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He H, He B, Guan L, Zhao Y, Jiang F, Chen G, Zhu Q, Chen CYC, Li T, Yao J. De novo generation of SARS-CoV-2 antibody CDRH3 with a pre-trained generative large language model. Nat Commun 2024; 15:6867. [PMID: 39127753 PMCID: PMC11316817 DOI: 10.1038/s41467-024-50903-y] [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: 11/14/2023] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Artificial Intelligence (AI) techniques have made great advances in assisting antibody design. However, antibody design still heavily relies on isolating antigen-specific antibodies from serum, which is a resource-intensive and time-consuming process. To address this issue, we propose a Pre-trained Antibody generative large Language Model (PALM-H3) for the de novo generation of artificial antibodies heavy chain complementarity-determining region 3 (CDRH3) with desired antigen-binding specificity, reducing the reliance on natural antibodies. We also build a high-precision model antigen-antibody binder (A2binder) that pairs antigen epitope sequences with antibody sequences to predict binding specificity and affinity. PALM-H3-generated antibodies exhibit binding ability to SARS-CoV-2 antigens, including the emerging XBB variant, as confirmed through in-silico analysis and in-vitro assays. The in-vitro assays validate that PALM-H3-generated antibodies achieve high binding affinity and potent neutralization capability against spike proteins of SARS-CoV-2 wild-type, Alpha, Delta, and the emerging XBB variant. Meanwhile, A2binder demonstrates exceptional predictive performance on binding specificity for various epitopes and variants. Furthermore, by incorporating the attention mechanism inherent in the Roformer architecture into the PALM-H3 model, we improve its interpretability, providing crucial insights into the fundamental principles of antibody design.
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Affiliation(s)
- Haohuai He
- AI Lab, Tencent, Shenzhen, 518052, China
- Artificial Intelligence Medical Research Center, School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Bing He
- AI Lab, Tencent, Shenzhen, 518052, China.
| | - Lei Guan
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Xi'an, China
| | - Yu Zhao
- AI Lab, Tencent, Shenzhen, 518052, China
| | - Feng Jiang
- AI Lab, Tencent, Shenzhen, 518052, China
| | - Guanxing Chen
- Artificial Intelligence Medical Research Center, School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Qingge Zhu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Xi'an, China
| | - Calvin Yu-Chian Chen
- AI for Science (AI4S)-Preferred Program, School of Electronic and Computer Engineering, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
- Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan.
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, 41354, Taiwan.
- Guangdong L-Med Biotechnology Co. Ltd, Meizhou, 514699, Guangdong, China.
| | - Ting Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Xi'an, China.
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2
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Izadi A, Karami Y, Bratanis E, Wrighton S, Khakzad H, Nyblom M, Olofsson B, Happonen L, Tang D, Sundwall M, Godzwon M, Chao Y, Toledo AG, Schmidt T, Ohlin M, Nilges M, Malmström J, Bahnan W, Shannon O, Malmström L, Nordenfelt P. The hinge-engineered IgG1-IgG3 hybrid subclass IgGh 47 potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies. Nat Commun 2024; 15:3600. [PMID: 38678029 PMCID: PMC11055898 DOI: 10.1038/s41467-024-47928-8] [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: 06/30/2023] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
Streptococcus pyogenes can cause invasive disease with high mortality despite adequate antibiotic treatments. To address this unmet need, we have previously generated an opsonic IgG1 monoclonal antibody, Ab25, targeting the bacterial M protein. Here, we engineer the IgG2-4 subclasses of Ab25. Despite having reduced binding, the IgG3 version promotes stronger phagocytosis of bacteria. Using atomic simulations, we show that IgG3's Fc tail has extensive movement in 3D space due to its extended hinge region, possibly facilitating interactions with immune cells. We replaced the hinge of IgG1 with four different IgG3-hinge segment subclasses, IgGhxx. Hinge-engineering does not diminish binding as with IgG3 but enhances opsonic function, where a 47 amino acid hinge is comparable to IgG3 in function. IgGh47 shows improved protection against S. pyogenes in a systemic infection mouse model, suggesting that IgGh47 has promise as a preclinical therapeutic candidate. Importantly, the enhanced opsonic function of IgGh47 is generalizable to diverse S. pyogenes strains from clinical isolates. We generated IgGh47 versions of anti-SARS-CoV-2 mAbs to broaden the biological applicability, and these also exhibit strongly enhanced opsonic function compared to the IgG1 subclass. The improved function of the IgGh47 subclass in two distant biological systems provides new insights into antibody function.
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Affiliation(s)
- Arman Izadi
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Yasaman Karami
- Université de Lorraine, CNRS, Inria, LORIA, F-54000, Nancy, France
- Institut Pasteur, Université Paris cite, CNRS UMR3528, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, F-75015, Paris, France
| | - Eleni Bratanis
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Sebastian Wrighton
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Hamed Khakzad
- Université de Lorraine, CNRS, Inria, LORIA, F-54000, Nancy, France
| | - Maria Nyblom
- Department of Biology & Lund Protein Production Platform (LP3), Lund University, Lund, Sweden
| | - Berit Olofsson
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Lotta Happonen
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Di Tang
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Martin Sundwall
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Magdalena Godzwon
- Department of Immunotechnology and SciLifeLab Drug Discovery and Development Platform, Lund University, Lund, Sweden
| | - Yashuan Chao
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Alejandro Gomez Toledo
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Tobias Schmidt
- Department of Clinical Sciences Lund, Division of Pediatrics, Faculty of Medicine, Lund University, Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology and SciLifeLab Drug Discovery and Development Platform, Lund University, Lund, Sweden
| | - Michael Nilges
- Institut Pasteur, Université Paris cite, CNRS UMR3528, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, F-75015, Paris, France
| | - Johan Malmström
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Wael Bahnan
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Oonagh Shannon
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
- Section for Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
| | - Lars Malmström
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Pontus Nordenfelt
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden.
- Department of Laboratory Medicine, Clinical Microbiology, Skåne University Hospital Lund, Lund University, Lund, Sweden.
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3
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Fernández-Quintero ML, Pomarici ND, Fischer ALM, Hoerschinger VJ, Kroell KB, Riccabona JR, Kamenik AS, Loeffler JR, Ferguson JA, Perrett HR, Liedl KR, Han J, Ward AB. Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines. Antibodies (Basel) 2023; 12:67. [PMID: 37873864 PMCID: PMC10594513 DOI: 10.3390/antib12040067] [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: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural features that drive antibody function and, consequently, their molecular recognition is critical for engineering antibodies. Here, we present the structural architecture of conventional IgG antibodies alongside other formats. We emphasize the importance of considering antibodies as conformational ensembles in solution instead of focusing on single-static structures because their functions and properties are strongly governed by their dynamic nature. Thus, in this review, we provide an overview of the unique structural and dynamic characteristics of antibodies with respect to their antigen recognition, biophysical properties, and effector functions. We highlight the numerous technical advances in antibody structure prediction and design, enabled by the vast number of experimentally determined high-quality structures recorded with cryo-EM, NMR, and X-ray crystallography. Lastly, we assess antibody and vaccine design strategies in the context of structure and dynamics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nancy D. Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna-Lena M. Fischer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Katharina B. Kroell
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna S. Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James A. Ferguson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailee R. Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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4
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Pacheco BLB, Nogueira CP, Venancio EJ. IgY Antibodies from Birds: A Review on Affinity and Avidity. Animals (Basel) 2023; 13:3130. [PMID: 37835736 PMCID: PMC10571861 DOI: 10.3390/ani13193130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
IgY antibodies are found in the blood and yolk of eggs. Several studies show the feasibility of utilising IgY for immunotherapy and immunodiagnosis. These antibodies have been studied because they fulfil the current needs for reducing, replacing, and improving the use of animals. Affinity and avidity represent the strength of the antigen-antibody interaction and directly influence antibody action. The aim of this review was to examine the factors that influence the affinity and avidity of IgY antibodies and the methodologies used to determine these variables. In birds, there are few studies on the maturation of antibody affinity and avidity, and these studies suggest that the use of an adjuvant-type of antigen, the animal lineage, the number of immunisations, and the time interfered with the affinity and avidity of IgY antibodies. Regarding the methodologies, most studies use chaotropic agents to determine the avidity index. Studies involving the solution phase and equilibrium titration reactions are also described. These results demonstrate the need for the standardisation of methodologies for the determination of affinity and avidity so that further studies can be performed to optimise the production of high avidity IgY antibodies.
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Affiliation(s)
| | - Camila Parada Nogueira
- Scientific Initiation Programme, Animal Science Course, State University of Londrina, Londrina 86038-350, Brazil;
| | - Emerson José Venancio
- Department of Pathological Sciences, State University of Londrina, Londrina 86038-350, Brazil
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5
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Bou-Jaoudeh M, Mimoun A, Delignat S, Peyron I, Capdevila L, Daventure V, Deligne C, Dimitrov JD, Christophe OD, Denis CV, Lenting PJ, Proulle V, Lacroix-Desmazes S. Imlifidase, a new option to optimize the management of patients with hemophilia A on emicizumab. J Thromb Haemost 2023; 21:2776-2783. [PMID: 37473843 DOI: 10.1016/j.jtha.2023.06.038] [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: 01/26/2023] [Revised: 06/07/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Emicizumab is a bispecific, chimeric, humanized immunoglobulin G (IgG)4 that mimics the procoagulant activity of factor (F) VIII (FVIII). Its long half-life and subcutaneous route of administration have been life-changing in treating patients with hemophilia A (HA) with or without FVIII inhibitors. However, emicizumab only partially mimics FVIII activity; it prevents but does not treat acute bleeds. Emergency management is particularly complicated in patients with FVIII inhibitors receiving emicizumab prophylaxis in whom exogenous FVIII is inefficient. We have shown recently that Imlifidase (IdeS), a bacterial IgG-degrading enzyme, efficiently eliminates human anti-FVIII IgG in a mouse model of severe HA with inhibitors and opens a therapeutic window for the administration of exogenous FVIII. OBJECTIVES To investigate the impact of IdeS treatment in inhibitor-positive HA mice injected with emicizumab. METHODS IdeS was injected to HA mice reconstituted with human neutralizing anti-FVIII IgG and treated with emicizumab. RESULTS IdeS hydrolyzed emicizumab in vitro and in vivo, albeit, at slower rates than another recombinant human monoclonal IgG4. While F(ab')2 fragments were rapidly cleared from the circulation, thus leading to a rapid loss of emicizumab procoagulant activity, low amounts of single-cleaved intermediate IgG persisted for several days. Moreover, the IdeS-mediated elimination of the neutralizing anti-FVIII IgG and restoration of the hemostatic efficacy of exogenous FVIII were not impaired by the presence of emicizumab and polyclonal human IgG in inhibitor-positive HA mice. CONCLUSION Our results suggest that IdeS could be administered to inhibitor-positive patients with HA receiving emicizumab prophylaxis to improve and ease the management of breakthrough bleeds or programmed major surgeries.
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Affiliation(s)
- Melissa Bou-Jaoudeh
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Angelina Mimoun
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Sandrine Delignat
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Ivan Peyron
- Laboratory for Hemostasis, Inflammation & Thrombosis, Unité Mixte de Recherche 1176, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, 94276 Le Kremlin-Bicêtre, France
| | - Ladislas Capdevila
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université Paris Cité, Paris, France; Service d'Hématologie Biologique et Unité Fonctionnelle d'Hémostase, Hôpital Cochin, AP-HP Centre, Université Paris Cité, Paris, France
| | - Victoria Daventure
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Claire Deligne
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Jordan D Dimitrov
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Olivier D Christophe
- Laboratory for Hemostasis, Inflammation & Thrombosis, Unité Mixte de Recherche 1176, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, 94276 Le Kremlin-Bicêtre, France
| | - Cécile V Denis
- Laboratory for Hemostasis, Inflammation & Thrombosis, Unité Mixte de Recherche 1176, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, 94276 Le Kremlin-Bicêtre, France
| | - Peter J Lenting
- Laboratory for Hemostasis, Inflammation & Thrombosis, Unité Mixte de Recherche 1176, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, 94276 Le Kremlin-Bicêtre, France
| | - Valérie Proulle
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université Paris Cité, Paris, France; Service d'Hématologie Biologique et Unité Fonctionnelle d'Hémostase, Hôpital Cochin, AP-HP Centre, Université Paris Cité, Paris, France
| | - Sébastien Lacroix-Desmazes
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université Paris Cité, Paris, France.
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6
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Shabani S, Rashidi M, Radgoudarzi S, Jebali A. The validation of artificial anti-monkeypox antibodies by in silico and experimental approaches. Immun Inflamm Dis 2023; 11:e834. [PMID: 37102640 PMCID: PMC10091375 DOI: 10.1002/iid3.834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/06/2023] [Accepted: 03/25/2023] [Indexed: 04/28/2023] Open
Abstract
As a result of smallpox immunization programs that ended more than 40 years ago, a significant portion of the world's population is not immune. Moreover, due to the lack of anti-monkeypox drugs and vaccines against monkeypox, the spread of this virus may be the beginning of another challenge. In this study, novel antibodies against monkeypox virus were modeled based on a heavy chain of human antibody and a small peptide fragment. Docking of modeled antibodies with C19L protein showed the range of docking energy, and root-mean-square deviation (RMSD) was from -124 to -154 kcal/mL and 4-6 angstrom, respectively. Also, docking of modeled antibodies-C19L complex with gamma Fc receptor type I illustrated the range of docking energy, and RMSD was from -132 to -155 kcal/ml and 5-7 angstrom, respectively. Moreover, molecular dynamics simulation showed that antibody 62 had the highest stability with the lowest energy level and RMSD. Interestingly, no modeled antibodies had immunogenicity, allergenicity, and toxicity. Although all of them had good stability, only antibodies 25, 28, 54, and 62 had a half-life of >10 h. Moreover, the interaction between C19L protein and anti-C19L antibodies (wild-type and synthetic) was evaluated by the SPR method. We found that KD in synthetic antibodies was lower than wild antibody. In terms of δH°, TδS°, and δG°, the results were consistent with binding parameters. Here, the lowest value of thermodynamic parameters was obtained for antibody 62. These data show that the synthetic antibodies, especially antibody 62, had a higher affinity than the wild-type antibody.
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Affiliation(s)
- Sadeq Shabani
- Department of Biological Sciences, Florida International University, Miami, Florida, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, USA
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Shakila Radgoudarzi
- I.M. Sechenov First Moscow State Medical University (Первый МГМУ им), Moscow, Russia
| | - Ali Jebali
- Department of Medical Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Science, Islamic Azad University, Tehran, Iran
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7
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Construction of a Fab Library Merging Chains from Semisynthetic and Immune Origin, Suitable for Developing New Tools for Gluten Immunodetection in Food. Foods 2022; 12:foods12010149. [PMID: 36613365 PMCID: PMC9818130 DOI: 10.3390/foods12010149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
The observed increase in the prevalence of gluten-related disorders has prompted the development of novel immunological systems for gluten detection in foodstuff. The innovation on these methods relies on the generation of new antibodies, which might alternatively be obtained by molecular evolution methods such as phage display. This work presents a novel approach for the generation of a Fab library by merging semi-synthetic heavy chains built-up from a pre-existent recombinant antibody fragment (dAb8E) with an immune light chain set derived from celiac donors. From the initial phage population (107 candidates) and after three rounds of selection and amplification, four different clones were isolated for further characterization. The phage Fab8E-4 presented the best features to be applied in an indirect ELISA for the detection of gluten in foods, resulting in improved specificity and sensitivity.
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8
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Lombard-Vadnais F, Chabot-Roy G, Zahn A, Rodriguez Torres S, Di Noia JM, Melichar HJ, Lesage S. Activation-induced cytidine deaminase expression by thymic B cells promotes T-cell tolerance and limits autoimmunity. iScience 2022; 26:105852. [PMID: 36654860 PMCID: PMC9840937 DOI: 10.1016/j.isci.2022.105852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/24/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Elimination of self-reactive T cells in the thymus is critical to establish T-cell tolerance. A growing body of evidence suggests a role for thymic B cells in the elimination of self-reactive thymocytes. To specifically address the role of thymic B cells in central tolerance, we investigated the phenotype of thymic B cells in various mouse strains, including non-obese diabetic (NOD) mice, a model of autoimmune diabetes. We noted that isotype switching of NOD thymic B cells is reduced as compared to other, autoimmune-resistant, mouse strains. To determine the impact of B cell isotype switching on thymocyte selection and tolerance, we generated NOD.AID-/- mice. Diabetes incidence was enhanced in these mice. Moreover, we observed reduced clonal deletion and a resulting increase in self-reactive CD4+ T cells in NOD.AID-/- mice relative to NOD controls. Together, this study reveals that AID expression in thymic B cells contributes to T-cell tolerance.
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Affiliation(s)
- Félix Lombard-Vadnais
- Immunologie-oncologie, Centre de recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC H1T 2M4, Canada,Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Geneviève Chabot-Roy
- Immunologie-oncologie, Centre de recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC H1T 2M4, Canada
| | - Astrid Zahn
- Unité de recherche en biologie moléculaire des cellules B, Institut de recherches cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Sahily Rodriguez Torres
- Immunologie-oncologie, Centre de recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC H1T 2M4, Canada,Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Javier M. Di Noia
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 0G4, Canada,Unité de recherche en biologie moléculaire des cellules B, Institut de recherches cliniques de Montréal, Montréal, QC H2W 1R7, Canada,Département de médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada,Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Heather J. Melichar
- Immunologie-oncologie, Centre de recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC H1T 2M4, Canada,Département de médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada,Corresponding author
| | - Sylvie Lesage
- Immunologie-oncologie, Centre de recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC H1T 2M4, Canada,Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC H3T 1J4, Canada,Corresponding author
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9
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Pomarici ND, Fernández-Quintero ML, Quoika PK, Waibl F, Bujotzek A, Georges G, Liedl KR. Bispecific antibodies-effects of point mutations on CH3-CH3 interface stability. Protein Eng Des Sel 2022; 35:6873150. [PMID: 36468666 PMCID: PMC9741699 DOI: 10.1093/protein/gzac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 12/12/2022] Open
Abstract
A new format of therapeutic proteins is bispecific antibodies, in which two different heavy chains heterodimerize to obtain two different binding sites. Therefore, it is crucial to understand and optimize the third constant domain (CH3-CH3) interface to favor heterodimerization over homodimerization, and to preserve the physicochemical properties, as thermal stability. Here, we use molecular dynamics simulations to investigate the dissociation process of 19 CH3-CH3 crystal structures that differ from each other in few point mutations. We describe the dissociation of the dimeric interface as a two-steps mechanism. As confirmed by a Markov state model, apart from the bound and the dissociated state, we observe an additional intermediate state, which corresponds to an encounter complex. The analysis of the interdomain contacts reveals key residues that stabilize the interface. We expect that our results will improve the understanding of the CH3-CH3 interface interactions and thus advance the developability and design of new antibodies formats.
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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, A-6020 Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-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, A-6020 Innsbruck, Austria,Center for Protein Assemblies (CPA), Department of Physics, Chair of Theoretical Biophysics, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Nonnenwald 2, Penzberg, 82377, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Nonnenwald 2, Penzberg, 82377, Germany
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10
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Moyo-Gwete T, Scheepers C, Makhado Z, Kgagudi P, Mzindle NB, Ziki R, Madzorera S, Manamela NP, Ayres F, Lambson BE, Richardson SI, Morris L, Moore PL. Enhanced neutralization potency of an identical HIV neutralizing antibody expressed as different isotypes is achieved through genetically distinct mechanisms. Sci Rep 2022; 12:16473. [PMID: 36182959 PMCID: PMC9526727 DOI: 10.1038/s41598-022-20141-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/09/2022] [Indexed: 11/25/2022] Open
Abstract
Antibodies with the same variable region can exist as multiple isotypes with varying neutralization potencies, though the mechanism for this is not fully defined. We previously isolated an HIV-directed IgA1 monoclonal antibody (mAb), CAP88-CH06, and showed that IgA1 and IgG3 isotypes of this antibody demonstrated enhanced neutralization compared to IgG1. To explore the mechanism behind this, hinge region and constant heavy chain (CH1) chimeras were constructed between the IgA1, IgG3 and IgG1 mAbs and assessed for neutralization activity, antibody-dependent cellular phagocytosis (ADCP) and antibody-dependent cellular cytotoxicity (ADCC). Hinge chimeras revealed that the increased neutralization potency and phagocytosis of the IgG3 isotype was attributed to its longer hinge region. In contrast, for IgA1, CH1 chimeras showed that this region was responsible both for enhanced neutralization potency and decreased ADCP, though ADCC was not affected. Overall, these data show that the enhanced neutralization potency of CAP88-CH06 IgG3 and IgA1, compared to IgG1, is achieved through distinct mechanisms. Understanding the influence of the hinge and CH1 regions on Fab domain function may provide insights into the engineering of therapeutic antibodies with increased neutralization potency.
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Affiliation(s)
- Thandeka Moyo-Gwete
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Cathrine Scheepers
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Makhado
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Prudence Kgagudi
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Nonkululeko B Mzindle
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Rutendo Ziki
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Sharon Madzorera
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Nelia P Manamela
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Frances Ayres
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Bronwen E Lambson
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Simone I Richardson
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa. .,SA MRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa. .,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa. .,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
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11
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Bolton MJ, Arevalo CP, Griesman T, Li SH, Bates P, Wilson PC, Hensley SE. IgG3 subclass antibodies recognize antigenically drifted influenza viruses and SARS-CoV-2 variants through efficient bivalent binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.27.509738. [PMID: 36203556 PMCID: PMC9536032 DOI: 10.1101/2022.09.27.509738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The constant domains of antibodies are important for effector functions, but less is known about how they can affect binding and neutralization of viruses. Here we evaluated a panel of human influenza virus monoclonal antibodies (mAbs) expressed as IgG1, IgG2 or IgG3. We found that many influenza virus-specific mAbs have altered binding and neutralization capacity depending on the IgG subclass encoded, and that these differences result from unique bivalency capacities of the subclasses. Importantly, subclass differences in antibody binding and neutralization were greatest when the affinity for the target antigen was reduced through antigenic mismatch. We found that antibodies expressed as IgG3 bound and neutralized antigenically drifted influenza viruses more effectively. We obtained similar results using a panel of SARS-CoV-2-specific mAbs and the antigenically advanced B.1.351 strain of SARS-CoV-2. We found that a licensed therapeutic mAb retained neutralization breadth against SARS-CoV-2 variants when expressed as IgG3, but not IgG1. These data highlight that IgG subclasses are not only important for fine-tuning effector functionality, but also for binding and neutralization of antigenically drifted viruses. Significance Influenza viruses and coronaviruses undergo continuous change, successfully evading human antibodies elicited from prior infections or vaccinations. It is important to identify features that allow antibodies to bind with increased breadth. Here we examined the effect that different IgG subclasses have on monoclonal antibody binding and neutralization. We show that IgG subclass is a determinant of antibody breadth, with IgG3 affording increased neutralization of antigenically drifted variants of influenza virus and SARS-CoV-2. Future studies should evaluate IgG3 therapeutic antibodies and vaccination strategies or adjuvants that may skew antibody responses toward broadly reactive isotypes.
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Affiliation(s)
- Marcus J. Bolton
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Claudia P. Arevalo
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Trevor Griesman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shuk Hang Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paul Bates
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Patrick C. Wilson
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Scott E. Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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12
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Noailly B, Yaugel-Novoa M, Werquin J, Jospin F, Drocourt D, Bourlet T, Rochereau N, Paul S. Antiviral Activities of HIV-1-Specific Human Broadly Neutralizing Antibodies Are Isotype-Dependent. Vaccines (Basel) 2022; 10:vaccines10060903. [PMID: 35746511 PMCID: PMC9227833 DOI: 10.3390/vaccines10060903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023] Open
Abstract
Broadly neutralizing antibodies (bNAbs) offer promising opportunities for preventing HIV-1 infection. The protection mechanisms of bNAbs involve the Fc domain, as well as their Fab counterpart. Here, different bNAb isotypes including IgG1, IgA1, IgA2, and IgA122 (IgA2 with the hinge of IgA1) were generated and then produced in CHO cells. Their ability to neutralize pseudovirus and primary HIV-1 isolates were measured, as well as their potential ADCC-like activity using a newly developed assay. In our work, gp41-specific IgA seems to be more efficient than IgG1 in inducing ADCC-like activity, but not in its virus neutralization effect. We show that either gp120-specific IgA or IgG1 isotypes are both efficient in neutralizing different viral strains. In contrast, gp120-specific IgG1 was a better ADCC-like inducer than IgA isotypes. These results provide new insights into the neutralization and ADCC-like activity of different bNAbs that might be taken into consideration when searching for new treatments or antibody-based vaccines.
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Affiliation(s)
- Blandine Noailly
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France; (B.N.); (M.Y.-N.); (J.W.); (F.J.); (T.B.); (N.R.)
| | - Melyssa Yaugel-Novoa
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France; (B.N.); (M.Y.-N.); (J.W.); (F.J.); (T.B.); (N.R.)
| | - Justine Werquin
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France; (B.N.); (M.Y.-N.); (J.W.); (F.J.); (T.B.); (N.R.)
| | - Fabienne Jospin
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France; (B.N.); (M.Y.-N.); (J.W.); (F.J.); (T.B.); (N.R.)
| | | | - Thomas Bourlet
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France; (B.N.); (M.Y.-N.); (J.W.); (F.J.); (T.B.); (N.R.)
| | - Nicolas Rochereau
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France; (B.N.); (M.Y.-N.); (J.W.); (F.J.); (T.B.); (N.R.)
| | - Stéphane Paul
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France; (B.N.); (M.Y.-N.); (J.W.); (F.J.); (T.B.); (N.R.)
- Correspondence:
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13
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Lindeman I, Polak J, Qiao S, Holmøy T, Høglund RA, Vartdal F, Berg‐Hansen P, Sollid LM, Lossius A. Stereotyped B‐cell responses are linked to IgG constant region polymorphisms in multiple sclerosis. Eur J Immunol 2022; 52:550-565. [DOI: 10.1002/eji.202149576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/19/2021] [Accepted: 01/10/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Ida Lindeman
- Department of Immunology Oslo University Hospital Oslo Norway
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Justyna Polak
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Shuo‐Wang Qiao
- Department of Immunology Oslo University Hospital Oslo Norway
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Trygve Holmøy
- Department of Neurology Akershus University Hospital Lørenskog Norway
- Department of Neurology Institute of Clinical Medicine University of Oslo Norway
| | - Rune A. Høglund
- Department of Neurology Akershus University Hospital Lørenskog Norway
- Department of Neurology Institute of Clinical Medicine University of Oslo Norway
| | - Frode Vartdal
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Pål Berg‐Hansen
- Department of Neurology Oslo University Hospital Oslo Norway
| | - Ludvig M. Sollid
- Department of Immunology Oslo University Hospital Oslo Norway
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Andreas Lossius
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
- Department of Neurology Akershus University Hospital Lørenskog Norway
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Norway
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14
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Le PJ, Miersch S, Forbes MW, Jarvik N, Ku A, Sidhu SS, Reilly RM, Winnik MA. Site-Specific Conjugation of Metal-Chelating Polymers to Anti-Frizzled-2 Antibodies via Microbial Transglutaminase. Biomacromolecules 2021; 22:2491-2504. [PMID: 33961407 DOI: 10.1021/acs.biomac.1c00246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metal-chelating polymer-based radioimmunoconjugates (RICs) are effective agents for radioimmunotherapy but are currently limited by nonspecific binding and off-target organ uptake. Nonspecific binding appears after conjugation of the polymer to the antibody and may be related to random lysine conjugation since the polymers themselves do not bind to cells. To investigate the role of conjugation sites on nonspecific binding of polymer RICs, we developed a microbial transglutaminase reaction to prepare site-specific antibody-polymer conjugates. The reaction was enabled by introducing a Q-tag (i.e., 7M48) into antibody (i.e., Fab) fragments and synthesizing a polyglutamide-based metal-chelating polymer with a PEG amine block to yield substrates. Mass spectrometric analyses confirmed that the microbial transglutaminase conjugation reaction was site-specific. For comparison, random lysine conjugation analogs with an average of one polymer per Fab were prepared by bis-aryl hydrazone conjugation. Conjugates were prepared from an anti-frizzled-2 Fab to target the Wnt pathway, along with a nonbinding specificity control, anti-Luciferase Fab. Fabs were engineered from a trastuzumab-based IgG1 framework and lack lysines in the antigen-binding site. Conjugates were analyzed for thermal conformational stability by differential scanning fluorimetry, which showed that the site-specific conjugate had a similar melting temperature to the parent Fab. Binding assays by biolayer interferometry showed that the site-specific anti-frizzled-2 conjugate maintained high affinity to the antigen, while the random conjugate showed a 10-fold decrease in affinity, which was largely due to changes in association rates. Radioligand cell-binding assays on frizzled-2+ PANC-1 cells and frizzled-2- CHO cells showed that the site-specific anti-frizzled-2 conjugate had ca. 4-fold lower nonspecific binding compared to the random conjugate. Site-specific conjugation appeared to reduce nonspecific binding associated with random conjugation of the polymer in polymer RICs.
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Affiliation(s)
- Penny J Le
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 1H6, Canada
| | - Shane Miersch
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Matthew W Forbes
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 1H6, Canada
| | - Nick Jarvik
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Anthony Ku
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Raymond M Reilly
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada.,Joint Department of Medical Imaging and Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Mitchell A Winnik
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 1H6, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E2, Canada
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15
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Benedetti F, Stracke F, Stadlmayr G, Stadlbauer K, Rüker F, Wozniak-Knopp G. Bispecific antibodies with Fab-arms featuring exchanged antigen-binding constant domains. Biochem Biophys Rep 2021; 26:100959. [PMID: 33718630 PMCID: PMC7920882 DOI: 10.1016/j.bbrep.2021.100959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/16/2020] [Accepted: 02/16/2021] [Indexed: 12/27/2022] Open
Abstract
Monoclonal antibodies can acquire the property of engagement of a second antigen via fusion methods or modification of their CDR loops, but also by modification of their constant domains, such as in the mAb2 format where a set of mutated amino acid residues in the CH3 domains enables a high-affinity specific interaction with the second antigen. We tested the possibility of introducing multiple binding sites for the second antigen by replacing the Fab CH1/CL domain pair with a pair of antigen-binding CH3 domains in a model scaffold with trastuzumab variable domains and VEGF-binding CH3 domains. Such bispecific molecules were produced in a “Fab-like” format and in a full-length antibody format. Novel constructs were of expected molecular composition using mass spectrometry. They were expressed at a high level in standard laboratory conditions, purified as monomers with Protein A and gel filtration and were of high thermostability. Their high-affinity binding to both target antigens was retained. Finally, the Her2/VEGF binding domain-exchanged bispecific antibody was able to mediate a potentiated surface Her2-internalization effect on the Her2-overexpressing cell line SK-BR-3 due to improved level of cross-linking with the endogenously secreted cytokine. To conclude, bispecific antibodies with Fabs featuring exchanged antigen-binding CH3 domains offer an alternative solution in positioning and valency of antigen binding sites. Fab constant domains can be efficiently exchanged for antigen-binding CH3 domains. Such mutagenesis results in bispecific antibodies with correct chain pairing. Domain-exchanged bispecific Fab- and IgG-like formats are of favorable biophysical properties. Resulting bispecific antibodies show high-affinity binding to both target antigens.
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Key Words
- Ab, antibody
- BLI, biolayer interferometry
- BSA, bovine serum albumin
- Bispecific antibody
- CDR, complementarity determining region
- DSC, differential scanning calorimetry
- Domain-exchanged antibody
- EC50, half-maximal effective concentration
- FBS, fetal bovine serum
- FITC, fluorescein isothiocyanate
- Fab constant domain exchange
- Fab, fragment antigen binding
- Fc, fragment crystallizable
- Fcab, Fc with antigen binding properties
- HPLC-SEC, high pressure liquid chromatography-size exclusion chromatography
- Her2 internalization
- IgG, immunoglobulin G
- LC-ESI-MS, liquid chromatography-electrospray ionization-mass spectrometry
- PBS, phosphate buffered saline
- PE, phycoerythrin
- PEI, polyethylenimine
- PNGase F, Peptide:N-glycosidase F
- RMSD, root mean square deviation
- TRA, trastuzumab
- Tm, melting temperature
- VEGF, vascular endothelial growth factor
- “Knobs-into-holes” heterodimerization
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Affiliation(s)
- Filippo Benedetti
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Florian Stracke
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Gerhard Stadlmayr
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Katharina Stadlbauer
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Florian Rüker
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Gordana Wozniak-Knopp
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
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16
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Immunoglobulin germline gene variation and its impact on human disease. Genes Immun 2021; 22:205-217. [PMID: 34175903 PMCID: PMC8234759 DOI: 10.1038/s41435-021-00145-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 02/06/2023]
Abstract
Immunoglobulins (Ig) play an important role in the immune system both when expressed as antigen receptors on the cell surface of B cells and as antibodies secreted into extracellular fluids. The advent of high-throughput sequencing methods has enabled the investigation of human Ig repertoires at unprecedented depth. This has led to the discovery of many previously unreported germline Ig alleles. Moreover, it is becoming clear that convergent and stereotypic antibody responses are common where different individuals recognise defined antigenic epitopes with the use of the same Ig V genes. Thus, germline V gene variation is increasingly being linked to the differential capacity of generating an effective immune response, which might lead to varying disease susceptibility. Here, we review recent evidence of how germline variation in Ig genes impacts the Ig repertoire and its subsequent effects on the adaptive immune response in vaccination, infection, and autoimmunity.
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17
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Abstract
We studied the molecular details of the recognition of antigens by the variable domain of their cognate antibodies in as well as those elicited by the constant domains, which do not directly interact with antigens. Such effects are difficult to study experimentally; however, molecular dynamics simulations and subsequent residue interaction network analysis provide insight into the allosteric communication between the antigen-binding CDR region and the constant domain. We performed MD simulations of the complex of Fab and prion-associated peptide in the apo and bound forms and follow the conformational changes in the antibody and cross-talk between its subunits and with antigens. These protocols could be generally applied for studies of other antigens-antibody recognition systems.
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Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA.
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18
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Domnowski M, Lo Presti K, Binder J, Reindl J, Lehmann L, Kummer F, Wolber M, Satzger M, Dehling M, Jaehrling J, Frieß W. Generation of mAb Variants with Less Attractive Self-Interaction but Preserved Target Binding by Well-Directed Mutation. Mol Pharm 2020; 18:236-245. [PMID: 33331157 DOI: 10.1021/acs.molpharmaceut.0c00848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Strongly attractive self-interaction of therapeutic protein candidates can impose challenges for manufacturing, filling, stability, and administration due to elevated viscosity or aggregation propensity. Suitable formulations can mitigate these issues to a certain extent. Understanding the self-interaction mechanism on a molecular basis and rational protein engineering provides a more fundamental approach, and it can save costs and efforts as well as alleviate risks at later stages of development. In this study, we used computational methods for the identification of aggregation-prone regions in a mAb and generated mutants based on these findings. We applied hydrogen-deuterium exchange mass spectrometry to identify distinct self-interaction hot spots. Ultimately, we generated mAb variants based on a combination of both approaches and identified mutants with low attractive self-interaction propensity, minimal off-target binding, and even improved target binding. Our data show that the introduction of arginine in spatial proximity to hydrophobic patches is highly beneficial on all these levels. For our mAb, variants that contain more than one aspartate residue flanking to the hydrophobic HCDR3 show decreased attractive self-interaction at unaffected off-target and target binding. The combined engineering strategy described here underlines the high potential of understanding self-interaction in the early stages of development to predict and reduce the risk of failure in subsequent development.
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Affiliation(s)
- Martin Domnowski
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig Maximilians-Universitaet, Munich 81377, Germany.,MorphoSys AG, Department of Protein Sciences (Research), Planegg 82152, Germany
| | - Ken Lo Presti
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig Maximilians-Universitaet, Munich 81377, Germany
| | - Jonas Binder
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig Maximilians-Universitaet, Munich 81377, Germany
| | - Josef Reindl
- MorphoSys AG, Department of Protein Sciences (Research), Planegg 82152, Germany
| | - Lucille Lehmann
- MorphoSys AG, Department of Protein Sciences (Research), Planegg 82152, Germany
| | - Felix Kummer
- MorphoSys AG, Department of Protein Sciences (Research), Planegg 82152, Germany
| | - Meike Wolber
- MorphoSys AG, Department of Protein Sciences (Research), Planegg 82152, Germany
| | - Marion Satzger
- MorphoSys AG, Department of Protein Sciences (Research), Planegg 82152, Germany
| | - Marco Dehling
- MorphoSys AG, Department of Protein Sciences (Research), Planegg 82152, Germany
| | - Jan Jaehrling
- MorphoSys AG, Department of Protein Sciences (Research), Planegg 82152, Germany
| | - Wolfgang Frieß
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig Maximilians-Universitaet, Munich 81377, Germany
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19
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Defining the structural basis for human leukocyte antigen reactivity in clinical transplantation. Sci Rep 2020; 10:18397. [PMID: 33110123 PMCID: PMC7591533 DOI: 10.1038/s41598-020-75355-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
The current state-of-the-art technology employed to assess anti-human leukocyte antigen antibodies (Anti-HLA Ab) for donor-recipient matching and patient risk stratification in renal transplantation is the single antigen bead (SAB) assay. However, there are limitations to the SAB assay as it is not quantitative and due to variations in techniques and reagents, there is no standardization across laboratories. In this study, a structurally-defined human monoclonal alloantibody was employed to provide a mechanistic explanation for how fundamental alloantibody biology influences the readout from the SAB assay. Performance of the clinical SAB assay was evaluated by altering Anti-HLA Ab concentration, subclass, and detection reagents. Tests were conducted in parallel by two internationally accredited laboratories using standardized protocols and reagents. We show that alloantibody concentration, subclass, laboratory-specific detection devices, subclass-specific detection reagents all contribute to a significant degree of variation in the readout. We report a significant prozone effect affecting HLA alleles that are bound strongly by the test alloantibody as opposed to those bound weakly and this phenomenon is independent of complement. These data highlight the importance for establishing international standards for SAB assay calibration and have significant implications for our understanding of discordance in previous studies that have analyzed its clinical relevance.
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20
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Rossini S, Noé R, Daventure V, Lecerf M, Justesen S, Dimitrov JD. V Region of IgG Controls the Molecular Properties of the Binding Site for Neonatal Fc Receptor. THE JOURNAL OF IMMUNOLOGY 2020; 205:2850-2860. [PMID: 33077645 DOI: 10.4049/jimmunol.2000732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/17/2020] [Indexed: 01/09/2023]
Abstract
Neonatal Fc receptor (FcRn) has a key role in the homeostasis of IgG. Despite its physiological and clinical importance, the interaction of IgG and FcRn remains not completely comprehended. Thus, IgG molecules with identical constant portions but with minor differences in their V regions have been demonstrated to interact with FcRn with a considerable heterogeneity in the binding affinity. To understand this discrepancy, we dissected the physicochemical mechanism of the interaction of 10 human IgG1 to human FcRn. The interactions of two Abs in the presence of their cognate Ags were also examined. Data from activation and equilibrium thermodynamics analyses as well as pH dependence of the kinetics revealed that the V region of IgG could modulate a degree of conformational changes and binding energy of noncovalent contacts at the FcRn binding interface. These results suggest that the V domains modulate FcRn binding site in Fc by allosteric effects. These findings contribute for a deeper understanding of the mechanism of IgG-FcRn interaction. They might also be of relevance for rational engineering of Abs for optimizing their pharmacokinetic properties.
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Affiliation(s)
- Sofia Rossini
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, F-75006 Paris, France; and
| | - Rémi Noé
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, F-75006 Paris, France; and
| | - Victoria Daventure
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, F-75006 Paris, France; and
| | - Maxime Lecerf
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, F-75006 Paris, France; and
| | | | - Jordan D Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, F-75006 Paris, France; and
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21
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Warrender AK, Kelton W. Beyond Allotypes: The Influence of Allelic Diversity in Antibody Constant Domains. Front Immunol 2020; 11:2016. [PMID: 32973808 PMCID: PMC7461860 DOI: 10.3389/fimmu.2020.02016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/24/2020] [Indexed: 01/25/2023] Open
Abstract
Polymorphic diversity in antibody constant domains has long been defined by allotypic motifs that cross react with the sera of other individuals. Improvements in sequencing technologies have led to the discovery of a large number of new allelic sequences that underlie this diversity. Many of the point mutations lie outside traditional allotypic motifs suggesting they do not elicit immunogenic responses. As antibodies play an important role in immune defense and biotechnology, understanding how this newly resolved diversity influences the function of antibodies is important. This review investigates the current known diversity of antibody alleles at a protein level for each antibody isotype as well as the kappa and lambda light chains. We focus on evidence emerging for how these mutations perturb antibody interactions with antigens and Fc receptors that are critical for function, as well as the influence this might have on the use of antibodies as therapeutics and reagents.
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Affiliation(s)
| | - William Kelton
- Te Huataki Waiora School of Health, The University of Waikato, Hamilton, New Zealand
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22
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Vankemmelbeke M, McIntosh RS, Chua JX, Kirk T, Daniels I, Patsalidou M, Moss R, Parsons T, Scott D, Harris G, Ramage JM, Spendlove I, Durrant LG. Engineering the Human Fc Region Enables Direct Cell Killing by Cancer Glycan-Targeting Antibodies without the Need for Immune Effector Cells or Complement. Cancer Res 2020; 80:3399-3412. [PMID: 32532823 DOI: 10.1158/0008-5472.can-19-3599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/25/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022]
Abstract
Murine IgG3 glycan-targeting mAb often induces direct cell killing in the absence of immune effector cells or complement via a proinflammatory mechanism resembling oncotic necrosis. This cancer cell killing is due to noncovalent association between Fc regions of neighboring antibodies, resulting in enhanced avidity. Human isotypes do not contain the residues underlying this cooperative binding mode; consequently, the direct cell killing of mouse IgG3 mAb is lost upon chimerization or humanization. Using the Lewisa/c/x -targeting 88mAb, we identified the murine IgG3 residues underlying the direct cell killing and increased avidity via a series of constant region shuffling and subdomain swapping approaches to create improved ("i") chimeric mAb with enhanced tumor killing in vitro and in vivo. Constant region shuffling identified a major CH3 and a minor CH2 contribution, which was further mapped to discontinuous regions among residues 286-306 and 339-378 that, when introduced in 88hIgG1, recapitulated the direct cell killing and avidity of 88mIgG3. Of greater interest was the creation of a sialyl-di-Lewisa-targeting i129G1 mAb via introduction of these selected residues into 129hIgG1, converting it into a direct cell killing mAb with enhanced avidity and significant in vivo tumor control. The human iG1 mAb, termed Avidimabs, retained effector functions, paving the way for the proinflammatory direct cell killing to promote antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity through relief of immunosuppression. Ultimately, Fc engineering of human glycan-targeting IgG1 mAb confers proinflammatory direct cell killing and enhanced avidity, an approach that could be used to improve the avidity of other mAb with therapeutic potential. SIGNIFICANCE: Fc engineering enhances avidity and direct cell killing of cancer-targeting anti-glycan antibodies to create superior clinical candidates for cancer immunotherapy.
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Affiliation(s)
- Mireille Vankemmelbeke
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom.,Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
| | - Richard S McIntosh
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
| | - Jia Xin Chua
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom.,Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
| | - Thomas Kirk
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom.,Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
| | - Ian Daniels
- Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
| | - Marilena Patsalidou
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
| | - Robert Moss
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
| | - Tina Parsons
- Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
| | - David Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, United Kingdom
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Judith M Ramage
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
| | - Ian Spendlove
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
| | - Lindy G Durrant
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom. .,Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, United Kingdom
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23
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Attallah C, Aguilar MF, Forno G, Etcheverrigaray M, Brigido MDM, Maranhão AQ, Oggero M. The glycosylation of anti-rhIFN-α2b recombinant antibodies influences the antigen-neutralizing activity. Biotechnol Lett 2020; 42:1369-1381. [PMID: 32285235 DOI: 10.1007/s10529-020-02879-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 03/29/2020] [Indexed: 01/17/2023]
Abstract
OBJECTIVES The influence of glycosylation on the antigen-neutralizing ability of two potential biotherapeutic anti-human IFN-α2b antibodies composed by murine and humanized single-chain Fv fused to human Fcγ1 (chimeric and humanized scFv-Fc, respectively) was studied. RESULTS Chimeric antibodies produced in CHO-K1 and HEK293 mammalian cells showed no differences in the antigen-antibody affinity but demonstrated differences in the in vitro neutralization of IFN-α2b activity. On the other hand, the humanized antibodies produced in the same cell types showed differences in both the antigen-antibody affinity and the antigen-neutralizing ability. These differences are due to the scFv domain, as evidenced by its expression in CHO-K1 and HEK293 cells. In order to determine if the Fc glycosylation influences the antigen binding ability, both parameters were analyzed on chimeric and humanized deglycosylated scFv-Fc. Surprisingly, no differences in the antigen-antibody affinity were observed, but differences in the antigen-neutralizing ability of both chimeric and humanized antibodies, and their respectively deglycosylated glycoforms were found. CONCLUSIONS Fc glycosylation influences the antigen neutralization ability of two anti-rhIFN-α2b recombinant antibodies. Although affinity is the widely accepted parameter to analyze antibody antigen binding, it does not appear to be sufficient to describe the behavior of recombinant antibodies in vitro. This work contributes with a high impact knowledge to develop therapeutic recombinant antibodies where glycosylation and producer cell lines must be taken into account for their influence on the antigen binding capacity and not only for their impact on the effector properties as it has been historically considered for antibodies.
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Affiliation(s)
- Carolina Attallah
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168 - Km 472.4 - C.C. 242, S3000ZAA, Santa Fe, Argentina
| | - María Fernanda Aguilar
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168 - Km 472.4 - C.C. 242, S3000ZAA, Santa Fe, Argentina
| | - Guillermina Forno
- R&D Zelltek S.A., UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168 - Km 472.4 - C.C. 242, S3000ZAA, Santa Fe, Argentina
| | - Marina Etcheverrigaray
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168 - Km 472.4 - C.C. 242, S3000ZAA, Santa Fe, Argentina
| | - Marcelo De Macedo Brigido
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Immunology Investigation Institute - iii - INCT, MCTIC, Brasilia, Brazil
| | - Andrea Queiroz Maranhão
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Immunology Investigation Institute - iii - INCT, MCTIC, Brasilia, Brazil
| | - Marcos Oggero
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168 - Km 472.4 - C.C. 242, S3000ZAA, Santa Fe, Argentina.
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24
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Ling WL, Lua WH, Gan SKE. Sagacity in antibody humanization for therapeutics, diagnostics and research purposes: considerations of antibody elements and their roles. Antib Ther 2020; 3:71-79. [PMID: 33928226 PMCID: PMC7990220 DOI: 10.1093/abt/tbaa005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/27/2020] [Accepted: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
The humanization of antibodies for therapeutics is a critical process that can determine the success of antibody drug development. However, the science underpinning this process remains elusive with different laboratories having very different methods. Well-funded laboratories can afford automated high-throughput screening methods to derive their best binder utilizing a very expensive initial set of equipment affordable only to a few. Often within these high-throughput processes, only standard key parameters, such as production, binding and aggregation are analyzed. Given the lack of suitable animal models, it is only at clinical trials that immunogenicity and allergy adverse effects are detected through anti-human antibodies as per FDA guidelines. While some occurrences that slip through can be mitigated by additional desensitization protocols, such adverse reactions to grafted humanized antibodies can be prevented at the humanization step. Considerations such as better antibody localization, avoidance of unspecific interactions to superantigens and the tailoring of antibody dependent triggering of immune responses, the antibody persistence on cells, can all be preemptively considered through a holistic sagacious approach, allowing for better outcomes in therapy and for research and diagnostic purposes.
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Affiliation(s)
- Wei-Li Ling
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Wai-Heng Lua
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- p53 Laboratory, ASTAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
- Experimental Drug Development Center, ASTAR, 10 Biopolis Road, #05-01, Chromos, Singapore 138670
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25
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Basauri A, González-Fernández C, Fallanza M, Bringas E, Fernandez-Lopez R, Giner L, Moncalián G, de la Cruz F, Ortiz I. Biochemical interactions between LPS and LPS-binding molecules. Crit Rev Biotechnol 2020; 40:292-305. [DOI: 10.1080/07388551.2019.1709797] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Arantza Basauri
- Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Santander, Spain
| | | | - Marcos Fallanza
- Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Santander, Spain
| | - Eugenio Bringas
- Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Santander, Spain
| | - Raúl Fernandez-Lopez
- Instituto de Biomedicina y Biotecnologia (IBBTEC), CSIC, Universidad de Cantabria, Santander, Spain
| | - Laura Giner
- Instituto de Biomedicina y Biotecnologia (IBBTEC), CSIC, Universidad de Cantabria, Santander, Spain
| | - Gabriel Moncalián
- Instituto de Biomedicina y Biotecnologia (IBBTEC), CSIC, Universidad de Cantabria, Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnologia (IBBTEC), CSIC, Universidad de Cantabria, Santander, Spain
| | - Inmaculada Ortiz
- Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Santander, Spain
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Abstract
In vertebrates, immunoglobulins (Igs), commonly known as antibodies, play an integral role in the armamentarium of immune defense against various pathogens. After an antigenic challenge, antibodies are secreted by differentiated B cells called plasma cells. Antibodies have two predominant roles that involve specific binding to antigens to launch an immune response, along with activation of other components of the immune system to fight pathogens. The ability of immunoglobulins to fight against innumerable and diverse pathogens lies in their intrinsic ability to discriminate between different antigens. Due to this specificity and high affinity for their antigens, antibodies have been a valuable and indispensable tool in research, diagnostics and therapy. Although seemingly a simple maneuver, the association between an antibody and its antigen, to make an antigen-antibody complex, is comprised of myriads of non-covalent interactions. Amino acid residues on the antigen binding site, the epitope, and on the antibody binding site, the paratope, intimately contribute to the energetics needed for the antigen-antibody complex stability. Structural biology methods to study antigen-antibody complexes are extremely valuable tools to visualize antigen-antibody interactions in detail; this helps to elucidate the basis of molecular recognition between an antibody and its specific antigen. The main scope of this chapter is to discuss the structure and function of different classes of antibodies and the various aspects of antigen-antibody interactions including antigen-antibody interfaces-with a special focus on paratopes, complementarity determining regions (CDRs) and other non-CDR residues important for antigen binding and recognition. Herein, we also discuss methods used to study antigen-antibody complexes, antigen recognition by antibodies, types of antigens in complexes, and how antigen-antibody complexes play a role in modern day medicine and human health. Understanding the molecular basis of antigen binding and recognition by antibodies helps to facilitate the production of better and more potent antibodies for immunotherapy, vaccines and various other applications.
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Affiliation(s)
- A Brenda Kapingidza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Krzysztof Kowal
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Department of Experimental Allergology and Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA.
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27
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In Vitro Characterization and Stability Profiles of Antibody-Fluorophore Conjugates Derived from Interchain Cysteine Cross-Linking or Lysine Bioconjugation. Pharmaceuticals (Basel) 2019; 12:ph12040176. [PMID: 31810248 PMCID: PMC6958397 DOI: 10.3390/ph12040176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 11/21/2022] Open
Abstract
Fluorescent labelling of monoclonal antibodies (mAbs) is classically performed by chemical bioconjugation methods. The most frequent labelling technique to generate antibody–fluorophore conjugates (AFCs) involves the bioconjugation onto the mAb lysines of a dye bearing an N-hydroxysuccinimide ester or an isothiocyanate group. However, discrepancies between labelling experiments or kits can be observed, related to reproducibility issues, alteration of antigen binding, or mAb properties. The lack of information on labelling kits and the incomplete characterization of the obtained labelled mAbs largely contribute to these issues. In this work, we generated eight AFCs through either lysine or interchain cysteine cross-linking bioconjugation of green-emitting fluorophores (fluorescein or BODIPY) onto either trastuzumab or rituximab. This strategy allowed us to study the influence of fluorophore solubility, bioconjugation technology, and antibody nature on two known labelling procedures. The structures of these AFCs were thoroughly analyzed by mass spectroscopy, and their antigen binding properties were studied. We then compared these AFCs in vitro by studying their respective spectral properties and stabilities. The shelf stability profiles and sensibility to pH variation of these AFCs prove to be dye-, antibody- and labelling-technology-dependent. Fluorescence emission in AFCs was higher when lysine labelling was used, but cross-linked AFCs were revealed to be more stable. This must be taken into account for the design of any biological study involving antibody labelling.
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28
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Karadag M, Arslan M, Kaleli NE, Kalyoncu S. Physicochemical determinants of antibody-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:85-114. [PMID: 32312427 DOI: 10.1016/bs.apcsb.2019.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Antibodies are specialized proteins generated by immune system for high specificity and affinity binding to target antigens. Because of their essential roles in immune system, antibodies have been successfully developed and engineered as biopharmaceuticals for treatment of various diseases. Analysis of antibody-protein interactions is always required to get detailed information on effectivity of such antibody-based therapeutics. Although physicochemical rules cannot be generalized for every antibody-protein interaction, there are some features which should be taken into account during antibody development and engineering efforts. In this chapter, physicochemical analysis of antibody paratope-protein epitope interactions will be discussed to highlight important characteristics. First, paratope and non-paratope regions of antibodies will be described and important roles of these regions on binding and biophysical features of antibodies will be discussed. Then, general features of epitope regions of protein antigens will be introduced along with several computational/experimental tools to identify them. Lastly, a rising star of antibody biopharmaceuticals, nanobodies, will be described to show importance of next-generation antibody fragment based biopharmaceuticals in drug development.
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Affiliation(s)
- Murat Karadag
- Izmir Biomedicine and Genome Center, İzmir, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylul University, İzmir, Turkey
| | - Merve Arslan
- Izmir Biomedicine and Genome Center, İzmir, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylul University, İzmir, Turkey
| | - Nazli Eda Kaleli
- Izmir Biomedicine and Genome Center, İzmir, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylul University, İzmir, Turkey
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29
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Maibom-Thomsen SL, Trier NH, Holm BE, Hansen KB, Rasmussen MI, Chailyan A, Marcatili P, Højrup P, Houen G. Immunoglobulin G structure and rheumatoid factor epitopes. PLoS One 2019; 14:e0217624. [PMID: 31199818 PMCID: PMC6568389 DOI: 10.1371/journal.pone.0217624] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 05/15/2019] [Indexed: 12/14/2022] Open
Abstract
Antibodies are important for immunity and exist in several classes (IgM, IgD, IgA, IgG, IgE). They are composed of symmetric dimeric molecules with two antigen binding regions (Fab) and a constant part (Fc), usually depicted as Y-shaped molecules. Rheumatoid factors found in patients with rheumatoid arthritis are autoantibodies binding to IgG and paradoxically appear to circulate in blood alongside with their antigen (IgG) without reacting with it. Here, it is shown that rheumatoid factors do not react with native IgG in solution, and that their epitopes only become accessible upon certain physico-chemical treatments (e.g. heat treatment at 57 °C), by physical adsorption on a hydrophobic surface or by antigen binding. Moreover, chemical cross-linking in combination with mass spectrometry showed that the native state of IgG is a compact (closed) form and that the Fab parts of IgG shield the Fc region and thereby control access of rheumatoid factors and presumably also some effector functions. It can be inferred that antibody binding to pathogen surfaces induces a conformational change, which exposes the Fc part with its effector sites and rheumatoid factor epitopes. This has strong implications for understanding antibody structure and physiology and necessitates a conceptual reformulation of IgG models.
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Affiliation(s)
| | - Nicole Hartwig Trier
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Autoimmunology, Statens Serum Institut, Copenhagen, Denmark
| | - Bettina Eide Holm
- Department of Autoimmunology, Statens Serum Institut, Copenhagen, Denmark
| | - Kirsten Beth Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Autoimmunology, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Ib Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Anna Chailyan
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Paolo Marcatili
- Department of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Gunnar Houen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Autoimmunology, Statens Serum Institut, Copenhagen, Denmark
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30
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Human Memory B Cells Harbor Diverse Cross-Neutralizing Antibodies against BK and JC Polyomaviruses. Immunity 2019; 50:668-676.e5. [PMID: 30824324 DOI: 10.1016/j.immuni.2019.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 10/26/2018] [Accepted: 02/04/2019] [Indexed: 12/15/2022]
Abstract
Human polyomaviruses cause a common childhood infection worldwide and typically elicit a neutralizing antibody and cellular immune response, while establishing a dormant infection in the kidney with minimal clinical manifestations. However, viral reactivation can cause severe pathology in immunocompromised individuals. We developed a high-throughput, functional antibody screen to examine the humoral response to BK polyomavirus. This approach enabled the isolation of antibodies from all peripheral B cell subsets and revealed the anti-BK virus antibody repertoire as clonally complex with respect to immunoglobulin sequences and isotypes (both IgM and IgG), including a high frequency of monoclonal antibodies that broadly neutralize BK virus subtypes and the related JC polyomavirus. Cryo-electron microscopy of a broadly neutralizing IgG single-chain variable fragment complexed with BK virus-like particles revealed the quaternary nature of a conserved viral epitope at the junction between capsid pentamers. These features unravel a potent modality for inhibiting polyomavirus infection in kidney transplant recipients and other immunocompromised patients.
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31
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Li C, Wang Y, Liu T, Niklasch M, Qiao K, Durand S, Chen L, Liang M, Baumert TF, Tong S, Nassal M, Wen YM, Wang YX. An E. coli-produced single-chain variable fragment (scFv) targeting hepatitis B virus surface protein potently inhibited virion secretion. Antiviral Res 2019; 162:118-129. [DOI: 10.1016/j.antiviral.2018.12.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 12/06/2018] [Accepted: 12/28/2018] [Indexed: 01/14/2023]
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32
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Iype J, Datta M, Khadour A, Übelhart R, Nicolò A, Rollenske T, Dühren-von Minden M, Wardemann H, Maity PC, Jumaa H. Differences in Self-Recognition between Secreted Antibody and Membrane-Bound B Cell Antigen Receptor. THE JOURNAL OF IMMUNOLOGY 2019; 202:1417-1427. [PMID: 30683703 DOI: 10.4049/jimmunol.1800690] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 12/20/2018] [Indexed: 11/19/2022]
Abstract
The random gene segment rearrangement during B cell development ensures Ab repertoire diversity. Because this process might generate autoreactive specificities, it has been proposed that stringent selection mechanisms prevent the development of autoreactive B cells. However, conventional assays to identify autoreactive B cells usually employ in vitro-generated Abs, which differ from membrane-bound BCRs. In this study, we used a cell-based assay to investigate the autoreactivity of membrane-bound BCRs derived from different B cell developmental stages of human peripheral blood. Contrasted to soluble Ab counterparts, only a few of the tested BCRs were autoreactive, although the cell-based assay sensitively detects feeble Ag recognition of a germline-reverted murine BCR that was selected after OVA immunization of mice, whereas conventional assays failed to do so. Together, these data suggest that proper identification of autoreactive B cells requires the membrane-bound BCR, as the soluble Ab may largely differ from its BCR counterpart in Ag binding.
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Affiliation(s)
- Joseena Iype
- Institute of Immunology, Ulm University Medical Center, 89081 Ulm, Germany; and
| | - Moumita Datta
- Institute of Immunology, Ulm University Medical Center, 89081 Ulm, Germany; and
| | - Ahmad Khadour
- Institute of Immunology, Ulm University Medical Center, 89081 Ulm, Germany; and
| | - Rudolf Übelhart
- Institute of Immunology, Ulm University Medical Center, 89081 Ulm, Germany; and
| | - Antonella Nicolò
- Institute of Immunology, Ulm University Medical Center, 89081 Ulm, Germany; and
| | - Tim Rollenske
- Division of B Cell Immunology, German Cancer Research Center, 69120 Heidelberg, Germany
| | | | - Hedda Wardemann
- Division of B Cell Immunology, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Palash C Maity
- Institute of Immunology, Ulm University Medical Center, 89081 Ulm, Germany; and
| | - Hassan Jumaa
- Institute of Immunology, Ulm University Medical Center, 89081 Ulm, Germany; and
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33
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Zhao J, Nussinov R, Ma B. Antigen binding allosterically promotes Fc receptor recognition. MAbs 2019; 11:58-74. [PMID: 30212263 PMCID: PMC6343797 DOI: 10.1080/19420862.2018.1522178] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/10/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022] Open
Abstract
A key question in immunology is whether antigen recognition and Fc receptor (FcR) binding are allosterically linked. This question is also relevant for therapeutic antibody design. Antibody Fab and Fc domains are connected by flexible unstructured hinge region. Fc chains have conserved glycosylation sites at Asn297, with each conjugated to a core heptasaccharide and forming biantennary Fc glycan. The glycans modulate the Fc conformations and functions. It is well known that the antibody Fab and Fc domains and glycan affect antibody activity, but whether these elements act independently or synergistically is still uncertain. We simulated four antibody complexes: free antibody, antigen-bound antibody, FcR-bound antibody, and an antigen-antibody-FcR complex. We found that, in the antibody's "T/Y" conformation, the glycans, and the Fc domain all respond to antigen binding, with the antibody population shifting to two dominant clusters, both with the Fc-receptor binding site open. The simulations reveal that the Fc-glycan-receptor complexes also segregate into two conformational clusters, one corresponding to the antigen-free antibody-FcR baseline binding, and the other with an antigen-enhanced antibody-FcR interaction. Our study confirmed allosteric communications in antibody-antigen recognition and following FcR activation. Even though we observed allosteric communications through the IgG domains, the most important mechanism that we observed is the communication via population shift, stimulated by antigen binding and propagating to influence FcR recognition.
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Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
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34
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Shan L, Mody N, Sormani P, Rosenthal KL, Damschroder MM, Esfandiary R. Developability Assessment of Engineered Monoclonal Antibody Variants with a Complex Self-Association Behavior Using Complementary Analytical and in Silico Tools. Mol Pharm 2018; 15:5697-5710. [DOI: 10.1021/acs.molpharmaceut.8b00867] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | - Pietro Sormani
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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35
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Zhao J, Nussinov R, Wu WJ, Ma B. In Silico Methods in Antibody Design. Antibodies (Basel) 2018; 7:E22. [PMID: 31544874 PMCID: PMC6640671 DOI: 10.3390/antib7030022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/28/2018] [Accepted: 06/28/2018] [Indexed: 01/10/2023] Open
Abstract
Antibody therapies with high efficiency and low toxicity are becoming one of the major approaches in antibody therapeutics. Based on high-throughput sequencing and increasing experimental structures of antibodies/antibody-antigen complexes, computational approaches can predict antibody/antigen structures, engineering the function of antibodies and design antibody-antigen complexes with improved properties. This review summarizes recent progress in the field of in silico design of antibodies, including antibody structure modeling, antibody-antigen complex prediction, antibody stability evaluation, and allosteric effects in antibodies and functions. We listed the cases in which these methods have helped experimental studies to improve the affinities and physicochemical properties of antibodies. We emphasized how the molecular dynamics unveiled the allosteric effects during antibody-antigen recognition and antibody-effector recognition.
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Affiliation(s)
- Jun Zhao
- Division of Biotechnology Review and Research I, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
- Interagency Oncology Task Force (IOTF) Fellowship: Oncology Product Research/Review Fellow, National Cancer Institute, Bethesda, MD 20892, USA.
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Wen-Jin Wu
- Division of Biotechnology Review and Research I, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
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36
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Friedensohn S, Lindner JM, Cornacchione V, Iazeolla M, Miho E, Zingg A, Meng S, Traggiai E, Reddy ST. Synthetic Standards Combined With Error and Bias Correction Improve the Accuracy and Quantitative Resolution of Antibody Repertoire Sequencing in Human Naïve and Memory B Cells. Front Immunol 2018; 9:1401. [PMID: 29973938 PMCID: PMC6019461 DOI: 10.3389/fimmu.2018.01401] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/06/2018] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing of immunoglobulin (Ig) repertoires (Ig-seq) is a powerful method for quantitatively interrogating B cell receptor sequence diversity. When applied to human repertoires, Ig-seq provides insight into fundamental immunological questions, and can be implemented in diagnostic and drug discovery projects. However, a major challenge in Ig-seq is ensuring accuracy, as library preparation protocols and sequencing platforms can introduce substantial errors and bias that compromise immunological interpretation. Here, we have established an approach for performing highly accurate human Ig-seq by combining synthetic standards with a comprehensive error and bias correction pipeline. First, we designed a set of 85 synthetic antibody heavy-chain standards (in vitro transcribed RNA) to assess correction workflow fidelity. Next, we adapted a library preparation protocol that incorporates unique molecular identifiers (UIDs) for error and bias correction which, when applied to the synthetic standards, resulted in highly accurate data. Finally, we performed Ig-seq on purified human circulating B cell subsets (naïve and memory), combined with a cellular replicate sampling strategy. This strategy enabled robust and reliable estimation of key repertoire features such as clonotype diversity, germline segment, and isotype subclass usage, and somatic hypermutation. We anticipate that our standards and error and bias correction pipeline will become a valuable tool for researchers to validate and improve accuracy in human Ig-seq studies, thus leading to potentially new insights and applications in human antibody repertoire profiling.
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Affiliation(s)
- Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - John M Lindner
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Enkelejda Miho
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Andreas Zingg
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Simon Meng
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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37
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Tanner JE, Hu J, Alfieri C. Construction and Characterization of a Humanized Anti-Epstein-Barr Virus gp350 Antibody with Neutralizing Activity in Cell Culture. Cancers (Basel) 2018; 10:cancers10040112. [PMID: 29642526 PMCID: PMC5923367 DOI: 10.3390/cancers10040112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/30/2018] [Accepted: 04/04/2018] [Indexed: 12/16/2022] Open
Abstract
Acute Epstein-Barr virus (EBV) infection in immunosuppressed transplant patients can give rise to a malignant B-cell proliferation known as post-transplant lymphoproliferative disease (PTLD). The EBV major virion surface glycoprotein (gp)350 is a principal target of naturally occurring neutralizing antibodies and is viewed as the best target to prevent acute infection and PTLD in at-risk transplant recipients. We have constructed a humanized (hu) version of the murine anti-gp350 neutralizing monoclonal antibody 72a1. The hu72a1 IgG1 antibody displayed no significant anti-mouse activity, recognized both gp350 and its splice variant gp220 as well as a gp350 peptide that was shown to constitute the principal EBV gp350 neutralizing epitope when tested in immunoassays. Hu72a1 antibody blocked in vitro EBV infection of B cells at a level which equaled that of a mouse-human chimeric 72a1 antibody construct. This work provides a further structural and immunological understanding of the 72a1 antibody interaction with EBV gp350, and constitutes a launch point for future anti-EBV therapeutic antibodies designed to block EBV infection and prevent PTLD while eliminating the deleterious antigenic murine features of the original 72a1 antibody.
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Affiliation(s)
- Jerome E Tanner
- Laboratory of Viral Pathogenesis, Research Centre, CHU Sainte-Justine, Montréal, QC H3T 1C5, Canada.
| | - Jing Hu
- Laboratory of Viral Pathogenesis, Research Centre, CHU Sainte-Justine, Montréal, QC H3T 1C5, Canada.
| | - Caroline Alfieri
- Laboratory of Viral Pathogenesis, Research Centre, CHU Sainte-Justine, Montréal, QC H3T 1C5, Canada.
- Department of Microbiology, Infectiology and Immunology, University of Montreal, 3175 Côte Ste-Catherine Road, Montreal, QC H3T 1C5, Canada.
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38
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Lua WH, Ling WL, Yeo JY, Poh JJ, Lane DP, Gan SKE. The effects of Antibody Engineering CH and CL in Trastuzumab and Pertuzumab recombinant models: Impact on antibody production and antigen-binding. Sci Rep 2018; 8:718. [PMID: 29335579 PMCID: PMC5768722 DOI: 10.1038/s41598-017-18892-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 12/19/2017] [Indexed: 12/17/2022] Open
Abstract
Current therapeutic antibodies such as Trastuzumab, are typically of the blood circulatory IgG1 class (Cκ/ CHγ1). Due to the binding to Her2 also present on normal cell surfaces, side effects such as cardiac failure can sometimes be associated with such targeted therapy. Using antibody isotype swapping, it may be possible to reduce systemic circulation through increased tissue localization, thereby minimising unwanted side effects. However, the effects of such modifications have yet to be fully characterized, particularly with regards to their biophysical properties in antigen binding. To do this, we produced all light and heavy chain human isotypes/subtypes recombinant versions of Trastuzumab and Pertuzumab, and studied them with respect to recombinant production and Her2 binding. Our findings show that while the light chain constant region changes have no major effects on production or Her2 binding, some heavy chain isotypes, in particularly, IgM and IgD isotypes, can modulate antigen binding. This study thus provides the groundwork for such isotype modifications to be performed in the future to yield therapeutics of higher efficacy and efficiency.
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Affiliation(s)
- Wai-Heng Lua
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wei-Li Ling
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Joshua Yi Yeo
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jun-Jie Poh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - David Philip Lane
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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39
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Di Bona D, Accardi G, Aiello A, Bilancia M, Candore G, Colomba C, Caruso C, Duro G, Gambino CM, Macchia L, Pandey JP. Association between γ marker, human leucocyte antigens and killer immunoglobulin-like receptors and the natural course of human cytomegalovirus infection: a pilot study performed in a Sicilian population. Immunology 2017; 153:523-531. [PMID: 29067686 DOI: 10.1111/imm.12855] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 09/07/2017] [Accepted: 10/19/2017] [Indexed: 12/21/2022] Open
Abstract
Natural killer (NK) cells provide a major defence against human cytomegalovirus (HCMV) infection through the interaction of their surface receptors, including the activating and inhibitory killer immunoglobulin-like receptors (KIRs), and human leucocyte antigen (HLA) class I molecules. Also γ marker (GM) allotypes, able to influence the NK antibody-dependent cell-mediated cytotoxicity, appear to be involved in the immunological control of virus infections, including HCMV. In some cases, their contribution requires epistatic interaction with other genes of the immune system, such as HLA. In the present report, with the aim of gaining insight into the immune mechanisms controlling HCMV, we have studied the possible associations among humoral and NK responses, and HCMV infections. In a previous study we assessed whether the KIR and HLA repertoire might influence the risk of developing symptomatic (n = 60) or asymptomatic (n = 60) disease after primary HCMV infection in the immunocompetent host. In the present study, the immunocompetent patients with primary symptomatic HCMV infection were genotyped for GM3/17 and GM23 allotypes, along with the 60 participants with a previous asymptomatic infection as controls. Notwithstanding the presence of missing data record, advanced missing data recovery techniques were able to show that individuals carrying the GM23 allotypes, both homozygous and heterozygous, GM17/17, HLA-C2 and Bw4T KIR-ligand groups are associated with the risk of developing symptomatic infection. Our findings on the role of both cellular and humoral immunity in the control of HCMV infection should be of value in guiding efforts to reduce HCMV-associated health complications in the elderly, including immunosenescence, and in transplantation.
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Affiliation(s)
- Danilo Di Bona
- Dipartimento dell'Emergenza e dei Trapianti d'Organo, Università di Bari Aldo Moro, Bari, Italy
| | - Giulia Accardi
- Dipartimento di Biopatologia e Biotecnologie Mediche, Università di Palermo, Palermo, Italy
| | - Anna Aiello
- Dipartimento di Biopatologia e Biotecnologie Mediche, Università di Palermo, Palermo, Italy
| | - Massimo Bilancia
- Dipartmento Jonico in Sistemi Giuridici ed Economici del Mediterraneo: società, ambiente, culture, Università di Bari Aldo Moro, Bari, Italy
| | - Giuseppina Candore
- Dipartimento di Biopatologia e Biotecnologie Mediche, Università di Palermo, Palermo, Italy
| | - Claudia Colomba
- Dipartimento di Scienze per la Promozione della Salute e Materno-Infantile "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Calogero Caruso
- Dipartimento di Biopatologia e Biotecnologie Mediche, Università di Palermo, Palermo, Italy
| | - Giovanni Duro
- Istituto di Biomedicina e Immunologia Molecolare, Consiglio Nazionale delle Ricerche, Palermo, Italy
| | - Caterina M Gambino
- Dipartimento di Biopatologia e Biotecnologie Mediche, Università di Palermo, Palermo, Italy
| | - Luigi Macchia
- Dipartimento dell'Emergenza e dei Trapianti d'Organo, Università di Bari Aldo Moro, Bari, Italy
| | - Janardan P Pandey
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, USA
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40
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Zhao J, Nussinov R, Ma B. Mechanisms of recognition of amyloid-β (Aβ) monomer, oligomer, and fibril by homologous antibodies. J Biol Chem 2017; 292:18325-18343. [PMID: 28924036 PMCID: PMC5672054 DOI: 10.1074/jbc.m117.801514] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/26/2017] [Indexed: 12/31/2022] Open
Abstract
Alzheimer's disease is one of the most devastating neurodegenerative diseases without effective therapies. Immunotherapy is a promising approach, but amyloid antibody structural information is limited. Here we simulate the recognition of monomeric, oligomeric, and fibril amyloid-β (Aβ) by three homologous antibodies (solanezumab, crenezumab, and their chimera, CreneFab). Solanezumab only binds the monomer, whereas crenezumab and CreneFab can recognize different oligomerization states; however, the structural basis for this observation is not understood. We successfully identified stable complexes of crenezumab with Aβ pentamer (oligomer model) and 16-mer (fibril model). It is noteworthy that solanezumab targets Aβ residues 16-26 preferentially in the monomeric state; conversely, crenezumab consistently targets residues 13-16 in different oligomeric states. Unlike the buried monomeric peptide in solanezumab's complementarity-determining region, crenezumab binds the oligomer's lateral and edge residues. Surprisingly, crenezumab's complementarity-determining region loops can effectively bind the Aβ fibril lateral surface around the same 13-16 region. The constant domain influences antigen recognition through entropy redistribution. Different constant domain residues in solanezumab/crenezumab/chimera influence the binding of Aβ aggregates. Collectively, we provide molecular insight into the recognition mechanisms facilitating antibody design.
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MESH Headings
- Amyloid/antagonists & inhibitors
- Amyloid/chemistry
- Amyloid/metabolism
- Amyloid beta-Peptides/antagonists & inhibitors
- Amyloid beta-Peptides/chemistry
- Amyloid beta-Peptides/metabolism
- Animals
- Antibodies/chemistry
- Antibodies/genetics
- Antibodies/metabolism
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal, Humanized/chemistry
- Antibodies, Monoclonal, Humanized/genetics
- Antibodies, Monoclonal, Humanized/metabolism
- Antibody Specificity
- Binding Sites, Antibody
- Complementarity Determining Regions/chemistry
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/metabolism
- Drug Design
- Humans
- Models, Molecular
- Molecular Docking Simulation
- Molecular Dynamics Simulation
- Molecular Weight
- Nootropic Agents/chemistry
- Nootropic Agents/metabolism
- Protein Aggregates
- Protein Aggregation, Pathological/metabolism
- Protein Conformation
- Protein Engineering
- Protein Multimerization
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/metabolism
- Structural Homology, Protein
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Affiliation(s)
- Jun Zhao
- From the Cancer and Inflammation Program, NCI-Frederick, Frederick, Maryland 21702
| | - Ruth Nussinov
- the Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, NCI-Frederick, Frederick, Maryland 21702, and
- the Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- the Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, NCI-Frederick, Frederick, Maryland 21702, and
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41
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Lossius A, Tomescu-Baciu A, Holmøy T, Vedeler CA, Røsjø E, Lorentzen ÅR, Casetta I, Vartdal F. Selective intrathecal enrichment of G1m1-positive B cells in multiple sclerosis. Ann Clin Transl Neurol 2017; 4:756-761. [PMID: 29046884 PMCID: PMC5634349 DOI: 10.1002/acn3.451] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/31/2017] [Indexed: 11/24/2022] Open
Abstract
Immunoglobulin gamma (IgG) heavy chain genes are associated with susceptibility to multiple sclerosis (MS) and IgG levels in the cerebrospinal fluid (CSF). However, how these variants are implicated in disease mechanisms remains unknown. Here, we show that proliferating plasmablasts expressing the G1m1 allotype of IgG1 are selectively enriched in CSF of G1m1/G1m3 heterozygous MS patients, whereas plasmablasts expressing either G1m1 or G1m3 are evenly distributed in blood. Moreover, there was a preferential intrathecal synthesis of oligoclonal IgG1 of the G1m1 allotype in heterozygous patients, whereas controls with Lyme neuroborreliosis displayed oligoclonal IgG1 of both allotypes. This points to a disease‐specific mechanism involved in B‐cell establishment within the central nervous system in MS.
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Affiliation(s)
- Andreas Lossius
- Department of Immunology and Transfusion Medicine Faculty of Medicine University of Oslo and Oslo University Hospital Rikshospitalet Oslo Norway.,Department of Neurology Oslo University Hospital Rikshospitalet Oslo Norway.,Department of Neurology Akershus University Hospital Lørenskog Norway
| | - Alina Tomescu-Baciu
- Department of Immunology and Transfusion Medicine Faculty of Medicine University of Oslo and Oslo University Hospital Rikshospitalet Oslo Norway
| | - Trygve Holmøy
- Department of Neurology Akershus University Hospital Lørenskog Norway.,Institute of Clinical Medicine University of Oslo Oslo Norway
| | - Christian A Vedeler
- Department of Clinical Medicine University of Bergen Bergen Norway.,Department of Neurology Haukeland University Hospital Bergen Norway
| | - Egil Røsjø
- Department of Neurology Akershus University Hospital Lørenskog Norway.,Institute of Clinical Medicine University of Oslo Oslo Norway
| | - Åslaug R Lorentzen
- Department of Neurology Sørlandet Hospital Trust Kristiansand Norway.,The Norwegian National Advisory Unit on Tick-borne diseases Arendal Norway
| | - Ilaria Casetta
- Department of Biomedical and Specialty Surgical Sciences Section of Neurology Psychiatry and Psychology University of Ferrara Ferrara Italy
| | - Frode Vartdal
- Department of Immunology and Transfusion Medicine Faculty of Medicine University of Oslo and Oslo University Hospital Rikshospitalet Oslo Norway
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42
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Capodicasa C, Catellani M, Moscetti I, Bromuro C, Chiani P, Torosantucci A, Benvenuto E. Comparative analysis of plant-produced, recombinant dimeric IgA against cell wall β-glucan of pathogenic fungi. Biotechnol Bioeng 2017; 114:2729-2738. [PMID: 28832951 DOI: 10.1002/bit.26403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/30/2017] [Accepted: 08/17/2017] [Indexed: 12/14/2022]
Abstract
Immunoglobulins A (IgA) are crucially involved in protection of human mucosal surfaces from microbial pathogens. In this work, we devised and expressed in plants recombinant chimeric antifungal antibodies (Abs) of isotype A (IgA1, IgA2, and scFvFcA1), derived from a murine mAb directed to the fungal cell wall polysaccharide β-glucan which had proven able to confer protection against multiple pathogenic fungi. All recombinant IgA (rIgA) were expressed and correctly assembled in dimeric form in plants and evaluated for yield, antigen-binding efficiency and antifungal properties in vitro, in comparison with a chimeric IgG1 version. Production yields and binding efficiency to purified β-glucans showed significant variations not only between Abs of different isotypes but also between the different IgA formats. Moreover, only the dimeric IgA1 was able to strongly bind cells of the fungal pathogen Candida albicans and to restrain its adhesion to human epithelial cells. Our data indicate that IgG to IgA switch and differences in molecular structure among different rIgA formats can impact expression in plant and biological activity of anti-β-glucans Abs and provide new insights for the design of recombinant IgA as anti-infective immunotherapeutics, whose potential is still poorly investigated.
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Affiliation(s)
- Cristina Capodicasa
- Laboratory of Biotechnology, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Research Center Casaccia, Rome, Italy
| | - Marcello Catellani
- Laboratory of Biotechnology, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Research Center Casaccia, Rome, Italy
| | - Ilaria Moscetti
- Laboratory of Biotechnology, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Research Center Casaccia, Rome, Italy
| | - Carla Bromuro
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Chiani
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonella Torosantucci
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Eugenio Benvenuto
- Laboratory of Biotechnology, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Research Center Casaccia, Rome, Italy
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43
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Yang D, Kroe-Barrett R, Singh S, Roberts CJ, Laue TM. IgG cooperativity - Is there allostery? Implications for antibody functions and therapeutic antibody development. MAbs 2017; 9:1231-1252. [PMID: 28812955 PMCID: PMC5680800 DOI: 10.1080/19420862.2017.1367074] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A central dogma in immunology is that an antibody's in vivo functionality is mediated by 2 independent events: antigen binding by the variable (V) region, followed by effector activation by the constant (C) region. However, this view has recently been challenged by reports suggesting allostery exists between the 2 regions, triggered by conformational changes or configurational differences. The possibility of allosteric signals propagating through the IgG domains complicates our understanding of the antibody structure-function relationship, and challenges the current subclass selection process in therapeutic antibody design. Here we review the types of cooperativity in IgG molecules by examining evidence for and against allosteric cooperativity in both Fab and Fc domains and the characteristics of associative cooperativity in effector system activation. We investigate the origin and the mechanism of allostery with an emphasis on the C-region-mediated effects on both V and C region interactions, and discuss its implications in biological functions. While available research does not support the existence of antigen-induced conformational allosteric cooperativity in IgGs, there is substantial evidence for configurational allostery due to glycosylation and sequence variations.
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Affiliation(s)
- Danlin Yang
- a Biotherapeutics Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield , Connecticut , USA
| | - Rachel Kroe-Barrett
- a Biotherapeutics Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield , Connecticut , USA
| | - Sanjaya Singh
- b Janssen BioTherapeutics, Janssen Research & Development, LLC, Spring House , Pennsylvania , USA
| | - Christopher J Roberts
- c Department of Chemical and Biomolecular Engineering , University of Delaware , Newark , Delaware , USA
| | - Thomas M Laue
- d Department of Molecular, Cellular, and Biomedical Sciences , University of New Hampshire , Durham , New Hampshire , USA
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44
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Zhao J, Nussinov R, Ma B. Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains. Protein Eng Des Sel 2017; 30:67-76. [PMID: 27899437 PMCID: PMC5157118 DOI: 10.1093/protein/gzw065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/05/2016] [Accepted: 11/14/2016] [Indexed: 12/12/2022] Open
Abstract
Molecular details of the recognition of disordered antigens by their cognate antibodies have not been studied as extensively as folded protein antigens and much is still unknown. To follow the conformational changes in the antibody and cross-talk between its subunits and with antigens, we performed molecular dynamics (MD) simulations of the complex of Fab and prion-associated peptide in the apo and bound forms. We observed that the inter-chain disulfide bond in constant domains restrains the conformational changes of Fab, especially the loops in the CH1 domain, resulting in inhibition of the cross-talk between Fab subdomains that thereby may prevent prion peptide binding. We further identified several negative and positive correlations of motions between the peptide and Fab constant domains, which suggested structural cross-talks between the constant domains and the antigen. The cross-talk was influenced by the inter-chain disulfide bond, which reduced the number of paths between them. Importantly, network analysis of the complex and its bound water molecules observed that those water molecules form an integral part of the Fab/peptide complex network and potential allosteric pathways. On-going work focuses on developing strategies aimed to incorporate these new network communications-including the associated water molecules-toward the grand challenge of antibody design.
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Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Genetics and Molecular Medicine, Sackler Institute of Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
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45
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Prigent J, Lorin V, Kök A, Hieu T, Bourgeau S, Mouquet H. Scarcity of autoreactive human blood IgA + memory B cells. Eur J Immunol 2016; 46:2340-2351. [PMID: 27469325 PMCID: PMC5113776 DOI: 10.1002/eji.201646446] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/17/2016] [Accepted: 07/26/2016] [Indexed: 12/17/2022]
Abstract
Class‐switched memory B cells are key components of the “reactive” humoral immunity, which ensures a fast and massive secretion of high‐affinity antigen‐specific antibodies upon antigenic challenge. In humans, IgA class‐switched (IgA+) memory B cells and IgA antibodies are abundant in the blood. Although circulating IgA+ memory B cells and their corresponding secreted immunoglobulins likely possess major protective and/or regulatory immune roles, little is known about their specificity and function. Here, we show that IgA+ and IgG+ memory B‐cell antibodies cloned from the same healthy humans share common immunoglobulin gene features. IgA and IgG memory antibodies have comparable lack of reactivity to vaccines, common mucosa‐tropic viruses and commensal bacteria. However, the IgA+ memory B‐cell compartment contains fewer polyreactive clones and importantly, only rare self‐reactive clones compared to IgG+ memory B cells. Self‐reactivity of IgAs is acquired following B‐cell affinity maturation but not antibody class switching. Together, our data suggest the existence of different regulatory mechanisms for removing autoreactive clones from the IgG+ and IgA+ memory B‐cell repertoires, and/or different maturation pathways potentially reflecting the distinct nature and localization of the cognate antigens recognized by individual B‐cell populations.
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Affiliation(s)
- Julie Prigent
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris, France.,CNRS-URA 1961, Paris, France
| | - Valérie Lorin
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris, France.,CNRS-URA 1961, Paris, France
| | - Ayrin Kök
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris, France.,CNRS-URA 1961, Paris, France
| | - Thierry Hieu
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris, France.,CNRS-URA 1961, Paris, France
| | - Salomé Bourgeau
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris, France.,CNRS-URA 1961, Paris, France
| | - Hugo Mouquet
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris, France. .,CNRS-URA 1961, Paris, France.
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46
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Simon B, Weseslindtner L, Görzer I, Pollak K, Jaksch P, Klepetko W, Puchhammer-Stöckl E. Subclass-specific antibody responses to human cytomegalovirus in lung transplant recipients and their association with constant heavy immunoglobulin G chain polymorphism and virus replication. J Heart Lung Transplant 2016; 35:370-377. [DOI: 10.1016/j.healun.2015.10.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/31/2015] [Accepted: 10/15/2015] [Indexed: 12/18/2022] Open
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47
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Zito A, Bromuro C, Mandili G, Chiani P, Horenstein AL, Malavasi F, Cauda R, Cassone A, Torosantucci A. A Murine, Bispecific Monoclonal Antibody Simultaneously Recognizing β-Glucan and MP65 Determinants in Candida Species. PLoS One 2016; 11:e0148714. [PMID: 26859561 PMCID: PMC4747543 DOI: 10.1371/journal.pone.0148714] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/20/2016] [Indexed: 12/28/2022] Open
Abstract
There is a real medical need of new diagnostic tools for the early recognition of invasive Candida infections. We exploited a rather simple and rapid redox methodology to construct a bispecific monoclonal antibody (bsmAb) that combines a monoclonal antibody (mAb) directed against 1,3-β-D-glucan, a well-known, pan-fungal diagnostic biomarker, with a mAb recognizing MP65, a major immunogenic mannoprotein secreted by C.albicans and other Candida species. The bsmAb (MP65/bglu mAb) was successfully produced and purified at high yields and proved to bind and reveal simultaneously, with high sensitivity, the β-glucan and MP65 antigens in both purified and native forms. The MP65/bglu mAb is the first bispecific antibody generated against a fungal microorganism and may prove useful for the concurrent detection of different and clinically significant Candida biomarkers in patient sera.
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Affiliation(s)
- Andrea Zito
- Laboratory of Immunogenetics and CeRMS, Department of Medical Sciences, University of Torino and Transplant Immunology, Città della Salute e della Scienza, Torino, Italy
| | - Carla Bromuro
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immune-mediated Diseases, Rome, Italy
| | - Giorgia Mandili
- Laboratory of Immunogenetics and CeRMS, Department of Medical Sciences, University of Torino and Transplant Immunology, Città della Salute e della Scienza, Torino, Italy
- Department of Molecular Biotechnology, University of Torino, Città della Salute e della Scienza, Torino, Italy
| | - Paola Chiani
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immune-mediated Diseases, Rome, Italy
| | - Alberto L. Horenstein
- Laboratory of Immunogenetics and CeRMS, Department of Medical Sciences, University of Torino and Transplant Immunology, Città della Salute e della Scienza, Torino, Italy
| | - Fabio Malavasi
- Laboratory of Immunogenetics and CeRMS, Department of Medical Sciences, University of Torino and Transplant Immunology, Città della Salute e della Scienza, Torino, Italy
| | - Roberto Cauda
- Institute of Infectious Diseases, Catholic University of Rome, Rome, Italy
| | - Antonio Cassone
- Center of Functional Genomics, Genetics and Biology, University of Perugia, Perugia, Italy
| | - Antonella Torosantucci
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immune-mediated Diseases, Rome, Italy
- * E-mail:
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48
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Janda A, Bowen A, Greenspan NS, Casadevall A. Ig Constant Region Effects on Variable Region Structure and Function. Front Microbiol 2016; 7:22. [PMID: 26870003 PMCID: PMC4740385 DOI: 10.3389/fmicb.2016.00022] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/11/2016] [Indexed: 01/02/2023] Open
Abstract
The adaptive humoral immune response is responsible for the generation of antimicrobial proteins known as immunoglobulin molecules or antibodies. Immunoglobulins provide a defense system against pathogenic microbes and toxins by targeting them for removal and/or destruction. Historically, antibodies have been thought to be composed of distinct structural domains known as the variable and constant regions that are responsible for antigen binding and mediating effector functions such as opsonization and complement activation, respectively. These domains were thought to be structurally and functionally independent. Recent work has revealed however, that in some families of antibodies, the two regions can influence each other. We will discuss the body of work that led to these observations, as well as the mechanisms that have been proposed to explain how these two different antibody regions may interact in the function of antigen binding.
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Affiliation(s)
- Alena Janda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine New York, NY, USA
| | - Anthony Bowen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine New York, NY, USA
| | - Neil S Greenspan
- Department of Pathology, Case Western Reserve University Cleveland, OH, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health Baltimore, MD, USA
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49
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Characterization of cetuximab Fc/2 dimers by off-line CZE-MS. Anal Chim Acta 2016; 908:168-76. [PMID: 26826699 DOI: 10.1016/j.aca.2015.12.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 12/12/2015] [Accepted: 12/17/2015] [Indexed: 11/30/2022]
Abstract
Monoclonal antibody (mAb) therapeutics attract the largest concern due to their strong therapeutic potency and specificity. The Fc region of mAbs is common to many new biotherapeutics as biosimilar, antibody drug conjugate or fusion protein. Fc region has consequences for Fc-mediated effector functions that might be desirable for therapeutic applications. As a consequence, there is a continuous need for improvement of analytical methods to enable fast and accurate characterization of biotherapeutics. Capillary zone electrophoresis-Mass spectrometry couplings (CZE-MS) appear really attractive methods for the characterization of biological samples. In this report, we used CZE-MS systems developed in house and native MS infusion to allow precise middle-up characterization of Fc/2 variant of cetuximab. Molecular weights were measured for three Fc/2 charge variants detected in the CZE separation of cetuximab subunits. Two Fc/2 C-terminal lysine variants were identified and separated. As the aim is to understand the presence of three peaks in the CZE separation for two Fc/2 subunits, we developed a strategy using CZE-UV/MALDI-MS and CZE-UV/ESI-MS to evaluate the role of N-glycosylation and C-terminal lysine truncation on the CZE separation. The chemical structure of N-glycosylation expressed on the Fc region of cetuximab does not influence CZE separation while C-terminal lysine is significantly influencing separation. In addition, native MS infusion demonstrated the characterization of Fc/2 dimers at pH 5.7 and 6.8 and the first separation of these dimers using CZE-MS.
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50
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Xia Y, Eryilmaz E, Zhang Q, Cowburn D, Putterman C. Anti-DNA antibody mediated catalysis is isotype dependent. Mol Immunol 2015; 69:33-43. [PMID: 26655427 DOI: 10.1016/j.molimm.2015.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/29/2015] [Accepted: 11/01/2015] [Indexed: 12/27/2022]
Abstract
Anti-DNA antibodies are the serological hallmark of systemic lupus erythematosus, and participate in the pathogenesis of lupus nephritis by cross-reacting with multiple renal antigens. Previously, using a panel of murine anti-DNA IgGs that share identical variable regions but that differ in the constant regions, we demonstrated that the cross-reaction and renal pathogenicity of anti-DNA antibodies are isotype dependent. In this study, we investigated the catalytic potential of this anti-DNA antibody panel, and determined its isotype dependency. The three isotype switch variants (IgG1, IgG2a, IgG2b) and the parent IgG3 PL9-11 anti-DNA antibodies were compared in their catalysis of 500 base pair linear double stranded DNA and a 12-mer peptide (ALWPPNLHAWVP), by gel analysis, MALDI-TOF mass spectrometry, and nuclear magnetic resonance spectroscopy. The binding affinity of anti-DNA antibodies to double stranded DNA and peptide antigens were assessed by ELISA and surface plasmon resonance. We found that the PL9-11 antibody isotypes vary significantly in their potential to catalyze the cleavage of both linear and double stranded DNA and the proteolysis of peptides. The degree of the cleavage and proteolysis increases with the incubation temperature and time. While different PL9-11 isotypes have the same initial attack sites within the ALWPPNLHAWVP peptide, there was no correlation between binding affinity to the peptide and proteolysis rates. In conclusion, the catalytic properties of anti-DNA antibodies are isotype dependent. This finding provides further evidence that antibodies that share the same variable region, but which have different constant regions, are functionally distinct. The catalytic effects modulated by antibody constant regions need to be considered in the design of therapeutic antibodies (abzymes) and peptides designed to block pathogenic autoantibodies.
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Affiliation(s)
- Yumin Xia
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Division of Rheumatology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Ertan Eryilmaz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Qiuting Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Chaim Putterman
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Division of Rheumatology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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