1
|
Thalén NB, Karlander M, Lundqvist M, Persson H, Hofström C, Turunen SP, Godzwon M, Volk AL, Malm M, Ohlin M, Rockberg J. Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping. Commun Biol 2024; 7:805. [PMID: 38961245 PMCID: PMC11222437 DOI: 10.1038/s42003-024-06508-8] [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: 11/29/2023] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
Precise epitope determination of therapeutic antibodies is of great value as it allows for further comprehension of mechanism of action, therapeutic responsiveness prediction, avoidance of unwanted cross reactivity, and vaccine design. The golden standard for discontinuous epitope determination is the laborious X-ray crystallography method. Here, we present a combinatorial method for rapid mapping of discontinuous epitopes by mammalian antigen display, eliminating the need for protein expression and purification. The method is facilitated by automated workflows and tailored software for antigen analysis and oligonucleotide design. These oligos are used in automated mutagenesis to generate an antigen receptor library displayed on mammalian cells for direct binding analysis by flow cytometry. Through automated analysis of 33930 primers an optimized single condition cloning reaction was defined allowing for mutation of all surface-exposed residues of the receptor binding domain of SARS-CoV-2. All variants were functionally expressed, and two reference binders validated the method. Furthermore, epitopes of three novel therapeutic antibodies were successfully determined followed by evaluation of binding also towards SARS-CoV-2 Omicron BA.2. We find the method to be highly relevant for rapid construction of antigen libraries and determination of antibody epitopes, especially for the development of therapeutic interventions against novel pathogens.
Collapse
Affiliation(s)
- Niklas Berndt Thalén
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Maximilian Karlander
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Magnus Lundqvist
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development Platform & School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Camilla Hofström
- Science for Life Laboratory, Drug Discovery and Development Platform & School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - S Pauliina Turunen
- Science for Life Laboratory, Drug Discovery and Development Platform & School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | - Anna-Luisa Volk
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Magdalena Malm
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Johan Rockberg
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden.
| |
Collapse
|
2
|
Struijf EM, De la O Becerra KI, Ruyken M, de Haas CJC, van Oosterom F, Siere DY, van Keulen JE, Heesterbeek DAC, Dolk E, Heukers R, Bardoel BW, Gros P, Rooijakkers SHM. Inhibition of cleavage of human complement component C5 and the R885H C5 variant by two distinct high affinity anti-C5 nanobodies. J Biol Chem 2023; 299:104956. [PMID: 37356719 PMCID: PMC10374974 DOI: 10.1016/j.jbc.2023.104956] [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: 03/06/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023] Open
Abstract
The human complement system plays a crucial role in immune defense. However, its erroneous activation contributes to many serious inflammatory diseases. Since most unwanted complement effector functions result from C5 cleavage into C5a and C5b, development of C5 inhibitors, such as clinically approved monoclonal antibody eculizumab, are of great interest. Here, we developed and characterized two anti-C5 nanobodies, UNbC5-1 and UNbC5-2. Using surface plasmon resonance, we determined a binding affinity of 119.9 pM for UNbC5-1 and 7.7 pM for UNbC5-2. Competition experiments determined that the two nanobodies recognize distinct epitopes on C5. Both nanobodies efficiently interfered with C5 cleavage in a human serum environment, as they prevented red blood cell lysis via membrane attack complexes (C5b-9) and the formation of chemoattractant C5a. The cryo-EM structure of UNbC5-1 and UNbC5-2 in complex with C5 (3.6 Å resolution) revealed that the binding interfaces of UNbC5-1 and UNbC5-2 overlap with known complement inhibitors eculizumab and RaCI3, respectively. UNbC5-1 binds to the MG7 domain of C5, facilitated by a hydrophobic core and polar interactions, and UNbC5-2 interacts with the C5d domain mostly by salt bridges and hydrogen bonds. Interestingly, UNbC5-1 potently binds and inhibits C5 R885H, a genetic variant of C5 that is not recognized by eculizumab. Altogether, we identified and characterized two different, high affinity nanobodies against human C5. Both nanobodies could serve as diagnostic and/or research tools to detect C5 or inhibit C5 cleavage. Furthermore, the residues targeted by UNbC5-1 hold important information for therapeutic inhibition of different polymorphic variants of C5.
Collapse
Affiliation(s)
- Eva M Struijf
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Karla I De la O Becerra
- Structural Biochemistry Group, Faculty of Science, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Maartje Ruyken
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Carla J C de Haas
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Fleur van Oosterom
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Danique Y Siere
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joanne E van Keulen
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dani A C Heesterbeek
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | | | - Bart W Bardoel
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Piet Gros
- Structural Biochemistry Group, Faculty of Science, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Suzan H M Rooijakkers
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
3
|
Jethva PN, Gross ML. Hydrogen Deuterium Exchange and other Mass Spectrometry-based Approaches for Epitope Mapping. FRONTIERS IN ANALYTICAL SCIENCE 2023; 3:1118749. [PMID: 37746528 PMCID: PMC10512744 DOI: 10.3389/frans.2023.1118749] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Antigen-antibody interactions are a fundamental subset of protein-protein interactions responsible for the "survival of the fittest". Determining the interacting interface of the antigen, called an epitope, and that on the antibody, called a paratope, is crucial to antibody development. Because each antigen presents multiple epitopes (unique footprints), sophisticated approaches are required to determine the target region for a given antibody. Although X-ray crystallography, Cryo-EM, and nuclear magnetic resonance can provide atomic details of an epitope, they are often laborious, poor in throughput, and insensitive. Mass spectrometry-based approaches offer rapid turnaround, intermediate structural resolution, and virtually no size limit for the antigen, making them a vital approach for epitope mapping. In this review, we describe in detail the principles of hydrogen deuterium exchange mass spectrometry in application to epitope mapping. We also show that a combination of MS-based approaches can assist or complement epitope mapping and push the limit of structural resolution to the residue level. We describe in detail the MS methods used in epitope mapping, provide our perspective about the approaches, and focus on elucidating the role that HDX-MS is playing now and in the future by organizing a discussion centered around several improvements in prototype instrument/applications used for epitope mapping. At the end, we provide a tabular summary of the current literature on HDX-MS-based epitope mapping.
Collapse
Affiliation(s)
- Prashant N. Jethva
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
| |
Collapse
|
4
|
Ma M, Qi H, Hu C, Xu Z, Wu F, Wang N, Lai D, Li Y, Zhang H, Jiang H, Meng Q, Guo S, Kang Y, Zhao X, Li H, Tao SC. The binding epitope of sintilimab on PD-1 revealed by AbMap. Acta Biochim Biophys Sin (Shanghai) 2021; 53:628-635. [PMID: 33637989 DOI: 10.1093/abbs/gmab020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 12/24/2022] Open
Abstract
PD-1 plays an important role as an immune checkpoint. Sintilimab is a newly approved PD-1 antibody for cancer immunotherapy with an unknown binding epitope on PD-1. In this study, to elucidate the molecular mechanism by which sintilimab blocks PD-1 activation, we applied Antibody binding epitope Mapping (AbMap) to identify the binding epitope of sintilimab. An epitope was successfully identified, i.e. SLAPKA, aa 127-132. By constructing a series of point mutations, the dominant residues S127, L128, A129, P130, and A132 of PD-1 were further validated by western blot analysis, biolayer interferometry, and flow cytometry. Structural analysis showed that the epitope is partially within the binding interface of PD-1 and PD-L1, and this epitope also partially overlaps with that of nivolumab and pembrolizumab. These results demonstrate that sintilimab can attenuate PD-1 activation by directly competing with the interaction between PD-1 and PD-L1 through binding with the key residues of the FG loop on PD-1. This study also demonstrates the high efficiency and accuracy of AbMap for determining the binding epitope of therapeutic antibodies.
Collapse
Affiliation(s)
- Mingliang Ma
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huan Qi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhaowei Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fanlin Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture, Lu Dong University, Yantai 264025, Shandong, China
| | - Nan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, China
| | - Danyun Lai
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hainan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hewei Jiang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingfeng Meng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shujuan Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yani Kang
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaodong Zhao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng-ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory for Oncogenes, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
5
|
Inflammation, immunity and potential target therapy of SARS-COV-2: A total scale analysis review. Food Chem Toxicol 2021; 150:112087. [PMID: 33640537 PMCID: PMC7905385 DOI: 10.1016/j.fct.2021.112087] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 12/18/2022]
Abstract
Coronavirus disease-19 (COVID-19) is a complex disease that causes illness ranging from mild to severe respiratory problems. It is caused by a novel coronavirus SARS-CoV-2 (Severe acute respiratory syndrome coronavirus-2) that is an enveloped positive-sense single-stranded RNA (+ssRNA) virus belongs to coronavirus CoV family. It has a fast-spreading potential worldwide, which leads to high mortality regardless of lows death rates. Now some vaccines or a specific drug are approved but not available for every country for disease prevention and/or treatment. Therefore, it is a high demand to identify the known drugs and test them as a possible therapeutic approach. In this critical situation, one or more of these drugs may represent the only option to treat or reduce the severity of the disease, until some specific drugs or vaccines will be developed and/or approved for everyone in this pandemic. In this updated review, the available repurpose immunotherapeutic treatment strategies are highlighted, elucidating the crosstalk between the immune system and SARS-CoV-2. Despite the reasonable data availability, the effectiveness and safety of these drugs against SARS-CoV-2 needs further studies and validations aiming for a better clinical outcome.
Collapse
|
6
|
Zelek WM, Menzies GE, Brancale A, Stockinger B, Morgan BP. Characterizing the original anti-C5 function-blocking antibody, BB5.1, for species specificity, mode of action and interactions with C5. Immunology 2020; 161:103-113. [PMID: 32557571 PMCID: PMC7496778 DOI: 10.1111/imm.13228] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/05/2020] [Accepted: 06/07/2020] [Indexed: 12/11/2022] Open
Abstract
The implication of complement in multiple diseases over the last 20 years has fuelled interest in developing anti-complement drugs. To date, the focus has been on C5; blocking cleavage of C5 prevents formation of two pro-inflammatory activities, C5a anaphylatoxin and membrane attack complex. The concept of C5 blockade to inhibit inflammation dates back 30 years to the description of BB5.1, an anti-C5 blocking monoclonal antibody raised in C5-deficient mice. This antibody proved an invaluable tool to demonstrate complement involvement in mouse disease models and catalysed enthusiasm for anti-complement drug development, culminating in the anti-human C5 monoclonal antibody eculizumab, the most successful anti-complement drug to date, already in clinical use for several rare diseases. Despite its key role in providing proof-of-concept for C5 blockade, the mechanism of BB5.1 inhibition remains poorly understood. Here, we characterized BB5.1 cross-species inhibition, C5 binding affinity and chain specificity. BB5.1 efficiently inhibited C5 in mouse serum but not in human or other rodent sera; it prevented C5 cleavage and C5a generation. BB5.1 bound the C5 α-chain with high affinity and slow off-rate. BB5.1 complementarity-determining regions were obtained and docking algorithms were used to predict the likely binding interface on mouse C5.
Collapse
Affiliation(s)
- Wioleta M. Zelek
- Systems Immunity University Research InstituteSchool of MedicineCardiff UniversityCardiffUK
| | | | - Andrea Brancale
- School of Pharmacy and Pharmaceutical SciencesCardiff UniversityCardiffUK
| | | | - Bryan Paul Morgan
- Systems Immunity University Research InstituteSchool of MedicineCardiff UniversityCardiffUK
- Dementia Research InstituteCardiff UniversityCardiffUK
| |
Collapse
|
7
|
Mohebnasab M, Eriksson O, Persson B, Sandholm K, Mohlin C, Huber-Lang M, Keating BJ, Ekdahl KN, Nilsson B. Current and Future Approaches for Monitoring Responses to Anti-complement Therapeutics. Front Immunol 2019; 10:2539. [PMID: 31787968 PMCID: PMC6856077 DOI: 10.3389/fimmu.2019.02539] [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: 04/28/2019] [Accepted: 10/14/2019] [Indexed: 01/13/2023] Open
Abstract
Aberrations in complement system functions have been identified as either direct or indirect pathophysiological mechanisms in many diseases and pathological conditions, such as infections, autoimmune diseases, inflammation, malignancies, and allogeneic transplantation. Currently available techniques to study complement include quantification of (a) individual complement components, (b) complement activation products, and (c) molecular mechanisms/function. An emerging area of major interest in translational studies aims to study and monitor patients on complement regulatory drugs for efficacy as well as adverse events. This area is progressing rapidly with several anti-complement therapeutics under development, in clinical trials, or already in clinical use. In this review, we summarized the appropriate indications, techniques, and interpretations of basic complement analyses, exemplified by a number of clinical disorders.
Collapse
Affiliation(s)
- Maedeh Mohebnasab
- Division of Transplantation, Department of Surgery, University of Pennsylvania, Philadelphia, PA, United States
| | - Oskar Eriksson
- Rudbeck Laboratory C5:3, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Barbro Persson
- Rudbeck Laboratory C5:3, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kerstin Sandholm
- Centre of Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden
| | - Camilla Mohlin
- Centre of Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden
| | - Markus Huber-Lang
- Institute for Clinical and Experimental Trauma Immunology, University Hospital of Ulm, Ulm, Germany
| | - Brendan J Keating
- Division of Transplantation, Department of Surgery, University of Pennsylvania, Philadelphia, PA, United States
| | - Kristina N Ekdahl
- Rudbeck Laboratory C5:3, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.,Centre of Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden
| | - Bo Nilsson
- Rudbeck Laboratory C5:3, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
8
|
Danquah BD, Röwer C, Opuni KM, El-Kased R, Frommholz D, Illges H, Koy C, Glocker MO. Intact Transition Epitope Mapping - Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE). Mol Cell Proteomics 2019; 18:1543-1555. [PMID: 31147491 PMCID: PMC6683010 DOI: 10.1074/mcp.ra119.001429] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Epitope mapping, which is the identification of antigenic determinants, is essential for the design of novel antibody-based therapeutics and diagnostic tools. ITEM-THREE is a mass spectrometry-based epitope mapping method that can identify epitopes on antigens upon generating an immune complex in electrospray-compatible solutions by adding an antibody of interest to a mixture of peptides from which at least one holds the antibody's epitope. This mixture is nano-electrosprayed without purification. Identification of the epitope peptide is performed within a mass spectrometer that provides an ion mobility cell sandwiched in-between two collision cells and where this ion manipulation setup is flanked by a quadrupole mass analyzer on one side and a time-of-flight mass analyzer on the other side. In a stepwise fashion, immune-complex ions are separated from unbound peptide ions and dissociated to release epitope peptide ions. Immune complex-released peptide ions are separated from antibody ions and fragmented by collision induced dissociation. Epitope-containing peptide fragment ions are recorded, and mass lists are submitted to unsupervised data base search thereby retrieving both, the amino acid sequence of the epitope peptide and the originating antigen. ITEM-THREE was developed with antiTRIM21 and antiRA33 antibodies for which the epitopes were known, subjecting them to mixtures of synthetic peptides of which one contained the respective epitope. ITEM-THREE was then successfully tested with an enzymatic digest of His-tagged recombinant human β-actin and an antiHis-tag antibody, as well as with an enzymatic digest of recombinant human TNFα and an antiTNFα antibody whose epitope was previously unknown.
Collapse
Affiliation(s)
- Bright D Danquah
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Claudia Röwer
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | - Reham El-Kased
- ¶Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - David Frommholz
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany
| | - Harald Illges
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany;; **University of Applied Sciences Bonn-Rhein-Sieg, Institute for Functional Gene Analytics, Rheinbach, Germany
| | - Cornelia Koy
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Michael O Glocker
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany.
| |
Collapse
|
9
|
Hu FJ, Volk AL, Persson H, Säll A, Borrebaeck C, Uhlen M, Rockberg J. Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders. N Biotechnol 2018; 45:80-88. [DOI: 10.1016/j.nbt.2017.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/28/2017] [Accepted: 07/31/2017] [Indexed: 10/19/2022]
|
10
|
Macpherson A, Liu X, Dedi N, Kennedy J, Carrington B, Durrant O, Heywood S, van den Elsen J, Lawson ADG. The rational design of affinity-attenuated OmCI for the purification of complement C5. J Biol Chem 2018; 293:14112-14121. [PMID: 30030376 PMCID: PMC6130949 DOI: 10.1074/jbc.ra118.004043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/03/2018] [Indexed: 12/04/2022] Open
Abstract
Complement component C5 is the target of the mAb eculizumab and is the focus of a sustained drug discovery effort to prevent complement-induced inflammation in a range of autoimmune diseases. The immune evasion protein OmCI binds to and potently inactivates C5; this tight-binding interaction can be exploited to affinity-purify C5 protein from serum, offering a vastly simplified protocol compared with existing methods. However, breaking the high-affinity interaction requires conditions that risk denaturing or activating C5. We performed structure-guided in silico mutagenesis to identify prospective OmCI residues that contribute significantly to the binding affinity. We tested our predictions in vitro, using site-directed mutagenesis, and characterized mutants using a range of biophysical techniques, as well as functional assays. Our biophysical analyses suggest that the C5–OmCI interaction is complex with potential for multiple binding modes. We present single mutations that lower the affinity of OmCI for C5 and combinations of mutations that significantly decrease or entirely abrogate formation of the complex. The affinity-attenuated forms of OmCI are suitable for affinity purification and allow elution under mild conditions that are nondenaturing or activating to C5. We present the rational design, biophysical characterization, and experimental validation of affinity-reduced forms of OmCI as tool reagents to enable the affinity purification of C5.
Collapse
Affiliation(s)
- Alex Macpherson
- From the UCB-Celltech, Slough SL1 3WE, United Kingdom and .,the Department of Biology and Biochemistry, University of Bath, Bath BA2 7AX, United Kingdom
| | - Xiaofeng Liu
- From the UCB-Celltech, Slough SL1 3WE, United Kingdom and
| | - Neesha Dedi
- From the UCB-Celltech, Slough SL1 3WE, United Kingdom and
| | | | | | - Oliver Durrant
- From the UCB-Celltech, Slough SL1 3WE, United Kingdom and
| | - Sam Heywood
- From the UCB-Celltech, Slough SL1 3WE, United Kingdom and
| | - Jean van den Elsen
- the Department of Biology and Biochemistry, University of Bath, Bath BA2 7AX, United Kingdom
| | | |
Collapse
|
11
|
Jo DH, Kim JH, Yang W, Kim H, Chang S, Kim D, Chang M, Lee K, Chung J, Kim JH. Anti-complement component 5 antibody targeting MG4 domain inhibits choroidal neovascularization. Oncotarget 2018; 8:45506-45516. [PMID: 28477014 PMCID: PMC5542204 DOI: 10.18632/oncotarget.17221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/15/2017] [Indexed: 12/27/2022] Open
Abstract
Age-related macular degeneration (AMD) is one of the main causes of visual impairment in adults. Visual deterioration is more prominent in neovascular AMD with choroidal neovascularization (CNV). Clinical and postmortem studies suggested that complement system activation might induce CNV. In this study, we demonstrated that an anti-mouse complement component 5 (C5) antibody targeting MG4 domain of β chain effectively inhibited CNV which was induced by laser photocoagulation in mice. The targeted epitope of this anti-C5 antibody was different from that of currently utilized anti-C5 antibody (eculizumab) in the MG7 domain in which a single nucleotide polymorphism (R885H/C) results in poor response to eculizumab. Even with targeting MG4 domain, this anti-C5 antibody reduced production of C5a, monocyte chemoattractant protein-1 and vascular endothelial growth factor to prevent infiltration of F4/80-positive cells into CNV lesions and formation of CNV. Furthermore, anti-C5 antibody targeting MG4 domain induced no definite toxicity in normal retina. These results demonstrated that anti-C5 antibody targeting MG4 domain inhibited CNV in neovascular AMD.
Collapse
Affiliation(s)
- Dong Hyun Jo
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Biomedical Sciences and Protein Metabolism, Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jin Hyoung Kim
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Wonjun Yang
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyori Kim
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Shinjae Chang
- Biotechnology Research Institute, Celltrion, Inc., Incheon, Republic of Korea
| | - Dongjo Kim
- Biotechnology Research Institute, Celltrion, Inc., Incheon, Republic of Korea
| | - Minseok Chang
- Biotechnology Research Institute, Celltrion, Inc., Incheon, Republic of Korea
| | - Kihwang Lee
- Department of Ophthalmology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong Hun Kim
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Biomedical Sciences and Protein Metabolism, Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
12
|
Abstract
Antibodies are protein molecules used routinely for therapeutic, diagnostic, and research purposes due to their exquisite ability to selectively recognize and bind a given antigen. The particular area of the antigen recognized by the antibody is called the epitope, and for proteinaceous antigens the epitope can be of complex nature. Information about the binding epitope of an antibody can provide important mechanistic insights and indicate for what applications an antibody might be useful. Therefore, a variety of epitope mapping techniques have been developed to localize such regions. Although the real picture is even more complex, epitopes in protein antigens are broadly grouped into linear or discontinuous epitopes depending on the positioning of the epitope residues in the antigen sequence and the requirement of structure. Specialized methods for mapping of the two different classes of epitopes, using high-throughput or high-resolution methods, have been developed. While different in their detail, all of the experimental methods rely on assessing the binding of the antibody to the antigen or a set of antigen mimics. Early approaches utilizing sets of truncated proteins, small numbers of synthesized peptides, and structural analyses of antibody-antigen complexes have been significantly refined. Current state-of-the-art methods involve combinations of mutational scanning, protein display, and high-throughput screening in conjunction with bioinformatic analyses of large datasets.
Collapse
Affiliation(s)
- Johan Nilvebrant
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health, Protein Engineering, Stockholm, Sweden.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
| | - Johan Rockberg
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health, Protein Technology, Stockholm, Sweden.
| |
Collapse
|
13
|
Löfblom J, Rosenstein R, Nguyen MT, Ståhl S, Götz F. Staphylococcus carnosus: from starter culture to protein engineering platform. Appl Microbiol Biotechnol 2017; 101:8293-8307. [PMID: 28971248 PMCID: PMC5694512 DOI: 10.1007/s00253-017-8528-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 02/04/2023]
Abstract
Since the 1950s, Staphylococcus carnosus is used as a starter culture for sausage fermentation where it contributes to food safety, flavor, and a controlled fermentation process. The long experience with S. carnosus has shown that it is a harmless and "food grade" species. This was confirmed by the genome sequence of S. carnosus TM300 that lacks genes involved in pathogenicity. Since the development of a cloning system in TM300, numerous genes have been cloned, expressed, and characterized and in particular, virulence genes that could be functionally validated in this non-pathogenic strain. A secretion system was developed for production and secretion of industrially important proteins and later modified to also enable display of heterologous proteins on the surface. The display system has been employed for various purposes, such as development of live bacterial delivery vehicles as well as microbial biocatalysts or bioadsorbents for potential environmental or biosensor applications. Recently, this surface display system has been utilized for display of peptide and protein libraries for profiling of protease substrates and for generation of various affinity proteins, e.g., Affibody molecules and scFv antibodies. In addition, by display of fragmented antigen-encoding genes, the surface expression system has been successfully used for epitope mapping of antibodies. Reviews on specific applications of S. carnosus have been published earlier, but here we provide a more extensive overview, covering a broad range of areas from food fermentation to sophisticated methods for protein-based drug discovery, which are all based on S. carnosus.
Collapse
Affiliation(s)
- John Löfblom
- Division of Protein Technology, School of Biotechnology, KTH-Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, 106 91, Stockholm, Sweden
| | - Ralf Rosenstein
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Minh-Thu Nguyen
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Stefan Ståhl
- Division of Protein Technology, School of Biotechnology, KTH-Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, 106 91, Stockholm, Sweden.
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
| |
Collapse
|