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Zhang Y, Mi J, Wu W, Fei J, Lv B, Yu X, Wen K, Shen J, Wang Z. Investigation of Antibody Tolerance in Methanol for Analytical Purposes: Methanol Effect Patterns and Molecular Mechanisms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402050. [PMID: 38889249 DOI: 10.1002/advs.202402050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/16/2024] [Indexed: 06/20/2024]
Abstract
The extraction of targets from biological samples for immunoassays using organic solvents, such as methanol, is often necessary. However, high concentrations of organic solvents in extracts invariably lead to instability of the employed antibody, resulting in poor performance of the immunoassay. Evaluating the tolerance ability and exploring the molecular mechanisms of antibody tolerance in organic solvents are essential for the development of robust immunoassays. In this work, 25 monoclonal antibodies and methanol are utilized as models to address these questions. A novel protocol is initially established to precisely and rapidly determine antibody tolerance in methanol, identifying two distinct methanol effect patterns. Through a detailed investigation of the structural basis, a novel hypothesis regarding methanol effect patterns is proposed, termed "folding-aggregation," which is subsequently validated through molecular dynamics simulations. Furthermore, the investigation of sequence basis reveals significant differences in residue types within the complementarity-determining regions and ligand-binding residues, distinguishing the two antibody methanol effect patterns. Moreover, the methanol effect patterns of the antibodies are defined by germline antibodies. This work represents the first exploration of antibody methanol effect patterns and associated molecular mechanisms, with potential implications for the discovery and engineering of tolerant antibodies for the development of robust immunoassays.
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Affiliation(s)
- Yingjie Zhang
- National Key Laboratory of Veterinary Public Health and Safety, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P. R. China
| | - Jiafei Mi
- National Key Laboratory of Veterinary Public Health and Safety, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P. R. China
| | - Weilin Wu
- National Key Laboratory of Veterinary Public Health and Safety, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P. R. China
| | - Jie Fei
- National Key Laboratory of Veterinary Public Health and Safety, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P. R. China
| | - Bochen Lv
- National Key Laboratory of Veterinary Public Health and Safety, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P. R. China
| | - Xuezhi Yu
- National Key Laboratory of Veterinary Public Health and Safety, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P. R. China
| | - Kai Wen
- National Key Laboratory of Veterinary Public Health and Safety, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P. R. China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and Safety, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P. R. China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health and Safety, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P. R. China
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2
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Herling TW, Invernizzi G, Ausserwöger H, Bjelke JR, Egebjerg T, Lund S, Lorenzen N, Knowles TPJ. Nonspecificity fingerprints for clinical-stage antibodies in solution. Proc Natl Acad Sci U S A 2023; 120:e2306700120. [PMID: 38109540 PMCID: PMC10756282 DOI: 10.1073/pnas.2306700120] [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: 04/28/2023] [Accepted: 11/06/2023] [Indexed: 12/20/2023] Open
Abstract
Monoclonal antibodies (mAbs) have successfully been developed for the treatment of a wide range of diseases. The clinical success of mAbs does not solely rely on optimal potency and safety but also require good biophysical properties to ensure a high developability potential. In particular, nonspecific interactions are a key developability parameter to monitor during discovery and development. Despite an increased focus on the detection of nonspecific interactions, their underlying physicochemical origins remain poorly understood. Here, we employ solution-based microfluidic technologies to characterize a set of clinical-stage mAbs and their interactions with commonly used nonspecificity ligands to generate nonspecificity fingerprints, providing quantitative data on the underlying physical chemistry. Furthermore, the solution-based analysis enables us to measure binding affinities directly, and we evaluate the contribution of avidity in nonspecific binding by mAbs. We find that avidity can increase the apparent affinity by two orders of magnitude. Notably, we find that a subset of these highly developed mAbs show nonspecific electrostatic interactions, even at physiological pH and ionic strength, and that they can form microscale particles with charge-complementary polymers. The group of mAb constructs flagged here for nonspecificity are among the worst performers in independent reports of surface and column-based screens. The solution measurements improve on the state-of-the-art by providing a stand-alone result for individual mAbs without the need to benchmark against cohort data. Based on our findings, we propose a quantitative solution-based nonspecificity score, which can be integrated in the development workflow for biological therapeutics and more widely in protein engineering.
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Affiliation(s)
- Therese W. Herling
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | | | - Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Jais Rose Bjelke
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Thomas Egebjerg
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Søren Lund
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Nikolai Lorenzen
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Department of Physics, University of Cambridge, CambridgeCB3 0HE, United Kingdom
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3
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Pang KT, Yang YS, Zhang W, Ho YS, Sormanni P, Michaels TCT, Walsh I, Chia S. Understanding and controlling the molecular mechanisms of protein aggregation in mAb therapeutics. Biotechnol Adv 2023; 67:108192. [PMID: 37290583 DOI: 10.1016/j.biotechadv.2023.108192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/09/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
In antibody development and manufacturing, protein aggregation is a common challenge that can lead to serious efficacy and safety issues. To mitigate this problem, it is important to investigate its molecular origins. This review discusses (1) our current molecular understanding and theoretical models of antibody aggregation, (2) how various stress conditions related to antibody upstream and downstream bioprocesses can trigger aggregation, and (3) current mitigation strategies employed towards inhibiting aggregation. We discuss the relevance of the aggregation phenomenon in the context of novel antibody modalities and highlight how in silico approaches can be exploited to mitigate it.
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Affiliation(s)
- Kuin Tian Pang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore; School of Chemistry, Chemical Engineering, and Biotechnology, Nanyang Technology University, Singapore
| | - Yuan Sheng Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wei Zhang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Pietro Sormanni
- Chemistry of Health, Yusuf Hamied Department of Chemistry, University of Cambridge, United Kingdom
| | - Thomas C T Michaels
- Department of Biology, Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland; Bringing Materials to Life Initiative, ETH Zurich, Switzerland
| | - Ian Walsh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - Sean Chia
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore.
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4
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Kunamneni A, Montera MA, Durvasula R, Alles SRA, Goyal S, Westlund KN. Rapid Generation and Molecular Docking Analysis of Single-Chain Fragment Variable (scFv) Antibody Selected by Ribosome Display Targeting Cholecystokinin B Receptor (CCK-BR) for Reduction of Chronic Neuropathic Pain. Int J Mol Sci 2023; 24:11035. [PMID: 37446213 DOI: 10.3390/ijms241311035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
A robust cell-free platform technology, ribosome display in combination with cloning, expression, and purification was utilized to develop single chain Fragment variable (scFv) antibody variants as pain therapy directed at the mouse cholecystokinin B (CCK-B) receptor. Three effective CCK-B peptide-specific scFvs were generated through ribosomal display technology. Soluble expression and ELISA analysis showed that one antibody, scFv77-2 had the highest binding and could be purified from bacterial cells in large quantities. Octet measurements further revealed that the CCK-B scFv77-2 antibody had binding kinetics of KD = 1.794 × 10-8 M. Molecular modeling and docking analyses suggested that the scFv77-2 antibody shaped a proper cavity to embed the whole CCK-B peptide molecule and that a steady-state complex was formed relying on intermolecular forces, including hydrogen bonding, electrostatic force, and hydrophobic interactions. Thus, the scFv antibody can be applied for mechanistic intermolecular interactions and functional in vivo studies of CCK-BR. The high affinity scFv77-2 antibody showed good efficacy with binding to CCK-BR tested in a chronic pain model. In vivo studies validated the efficacy of the CCK-B receptor (CCK-BR) scFv77-2 antibody as a potential therapy for chronic trigeminal nerve injury-induced pain. Mice were given a single dose of the CCK-B receptor (CCK-BR) scFv antibody 3 weeks after induction of a chronic trigeminal neuropathic pain model, during the transition from acute to chronic pain. The long-term effectiveness for the reduction of mechanical hypersensitivity was evident, persisting for months. The anxiety- and depression-related behaviors typically accompanying persisting hypersensitivity subsequently never developed in the mice given CCK-BR scFv. The effectiveness of the antibody is the basis for further development of the lead CCK-BR scFv as a promising non-opioid therapeutic for chronic pain and the long-term reduction of chronic pain- and anxiety-related behaviors.
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Affiliation(s)
- Adinarayana Kunamneni
- Department of Internal Medicine, Mayo Clinic, Jacksonville, FL 32224-1865, USA
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153-3328, USA
| | - Marena A Montera
- Department of Anesthesiology & Critical Care Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131-0001, USA
| | - Ravi Durvasula
- Department of Internal Medicine, Mayo Clinic, Jacksonville, FL 32224-1865, USA
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153-3328, USA
| | - Sascha R A Alles
- Department of Anesthesiology & Critical Care Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131-0001, USA
| | - Sachin Goyal
- Department of Anesthesiology & Critical Care Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131-0001, USA
| | - Karin N Westlund
- Department of Anesthesiology & Critical Care Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131-0001, USA
- Biomedical Laboratory Research & Development (121F), New Mexico VA Health Care System, Albuquerque, NM 87108-5153, USA
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5
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Chang J, Rader C, Peng H. A mammalian cell display platform based on scFab transposition. Antib Ther 2023; 6:157-169. [PMID: 37492588 PMCID: PMC10365156 DOI: 10.1093/abt/tbad009] [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: 12/27/2022] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 07/27/2023] Open
Abstract
In vitro display technologies have been successfully utilized for the discovery and evolution of monoclonal antibodies (mAbs) for diagnostic and therapeutic applications, with phage display and yeast display being the most commonly used platforms due to their simplicity and high efficiency. As their prokaryotic or lower eukaryotic host organisms typically have no or different post-translational modifications, several mammalian cell-based display and screening technologies for isolation and optimization of mAbs have emerged and are being developed. We report here a novel and useful mammalian cell display platform based on the PiggyBac transposon system to display mAbs in a single-chain Fab (scFab) format on the surface of HEK293F cells. Immune rabbit antibody libraries encompassing ~7 × 107 independent clones were generated in an all-in-one transposon vector, stably delivered into HEK293F cells and displayed as an scFab with rabbit variable and human constant domains. After one round of magnetic activated cell sorting and two rounds of fluorescence activated cell sorting, mAbs with high affinity in the subnanomolar range and cross-reactivity to the corresponding human and mouse antigens were identified, demonstrating the power of this platform for antibody discovery. We developed a highly efficient mammalian cell display platform based on the PiggyBac transposon system for antibody discovery, which could be further utilized for humanization as well as affinity and specificity maturation.
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Affiliation(s)
- Jing Chang
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, USA
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, USA
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6
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Ausserwöger H, Krainer G, Welsh TJ, Thorsteinson N, de Csilléry E, Sneideris T, Schneider MM, Egebjerg T, Invernizzi G, Herling TW, Lorenzen N, Knowles TPJ. Surface patches induce nonspecific binding and phase separation of antibodies. Proc Natl Acad Sci U S A 2023; 120:e2210332120. [PMID: 37011217 PMCID: PMC10104583 DOI: 10.1073/pnas.2210332120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/06/2023] [Indexed: 04/05/2023] Open
Abstract
Nonspecific interactions are a key challenge in the successful development of therapeutic antibodies. The tendency for nonspecific binding of antibodies is often difficult to reduce by rational design, and instead, it is necessary to rely on comprehensive screening campaigns. To address this issue, we performed a systematic analysis of the impact of surface patch properties on antibody nonspecificity using a designer antibody library as a model system and single-stranded DNA as a nonspecificity ligand. Using an in-solution microfluidic approach, we find that the antibodies tested bind to single-stranded DNA with affinities as high as KD = 1 µM. We show that DNA binding is driven primarily by a hydrophobic patch in the complementarity-determining regions. By quantifying the surface patches across the library, the nonspecific binding affinity is shown to correlate with a trade-off between the hydrophobic and total charged patch areas. Moreover, we show that a change in formulation conditions at low ionic strengths leads to DNA-induced antibody phase separation as a manifestation of nonspecific binding at low micromolar antibody concentrations. We highlight that phase separation is driven by a cooperative electrostatic network assembly mechanism of antibodies with DNA, which correlates with a balance between positive and negative charged patches. Importantly, our study demonstrates that both nonspecific binding and phase separation are controlled by the size of the surface patches. Taken together, these findings highlight the importance of surface patches and their role in conferring antibody nonspecificity and its macroscopic manifestation in phase separation.
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Affiliation(s)
- Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Georg Krainer
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Timothy J. Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Nels Thorsteinson
- Research and Development, Chemical Computing Group, Montreal, QuebecH3A 2R7, Canada
| | - Ella de Csilléry
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Tomas Sneideris
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Matthias M. Schneider
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Thomas Egebjerg
- Global Research Technologies, Novo Nordisk A/S2760Måløv, Denmark
| | | | - Therese W. Herling
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Nikolai Lorenzen
- Global Research Technologies, Novo Nordisk A/S2760Måløv, Denmark
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Department of Physics, Cavendish Laboratory, University of Cambridge, CambridgeCB3 0HE, United Kingdom
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7
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Svilenov HL, Arosio P, Menzen T, Tessier P, Sormanni P. Approaches to expand the conventional toolbox for discovery and selection of antibodies with drug-like physicochemical properties. MAbs 2023; 15:2164459. [PMID: 36629855 PMCID: PMC9839375 DOI: 10.1080/19420862.2022.2164459] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
Antibody drugs should exhibit not only high-binding affinity for their target antigens but also favorable physicochemical drug-like properties. Such drug-like biophysical properties are essential for the successful development of antibody drug products. The traditional approaches used in antibody drug development require significant experimentation to produce, optimize, and characterize many candidates. Therefore, it is attractive to integrate new methods that can optimize the process of selecting antibodies with both desired target-binding and drug-like biophysical properties. Here, we summarize a selection of techniques that can complement the conventional toolbox used to de-risk antibody drug development. These techniques can be integrated at different stages of the antibody development process to reduce the frequency of physicochemical liabilities in antibody libraries during initial discovery and to co-optimize multiple antibody features during early-stage antibody engineering and affinity maturation. Moreover, we highlight biophysical and computational approaches that can be used to predict physical degradation pathways relevant for long-term storage and in-use stability to reduce the need for extensive experimentation.
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Affiliation(s)
- Hristo L. Svilenov
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Gent, Belgium
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tim Menzen
- Coriolis Pharma Research GmbH, Martinsried, 82152, Germany
| | - Peter Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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8
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Ausserwöger H, Schneider MM, Herling TW, Arosio P, Invernizzi G, Knowles TPJ, Lorenzen N. Non-specificity as the sticky problem in therapeutic antibody development. Nat Rev Chem 2022; 6:844-861. [PMID: 37117703 DOI: 10.1038/s41570-022-00438-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/16/2022]
Abstract
Antibodies are highly potent therapeutic scaffolds with more than a hundred different products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins. We discuss the role of surface patches - clusters of surface-exposed amino acid residues with similar physicochemical properties - as inducers of non-specific interactions. These patches collectively drive interactions including dipole-dipole, π-stacking and hydrophobic interactions to complementary moieties. We elucidate links between these supramolecular assembly processes and macroscopic development issues, such as decreased physical stability and poor in vivo half-life. Finally, we highlight challenges and opportunities for optimizing protein binding specificity and minimizing non-specificity for future generations of therapeutics.
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2021 White Paper on Recent Issues in Bioanalysis: ISR for Biomarkers, Liquid Biopsies, Spectral Cytometry, Inhalation/Oral & Multispecific Biotherapeutics, Accuracy/LLOQ for Flow Cytometry ( Part 2 - Recommendations on Biomarkers/CDx Assays Development & Validation, Cytometry Validation & Innovation, Biotherapeutics PK LBA Regulated Bioanalysis, Critical Reagents & Positive Controls Generation). Bioanalysis 2022; 14:627-692. [PMID: 35578974 DOI: 10.4155/bio-2022-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The 15th edition of the Workshop on Recent Issues in Bioanalysis (15th WRIB) was held on 27 September to 1 October 2021. Even with a last-minute move from in-person to virtual, an overwhelmingly high number of nearly 900 professionals representing pharma and biotech companies, contract research organizations (CROs), and multiple regulatory agencies still eagerly convened to actively discuss the most current topics of interest in bioanalysis. The 15th WRIB included three Main Workshops and seven Specialized Workshops that together spanned 1 week in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccines. Moreover, in-depth workshops on biomarker assay development and validation (BAV) (focused on clarifying the confusion created by the increased use of the term "context of use" [COU]); mass spectrometry of proteins (therapeutic, biomarker and transgene); state-of-the-art cytometry innovation and validation; and critical reagent and positive control generation were the special features of the 15th edition. This 2021 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2021 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 2) covers the recommendations on ISR for Biomarkers, Liquid Biopsies, Spectral Cytometry, Inhalation/Oral & Multispecific Biotherapeutics, Accuracy/LLOQ for Flow Cytometry. Part 1A (Endogenous Compounds, Small Molecules, Complex Methods, Regulated Mass Spec of Large Molecules, Small Molecule, PoC), Part 1B (Regulatory Agencies' Inputs on Bioanalysis, Biomarkers, Immunogenicity, Gene & Cell Therapy and Vaccine) and Part 3 (TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness) are published in volume 14 of Bioanalysis, issues 9 and 11 (2022), respectively.
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10
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Pedrioli A, Oxenius A. Single B cell technologies for monoclonal antibody discovery. Trends Immunol 2021; 42:1143-1158. [PMID: 34743921 DOI: 10.1016/j.it.2021.10.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022]
Abstract
Monoclonal antibodies (mAbs) are often selected from antigen-specific single B cells derived from different hosts, which are notably short-lived in ex vivo culture conditions and hence, arduous to interrogate. The development of several new techniques and protocols has facilitated the isolation and retrieval of antibody-coding sequences of antigen-specific B cells by also leveraging miniaturization of reaction volumes. Alternatively, mAbs can be generated independently of antigen-specific B cells, comprising display technologies and, more recently, artificial intelligence-driven algorithms. Consequently, a considerable variety of techniques are used, raising the demand for better consolidation. In this review, we present and discuss the major techniques available to interrogate antigen-specific single B cells to isolate antigen-specific mAbs, including their main advantages and disadvantages.
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Affiliation(s)
- Alessandro Pedrioli
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.
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11
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Prabakaran P, Rao SP, Wendt M. Animal immunization merges with innovative technologies: A new paradigm shift in antibody discovery. MAbs 2021; 13:1924347. [PMID: 33947305 PMCID: PMC8118498 DOI: 10.1080/19420862.2021.1924347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Animal-derived antibody sources, particularly, transgenic mice that are engineered with human immunoglobulin loci, along with advanced antibody generation technology platforms have facilitated the discoveries of human antibody therapeutics. For example, isolation of antigen-specific B cells, microfluidics, and next-generation sequencing have emerged as powerful tools for identifying and developing monoclonal antibodies (mAbs). These technologies enable not only antibody drug discovery but also lead to the understanding of B cell biology, immune mechanisms and immunogenetics of antibodies. In this perspective article, we discuss the scientific merits of animal immunization combined with advanced methods for antibody generation as compared to animal-free alternatives through in-vitro-generated antibody libraries. The knowledge gained from animal-derived antibodies concerning the recombinational diversity, somatic hypermutation patterns, and physiochemical properties is found more valuable and prerequisite for developing in vitro libraries, as well as artificial intelligence/machine learning methods to discover safe and effective mAbs.
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Affiliation(s)
- Ponraj Prabakaran
- Biologics Research US, Global Large Molecules Research, Sanofi, Framingham, MA, USA
| | - Sambasiva P Rao
- Biologics Research US, Global Large Molecules Research, Sanofi, Framingham, MA, USA
| | - Maria Wendt
- Biologics Research US, Global Large Molecules Research, Sanofi, Framingham, MA, USA
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12
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Laustsen AH, Greiff V, Karatt-Vellatt A, Muyldermans S, Jenkins TP. Animal Immunization, in Vitro Display Technologies, and Machine Learning for Antibody Discovery. Trends Biotechnol 2021; 39:1263-1273. [PMID: 33775449 DOI: 10.1016/j.tibtech.2021.03.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
Abstract
For years, a discussion has persevered on the benefits and drawbacks of antibody discovery using animal immunization versus in vitro selection from non-animal-derived recombinant repertoires using display technologies. While it has been argued that using recombinant display libraries can reduce animal consumption, we hold that the number of animals used in immunization campaigns is dwarfed by the number sacrificed during preclinical studies. Thus, improving quality control of antibodies before entering in vivo studies will have a larger impact on animal consumption. Both animal immunization and recombinant repertoires present unique advantages for discovering antibodies that are fit for purpose. Furthermore, we anticipate that machine learning will play a significant role within discovery workflows, refining current antibody discovery practices.
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Affiliation(s)
- Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | | | - Serge Muyldermans
- Department of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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13
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Gorovits B, Hays A, Jani D, Jones C, King C, Lundequist A, Mora J, Partridge M, Pathania D, Ramaswamy SS, Rutwij D, Shen H, Starling G. AAPS Perspective on the EURL Recommendation on the use of Non-Animal-Derived Antibodies. AAPS JOURNAL 2021; 23:34. [PMID: 33649990 DOI: 10.1208/s12248-021-00567-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022]
Abstract
In May 2020, the EU Reference Laboratory for alternatives to animal testing (EURL ECVAM) published a recommendation report entitled "Recommendation on nonanimal-derived antibodies". In this report, the EURL ECVAM specifically states: "Therefore, taking into consideration the ESAC Opinion on the scientific validity of replacements for animal-derived antibodies, EURL ECVAM recommends that animals should no longer be used for the development and production of antibodies for research, regulatory, diagnostic and therapeutic applications. The provisions of Directive 2010/63/EU should be respected, and EU countries should no longer authorise the development and production of antibodies through animal immunisation, where robust, legitimate scientific justification is lacking." (1). Here, we are providing the American Association of Pharmaceutical Scientists (AAPS) opinion on the EURL ECVAM recommendation report. In brief, there has been a clear and strong progress in reduction of animal use in the drug discovery and development process, including significant reduction of animal use in production of antibody reagents. Yet, it is proposed that more data need to be generated, shared and discussed within the scientific community before a decision to implement the change to non-animal derived antibodies is made.
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Affiliation(s)
- B Gorovits
- Sana Biotechnology, 300 Tech Square, Suite 700, Cambridge, MA, 02139, USA.
| | - A Hays
- PRA Health Sciences, Raleigh, North Carolina, USA
| | - D Jani
- Agenus Inc, Lexington, Massachusetts, USA
| | - C Jones
- Mercodia AB, Uppsala, Sweden
| | - C King
- Amgen Inc, Thousand Oaks, CA, USA
| | | | - J Mora
- Bristol Myers Squibb, New York, NY, USA
| | - M Partridge
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | | | | | - D Rutwij
- Gilead Sciences, Foster City, CA, USA
| | - H Shen
- Teva Pharmaceuticals, Petah Tikva, Israel
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14
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Makowski EK, Wu L, Gupta P, Tessier PM. Discovery-stage identification of drug-like antibodies using emerging experimental and computational methods. MAbs 2021; 13:1895540. [PMID: 34313532 PMCID: PMC8346245 DOI: 10.1080/19420862.2021.1895540] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 11/30/2022] Open
Abstract
There is intense and widespread interest in developing monoclonal antibodies as therapeutic agents to treat diverse human disorders. During early-stage antibody discovery, hundreds to thousands of lead candidates are identified, and those that lack optimal physical and chemical properties must be deselected as early as possible to avoid problems later in drug development. It is particularly challenging to characterize such properties for large numbers of candidates with the low antibody quantities, concentrations, and purities that are available at the discovery stage, and to predict concentrated antibody properties (e.g., solubility, viscosity) required for efficient formulation, delivery, and efficacy. Here we review key recent advances in developing and implementing high-throughput methods for identifying antibodies with desirable in vitro and in vivo properties, including favorable antibody stability, specificity, solubility, pharmacokinetics, and immunogenicity profiles, that together encompass overall drug developability. In particular, we highlight impressive recent progress in developing computational methods for improving rational antibody design and prediction of drug-like behaviors that hold great promise for reducing the amount of required experimentation. We also discuss outstanding challenges that will need to be addressed in the future to fully realize the great potential of using such analysis for minimizing development times and improving the success rate of antibody candidates in the clinic.
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Affiliation(s)
- Emily K. Makowski
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering
| | - Priyanka Gupta
- Department of Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, USA
- Biotherapeutics Discovery Department, Boehringer Ingelheim, Ridgefield, CT, USA
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
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15
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Alfaleh MA, Alsaab HO, Mahmoud AB, Alkayyal AA, Jones ML, Mahler SM, Hashem AM. Phage Display Derived Monoclonal Antibodies: From Bench to Bedside. Front Immunol 2020; 11:1986. [PMID: 32983137 PMCID: PMC7485114 DOI: 10.3389/fimmu.2020.01986] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Monoclonal antibodies (mAbs) have become one of the most important classes of biopharmaceutical products, and they continue to dominate the universe of biopharmaceutical markets in terms of approval and sales. They are the most profitable single product class, where they represent six of the top ten selling drugs. At the beginning of the 1990s, an in vitro antibody selection technology known as antibody phage display was developed by John McCafferty and Sir. Gregory Winter that enabled the discovery of human antibodies for diverse applications, particularly antibody-based drugs. They created combinatorial antibody libraries on filamentous phage to be utilized for generating antigen specific antibodies in a matter of weeks. Since then, more than 70 phage–derived antibodies entered clinical studies and 14 of them have been approved. These antibodies are indicated for cancer, and non-cancer medical conditions, such as inflammatory, optical, infectious, or immunological diseases. This review will illustrate the utility of phage display as a powerful platform for therapeutic antibodies discovery and describe in detail all the approved mAbs derived from phage display.
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Affiliation(s)
- Mohamed A Alfaleh
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad Bakur Mahmoud
- College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Almohanad A Alkayyal
- Department of Medical Laboratory Technology, University of Tabuk, Tabuk, Saudi Arabia
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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16
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Arslan M, Karadag D, Kalyoncu S. Conformational changes in a Vernier zone region: Implications for antibody dual specificity. Proteins 2020; 88:1447-1457. [PMID: 32526069 DOI: 10.1002/prot.25964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/23/2020] [Accepted: 06/06/2020] [Indexed: 11/07/2022]
Abstract
Understanding the determinants of antibody specificity is one of the challenging tasks in antibody development. Monospecific antibodies are still dominant in approved antibody therapeutics but there is a significant body of work to show that multispecific antibodies can increase the overall therapeutic effect. Dual-specific or "Two-in-One" antibodies can bind to two different antigens separately with the same antigen-binding site as opposed to bispecifics, which simultaneously bind to two different antigens through separate antigen-binding units. These nonstandard dual-specific antibodies were recently shown to be promising for new antibody-based therapeutics. Here, we physicochemically and structurally analyzed six different antibodies of which two are monospecific and four are dual-specific antibodies derived from monospecific templates to gain insight about dual-specificity determinants. These dual-specific antibodies can target both human epidermal growth factor receptor 2 and vascular endothelial growth factor at different binding affinities. We showed that a particular region of clustered Vernier zone residues might play key roles in gaining dual specificity. While there are minimal intramolecular interactions between a certain Vernier zone region, namely LV4 and LCDR1 of monospecific template, there is a significant structural change and consequently close contact formation between LV4-LCDR1 loops of derived dual-specific antibodies. Although Vernier zone residues were previously shown to be important for humanization applications, they are mostly underestimated in the literature. Here, we also aim to resurrect Vernier zone residues for antibody engineering efforts.
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Affiliation(s)
- Merve Arslan
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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17
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Willis LF, Kumar A, Jain T, Caffry I, Xu Y, Radford SE, Kapur N, Vásquez M, Brockwell DJ. The uniqueness of flow in probing the aggregation behavior of clinically relevant antibodies. ENGINEERING REPORTS : OPEN ACCESS 2020; 2:e12147. [PMID: 34901768 PMCID: PMC8638667 DOI: 10.1002/eng2.12147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
The development of therapeutic monoclonal antibodies (mAbs) can be hindered by their tendency to aggregate throughout their lifetime, which can illicit immunogenic responses and render mAb manufacturing unfeasible. Consequently, there is a need to identify mAbs with desirable thermodynamic stability, solubility, and lack of self-association. These behaviors are assessed using an array of in silico and in vitro assays, as no single assay can predict aggregation and developability. We have developed an extensional and shear flow device (EFD), which subjects proteins to defined hydrodynamic forces which mimic those experienced in bioprocessing. Here, we utilize the EFD to explore the aggregation propensity of 33 IgG1 mAbs, whose variable domains are derived from clinical antibodies. Using submilligram quantities of material per replicate, wide-ranging EFD-induced aggregation (9-81% protein in pellet) was observed for these mAbs, highlighting the EFD as a sensitive method to assess aggregation propensity. By comparing the EFD-induced aggregation data to those obtained previously from 12 other biophysical assays, we show that the EFD provides distinct information compared with current measures of adverse biophysical behavior. Assessing a candidate's liability to hydrodynamic force thus adds novel insight into the rational selection of developable mAbs that complements other assays.
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Affiliation(s)
- Leon F. Willis
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Amit Kumar
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
- Department of Life SciencesImperial College LondonLondonUK
| | | | - Isabelle Caffry
- Adimab LLCLebanonNew HampshireUSA
- Cornell Johnson Graduate School of ManagementIthacaNew YorkUSA
| | - Yingda Xu
- Adimab LLCLebanonNew HampshireUSA
- Biotheus Inc.ZhuhaiGuangdong ProvinceChina
| | - Sheena E. Radford
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Nikil Kapur
- School of Mechanical Engineering, Faculty of EngineeringUniversity of LeedsLeedsUK
| | | | - David J. Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
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18
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Function-based high-throughput screening for antibody antagonists and agonists against G protein-coupled receptors. Commun Biol 2020; 3:146. [PMID: 32218528 PMCID: PMC7099005 DOI: 10.1038/s42003-020-0867-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Hybridoma and phage display are two powerful technologies for isolating target-specific monoclonal antibodies based on the binding. However, for complex membrane proteins, such as G protein-coupled receptors (GPCRs), binding-based screening rarely results in functional antibodies. Here we describe a function-based high-throughput screening method for quickly identifying antibody antagonists and agonists against GPCRs by combining glycosylphosphatidylinositol-anchored antibody cell display with β-arrestin recruitment-based cell sorting and screening. This method links antibody genotype with phenotype and is applicable to all GPCR targets. We validated this method by identifying a panel of antibody antagonists and an antibody agonist to the human apelin receptor from an immune antibody repertoire. In contrast, we obtained only neutral binders and antibody antagonists from the same repertoire by phage display, suggesting that the new approach described here is more efficient than traditional methods in isolating functional antibodies. This new method may create a new paradigm in antibody drug discovery. Ren et al. develop a function-based high-throughput screening method for identifying antibody antagonists and agonists against GPCRs by combining GPI-anchored antibody cell surface display and β-arrestin recruitment reporter assay. They identify a panel of antibody antagonists and an agonist to the human apelin receptor, which is not obtainable from phage display technology.
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19
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Alfaleh MA, Alsaab HO, Mahmoud AB, Alkayyal AA, Jones ML, Mahler SM, Hashem AM. Phage Display Derived Monoclonal Antibodies: From Bench to Bedside. Front Immunol 2020. [PMID: 32983137 DOI: 10.3389/fimmu.2020.01986/bibtex] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Monoclonal antibodies (mAbs) have become one of the most important classes of biopharmaceutical products, and they continue to dominate the universe of biopharmaceutical markets in terms of approval and sales. They are the most profitable single product class, where they represent six of the top ten selling drugs. At the beginning of the 1990s, an in vitro antibody selection technology known as antibody phage display was developed by John McCafferty and Sir. Gregory Winter that enabled the discovery of human antibodies for diverse applications, particularly antibody-based drugs. They created combinatorial antibody libraries on filamentous phage to be utilized for generating antigen specific antibodies in a matter of weeks. Since then, more than 70 phage-derived antibodies entered clinical studies and 14 of them have been approved. These antibodies are indicated for cancer, and non-cancer medical conditions, such as inflammatory, optical, infectious, or immunological diseases. This review will illustrate the utility of phage display as a powerful platform for therapeutic antibodies discovery and describe in detail all the approved mAbs derived from phage display.
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Affiliation(s)
- Mohamed A Alfaleh
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad Bakur Mahmoud
- College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Almohanad A Alkayyal
- Department of Medical Laboratory Technology, University of Tabuk, Tabuk, Saudi Arabia
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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20
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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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21
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Miller MS, Douglass J, Hwang MS, Skora AD, Murphy M, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S, Gabelli SB. An engineered antibody fragment targeting mutant β-catenin via major histocompatibility complex I neoantigen presentation. J Biol Chem 2019; 294:19322-19334. [PMID: 31690625 PMCID: PMC6916501 DOI: 10.1074/jbc.ra119.010251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/04/2019] [Indexed: 12/18/2022] Open
Abstract
Mutations in CTNNB1, the gene encoding β-catenin, are common in colon and liver cancers, the most frequent mutation affecting Ser-45 in β-catenin. Peptides derived from WT β-catenin have previously been shown to be presented on the cell surface as part of major histocompatibility complex (MHC) class I, suggesting an opportunity for targeting this common driver gene mutation with antibody-based therapies. Here, crystal structures of both the WT and S45F mutant peptide bound to HLA-A*03:01 at 2.20 and 2.45 Å resolutions, respectively, confirmed the accessibility of the phenylalanine residue for antibody recognition. Phage display was then used to identify single-chain variable fragment clones that selectively bind the S45F mutant peptide presented in HLA-A*03:01 and have minimal WT or other off-target binding. Following the initial characterization of five clones, we selected a single clone, E10, for further investigation. We developed a computational model of the binding of E10 to the mutant peptide-bound HLA-A3, incorporating data from affinity maturation as initial validation. In the future, our model may be used to design clones with maintained specificity and higher affinity. Such derivatives could be adapted into either cell-based (CAR-T) or protein-based (bispecific T-cell engagers) therapies to target cancer cells harboring the S45F mutation in CTNNB1.
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Affiliation(s)
- Michelle S Miller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Andrew D Skora
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Michael Murphy
- GE Healthcare Life Sciences, Marlborough, Massachusetts 01752
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 .,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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