoishi S, Tanaka Y, Nakagawa I, Tsumoto K. Characterization of a novel format scFv×VHH single-chain biparatopic antibody against metal binding protein MtsA. Protein Sci 2024; 33:e5017. [PMID: 38747382 PMCID: PMC11094767 DOI: 10.1002/pro.5017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024]
Abstract
Biparatopic antibodies (bpAbs) are engineered antibodies that bind to multiple different epitopes within the same antigens. bpAbs comprise diverse formats, including fragment-based formats, and choosing the appropriate molecular format for a desired function against a target molecule is a challenging task. Moreover, optimizing the design of constructs requires selecting appropriate antibody modalities and adjusting linker length for individual bpAbs. Therefore, it is crucial to understand the characteristics of bpAbs at the molecular level. In this study, we first obtained single-chain variable fragments and camelid heavy-chain variable domains targeting distinct epitopes of the metal binding protein MtsA and then developed a novel format single-chain bpAb connecting these fragment antibodies with various linkers. The physicochemical properties, binding activities, complex formation states with antigen, and functions of the bpAb were analyzed using multiple approaches. Notably, we found that the assembly state of the complexes was controlled by a linker and that longer linkers tended to form more compact complexes. These observations provide detailed molecular information that should be considered in the design of bpAbs.
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Affiliation(s)
- Risa Asano
- Department of BioengineeringSchool of Engineering, The University of TokyoTokyoJapan
| | - Miyu Takeuchi
- Department of BioengineeringSchool of Engineering, The University of TokyoTokyoJapan
| | - Makoto Nakakido
- Department of BioengineeringSchool of Engineering, The University of TokyoTokyoJapan
- Department of Chemistry and BiotechnologySchool of Engineering, The University of TokyoTokyoJapan
| | - Sho Ito
- Rigaku Corporation ROD Single Crystal Analysis Group Application LaboratoriesTokyoJapan
| | - Chihiro Aikawa
- Section of Applied Veterinary Sciences, Division of Veterinary Sciences, Department of Veterinary MedicineObihiro University of Agriculture and Veterinary MedicineHokkaidoJapan
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku UniversityMiyagiJapan
- The advanced center for innovations in next‐generation medicine (INGEM)Tohoku UniversityMiyagiJapan
| | - Akinobu Senoo
- Department of Chemistry and BiotechnologySchool of Engineering, The University of TokyoTokyoJapan
| | - Go Ueno
- RIKEN SPring‐8 CenterHyogoJapan
| | - Satoru Nagatoishi
- Medical Device Development and Regulation Research CenterSchool of Engineering, The University of TokyoTokyoJapan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku UniversityMiyagiJapan
- The advanced center for innovations in next‐generation medicine (INGEM)Tohoku UniversityMiyagiJapan
| | - Ichiro Nakagawa
- Department of MicrobiologyGraduate School of Medicine, Kyoto UniversityKyotoJapan
| | - Kouhei Tsumoto
- Department of BioengineeringSchool of Engineering, The University of TokyoTokyoJapan
- Department of Chemistry and BiotechnologySchool of Engineering, The University of TokyoTokyoJapan
- Medical Device Development and Regulation Research CenterSchool of Engineering, The University of TokyoTokyoJapan
- The Institute of Medical Science, The University of TokyoTokyoJapan
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Krishna S, Jung ST, Lee EY. Escherichia coli and Pichia pastoris: microbial cell-factory platform for -full-length IgG production. Crit Rev Biotechnol 2024:1-23. [PMID: 38797692 DOI: 10.1080/07388551.2024.2342969] [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: 12/13/2023] [Accepted: 03/18/2024] [Indexed: 05/29/2024]
Abstract
Owing to the unmet demand, the pharmaceutical industry is investigating an alternative host to mammalian cells to produce antibodies for a variety of therapeutic and research applications. Regardless of some disadvantages, Escherichia coli and Pichia pastoris are the preferred microbial hosts for antibody production. Despite the fact that the production of full-length antibodies has been successfully demonstrated in E. coli, which has mostly been used to produce antibody fragments, such as: antigen-binding fragments (Fab), single-chain fragment variable (scFv), and nanobodies. In contrast, Pichia, a eukaryotic microbial host, is mostly used to produce glycosylated full-length antibodies, though hypermannosylated glycan is a major challenge. Advanced strategies, such as the introduction of human-like glycosylation in endotoxin-edited E. coli and cell-free system-based glycosylation, are making progress in creating human-like glycosylation profiles of antibodies in these microbes. This review begins by explaining the structural and functional requirements of antibodies and continues by describing and analyzing the potential of E. coli and P. pastoris as hosts for providing a favorable environment to create a fully functional antibody. In addition, authors compare these microbes on certain features and predict their future in antibody production. Briefly, this review analyzes, compares, and highlights E. coli and P. pastoris as potential hosts for antibody production.
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Affiliation(s)
- Shyam Krishna
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Sang Taek Jung
- BK21 Graduate Program, Department of Biomedical Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
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Liang WC, Xi H, Sun D, D’Ascenzo L, Zarzar J, Stephens N, Cook R, Li Y, Ye Z, Matsumoto M, Payandeh J, Masureel M, Wu Y. Structure- and machine learning-guided engineering demonstrate that a non-canonical disulfide in an anti-PD-1 rabbit antibody does not impede antibody developability. MAbs 2024; 16:2309685. [PMID: 38356181 PMCID: PMC10877986 DOI: 10.1080/19420862.2024.2309685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/21/2024] [Indexed: 02/16/2024] Open
Abstract
Rabbits produce robust antibody responses and have unique features in their antibody repertoire that make them an attractive alternative to rodents for in vivo discovery. However, the frequent occurrence of a non-canonical disulfide bond between complementarity-determining region (CDR) H1 (C35a) and CDRH2 (C50) is often seen as a liability for therapeutic antibody development, despite limited reports of its effect on antibody binding, function, and stability. Here, we describe the discovery and humanization of a human-mouse cross-reactive anti-programmed cell death 1 (PD-1) monoclonal rabbit antibody, termed h1340.CC, which possesses this non-canonical disulfide bond. Initial removal of the non-canonical disulfide resulted in a loss of PD-1 affinity and cross-reactivity, which led us to explore protein engineering approaches to recover these. First, guided by the sequence of a related clone and the crystal structure of h1340.CC in complex with PD-1, we generated variant h1340.SA.LV with a potency and cross-reactivity similar to h1340.CC, but only partially recovered affinity. Side-by-side developability assessment of both h1340.CC and h1340.SA.LV indicate that they possess similar, favorable properties. Next, and prompted by recent developments in machine learning (ML)-guided protein engineering, we used an unbiased ML- and structure-guided approach to rapidly and efficiently generate a different variant with recovered affinity. Our case study thus indicates that, while the non-canonical inter-CDR disulfide bond found in rabbit antibodies does not necessarily constitute an obstacle to therapeutic antibody development, combining structure- and ML-guided approaches can provide a fast and efficient way to improve antibody properties and remove potential liabilities.
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Affiliation(s)
- Wei-Ching Liang
- Department of Antibody Engineering, Genentech Inc, South San Francisco, CA, USA
| | - Hongkang Xi
- Department of Antibody Engineering, Genentech Inc, South San Francisco, CA, USA
| | - Dawei Sun
- Department of Structural Biology, Genentech Inc, South San Francisco, CA, USA
| | - Luigi D’Ascenzo
- Department of Structural Biology, Genentech Inc, South San Francisco, CA, USA
| | - Jonathan Zarzar
- Department of Pharma Technical Development, Genentech Inc, South San Francisco, CA, USA
| | - Nicole Stephens
- Department of Pharma Technical Development, Genentech Inc, South San Francisco, CA, USA
| | - Ryan Cook
- Department of Biochemical and Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Yinyin Li
- Department of Biochemical and Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Zhengmao Ye
- Department of Biochemical and Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
- Discovery Science & Technology Department, Gilead Sciences Inc, Foster City, CA, USA
| | - Marissa Matsumoto
- Department of Structural Biology, Genentech Inc, South San Francisco, CA, USA
- Asher Biotherapeutics, South San Francisco, CA, USA
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc, South San Francisco, CA, USA
- Exelixis Inc, Alameda, CA, USA
| | - Matthieu Masureel
- Department of Structural Biology, Genentech Inc, South San Francisco, CA, USA
| | - Yan Wu
- Department of Antibody Engineering, Genentech Inc, South San Francisco, CA, USA
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Banik SSR, Kushnir N, Doranz BJ, Chambers R. Breaking barriers in antibody discovery: harnessing divergent species for accessing difficult and conserved drug targets. MAbs 2023; 15:2273018. [PMID: 38050985 DOI: 10.1080/19420862.2023.2273018] [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: 05/31/2023] [Accepted: 10/16/2023] [Indexed: 12/07/2023] Open
Abstract
To exploit highly conserved and difficult drug targets, including multipass membrane proteins, monoclonal antibody discovery efforts increasingly rely on the advantages offered by divergent species such as rabbits, camelids, and chickens. Here, we provide an overview of antibody discovery technologies, analyze gaps in therapeutic antibodies that stem from the historic use of mice, and examine opportunities to exploit previously inaccessible targets through discovery now possible in alternate species. We summarize the clinical development of antibodies raised from divergent species, discussing how these animals enable robust immune responses against highly conserved binding sites and yield antibodies capable of penetrating functional pockets via long HCDR3 regions. We also discuss the value of pan-reactive molecules often produced by these hosts, and how these antibodies can be tested in accessible animal models, offering a faster path to clinical development.
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Brücksken KA, Loreto Palacio P, Hanschmann EM. Thiol Modifications in the Extracellular Space—Key Proteins in Inflammation and Viral Infection. Front Immunol 2022; 13:932525. [PMID: 35833136 PMCID: PMC9271835 DOI: 10.3389/fimmu.2022.932525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Posttranslational modifications (PTMs) allow to control molecular and cellular functions in response to specific signals and changes in the microenvironment of cells. They regulate structure, localization, stability, and function of proteins in a spatial and temporal manner. Among them, specific thiol modifications of cysteine (Cys) residues facilitate rapid signal transduction. In fact, Cys is unique because it contains the highly reactive thiol group that can undergo different reversible and irreversible modifications. Upon inflammation and changes in the cellular microenvironment, many extracellular soluble and membrane proteins undergo thiol modifications, particularly dithiol–disulfide exchange, S-glutathionylation, and S-nitrosylation. Among others, these thiol switches are essential for inflammatory signaling, regulation of gene expression, cytokine release, immunoglobulin function and isoform variation, and antigen presentation. Interestingly, also the redox state of bacterial and viral proteins depends on host cell-mediated redox reactions that are critical for invasion and infection. Here, we highlight mechanistic thiol switches in inflammatory pathways and infections including cholera, diphtheria, hepatitis, human immunodeficiency virus (HIV), influenza, and coronavirus disease 2019 (COVID-19).
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Ma H, Ó'Fágáin C, O'Kennedy R. Antibody stability: A key to performance - Analysis, influences and improvement. Biochimie 2020; 177:213-225. [PMID: 32891698 DOI: 10.1016/j.biochi.2020.08.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 02/01/2023]
Abstract
An antibody's stability greatly influences its performance (i.e. its specificity and affinity). Thus, stability is a major issue for researchers and manufacturers, especially with the increasing use of antibodies in therapeutics, diagnostics and rapid analytical platforms. Here we review antibody stability under five headings: (i) measurement techniques; (ii) stability issues in expression and production (expression, proteolysis, aggregation); (iii) effects of antibody format and engineering on stability and (iv) formulation, drying and storage conditions. We consider more than 100 sources, including patents, and conclude with (v) recommendations to promote antibody stability.
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Affiliation(s)
- Hui Ma
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland
| | - Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland.
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland; Qatar Foundation, Research Complex, And Hamad Bin Khalifa University, Education City, Doha, Qatar
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Akiba H, Satoh R, Nagata S, Tsumoto K. Effect of allotypic variation of human IgG1 on the thermal stability of disulfide-linked knobs-into-holes mutants of the Fc for stable bispecific antibody design. Antib Ther 2019; 2:65-69. [PMID: 33928224 PMCID: PMC7990158 DOI: 10.1093/abt/tbz008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/29/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022] Open
Abstract
Background Disulfide-linked knobs-into-holes (dKiH) mutation is a well-validated antibody engineering technique to force heterodimer formation of different Fcs for efficient production of bispecific antibodies. An artificial disulfide bond is created between mutated cysteine residues in CH3 domain of human IgG1 Fc whose positions are 354 of the “knob” and 349 of the “hole” heavy chains. The disulfide bond is located adjacent to the exposed loop with allotypic variations at positions 356 and 358. Effects of the variation on the biophysical property of the Fc protein with dKiH mutations have not been reported. Methods We produced dKiH Fc proteins of high purity by affinity-tag fusion to the hole chain and IdeS treatment, which enabled removal of mispaired side products. Thermal stability was analyzed in a differential scanning calorimetry instrument. Results We firstly analyzed the effect of the difference in allotypes of the Fcs on the thermal stability of the heterodimeric Fc. We observed different melting profiles of the two allotypes (G1m1 and nG1m1) showing slightly higher melting temperature of G1m1 than nG1m1. Additionally, we showed different characteristics among heterodimers with different combinations of the allotypes in knob and hole chains. Conclusion Allotypic variations affected melting profiles of dKiH Fc proteins possibly with larger contribution of variations adjacent to the disulfide linkage.
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Affiliation(s)
- Hiroki Akiba
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Reiko Satoh
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Satoshi Nagata
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Kouhei Tsumoto
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.,Medical Proteomics Laboratory, The Institute of Medical Sciences, The University of Tokyo, Tokyo, 108-8639, Japan
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Ning J, Ahmed S, Cheng G, Chen T, Wang Y, Peng D, Yuan Z. Analysis of the stability and affinity of BlaR-CTD protein to β-lactam antibiotics based on docking and mutagenesis studies. J Biol Eng 2019; 13:27. [PMID: 30976316 PMCID: PMC6441189 DOI: 10.1186/s13036-019-0157-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/14/2019] [Indexed: 12/20/2022] Open
Abstract
Owing to the thermal instability and low affinity of BlaR-CTD to some β-lactams, the receptor assay based on BlaR-CTD is limited in the detection of abundant variety of drugs and the result is often unstable. In this study, the three-dimensional structure of BlaR-CTD from Bacillus licheniformis ATCC14580 was constructed by homologous modeling based on the crystal structure of BlaR-CTD from B. licheniformis 749/I, and the binding sites of this protein to 40 β-lactams were also obtained by molecular docking. To improve the stability and affinity of the protein, 23 mutant proteins were designed based on docking and homologous alignment results as well as by inserting disulfide bond and building the salt bridge. The mutation was rationality evaluated by SIFT and PloyPhen2 software. The heterologous expressed and purified mutant proteins were then subjected to the activity and stability assay. It was shown that among all mutant proteins, I188K/S19C/G24C, A138E/R50C/Q147C and S190Y/E183C/I188K respectively exhibited a higher affinity to 33, 22 and 21 β-lactams than the wild-type protein, while I188K/S19C/G24C exhibited the best stability. This may due to that the conformation of the active site in mutant protein I188K/S19C/G24C changed, and the random coli in the surface of protein activity increased. Our study suggests a possible structure-function relationship on the stability and affinity of BlaR-CTD, which provides new insights into protein rational design study and lays a solid foundation for establishing the receptor-based screening assay for the detection of β-lactam residues.
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Affiliation(s)
- Jianan Ning
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Saeed Ahmed
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Guyue Cheng
- 2MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ting Chen
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yulian Wang
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Dapeng Peng
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zonghui Yuan
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China.,2MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
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