1
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Koçer İ, Çelik E. In silico analysis of the different variable domain oriented single-chain variable fragment antibody-antigen complexes. J Biomol Struct Dyn 2024; 42:4699-4709. [PMID: 37288797 DOI: 10.1080/07391102.2023.2222191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023]
Abstract
Single-chain variable fragment (scFv) antibodies hold great potential as diagnostic tools and therapeutic agents, especially for tumor cells. Since these applications require their production with improved properties, the design strategy of scFvs is crucial for their active, soluble, and high yield expression with high affinity towards their antigens. The order of VL and VH domains is one of the important parameters that affect the expression and binding affinity properties of scFvs. In addition, the optimum order of VL and VH domains could change for each scFv. In the present study, we used computer simulation tools to evaluate the effect of variable domain orientation on structure, stability, interacting residues of scFvs, and binding free energies of scFv-antigen complexes. We selected anti-HER2 scFv, which is specific for human epidermal growth receptor 2 (HER2) overexpressed in breast cancer, and anti-IL-1β scFv against IL-1β which is an important inflammatory biomarker, as model scFvs. Molecular dynamics simulations of the scFv-antigen complexes for 100 ns resulted in stability and compactness for both scFv constructs. Interaction and binding free energies calculated by the Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) approach suggested that the relative binding energies of anti-HER2 scFv-VLVH and anti-HER2 scFv-VHVL constructs had similar binding affinity towards HER2, while a relatively more negative binding free energy obtained between anti-IL-1β scFv-VHVL and IL-1β pointed to a higher binding affinity. The in silico approach and the results obtained here could be applied as a guide for future experimental interaction studies for highly specific scFvs used as biotechnological tools.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- İlkay Koçer
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey
- Institute of Science, Hacettepe University, Ankara, Turkey
| | - Eda Çelik
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey
- Institute of Science, Division of Bioengineering, Hacettepe University, Ankara, Turkey
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2
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Liu Z, Kim D, Kang S, Jung JU. A Detailed Protocol for Constructing a Human Single-Chain Variable Fragment (scFv) Library and Downstream Screening via Phage Display. Methods Protoc 2024; 7:13. [PMID: 38392687 PMCID: PMC10893473 DOI: 10.3390/mps7010013] [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: 12/04/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
The development of monoclonal antibodies (mAbs) represents a significant milestone in both basic research and clinical applications due to their target specificity and versatility in therapeutic and diagnostic applications. The innovative strategy of mAb screening, utilizing phage display, facilitates the in vitro screening of antibodies with high affinity to target antigens. The single-chain variable fragment (scFv) is a subset of mAb derivatives, known for its high binding affinity and smaller size-just one-third of that of human IgG. This report outlines a detailed and comprehensive procedure for constructing a scFv phagemid library derived from human patients, followed by screening via phage display affinity selection. The protocol utilizes 348 primer combinations spanning the entire human antibody repertoire to minimize sequence bias and maintain library diversity during polymerase chain reaction (PCR) for scFv generation, resulting in a library size greater than 1 × 108. Furthermore, we describe a high-throughput phage display screening protocol using enzyme-linked immunosorbent assay (ELISA) to evaluate more than 1200 scFv candidates. The generation of a highly diverse scFv library, coupled with the implementation of a phage display screening methodology, is expected to provide a valuable resource for researchers in pursuit of scFvs with high affinity for target antigens, thus advancing both research and clinical endeavors.
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Affiliation(s)
- Ziyi Liu
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dokyun Kim
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Seokmin Kang
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jae U. Jung
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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3
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Rodríguez-Nava C, Ortuño-Pineda C, Illades-Aguiar B, Flores-Alfaro E, Leyva-Vázquez MA, Parra-Rojas I, Del Moral-Hernández O, Vences-Velázquez A, Cortés-Sarabia K, Alarcón-Romero LDC. Mechanisms of Action and Limitations of Monoclonal Antibodies and Single Chain Fragment Variable (scFv) in the Treatment of Cancer. Biomedicines 2023; 11:1610. [PMID: 37371712 DOI: 10.3390/biomedicines11061610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Monoclonal antibodies are among the most effective tools for detecting tumor-associated antigens. The U.S. Food and Drug Administration (FDA) has approved more than 36 therapeutic antibodies for developing novel alternative therapies that have significant success rates in fighting cancer. However, some functional limitations have been described, such as their access to solid tumors and low interaction with the immune system. Single-chain variable fragments (scFv) are versatile and easy to produce, and being an attractive tool for use in immunotherapy models. The small size of scFv can be advantageous for treatment due to its short half-life and other characteristics related to the structural and functional aspects of the antibodies. Therefore, the main objective of this review was to describe the current situation regarding the mechanisms of action, applications, and limitations of monoclonal antibodies and scFv in the treatment of cancer.
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Affiliation(s)
- Cynthia Rodríguez-Nava
- Laboratorio de Investigación en Citopatología e Histoquímica, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Mexico
- Laboratorio de Investigación en Inmunobiología y Diagnóstico Molecular, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Mexico
| | - Carlos Ortuño-Pineda
- Laboratorio de Proteínas y Ácidos Nucleicos, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Mexico
| | - Berenice Illades-Aguiar
- Laboratorio de Investigación en Biomedicina Molecular, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Mexico
| | - Eugenia Flores-Alfaro
- Laboratorio de Investigación en Epidemiología Clínica y Molecular, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Mexico
| | - Marco Antonio Leyva-Vázquez
- Laboratorio de Investigación en Biomedicina Molecular, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Mexico
| | - Isela Parra-Rojas
- Laboratorio de Investigación en Obesidad y Diabetes, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Mexico
| | | | - Amalia Vences-Velázquez
- Laboratorio de Investigación en Inmunobiología y Diagnóstico Molecular, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Mexico
| | - Karen Cortés-Sarabia
- Laboratorio de Investigación en Inmunobiología y Diagnóstico Molecular, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Mexico
| | - Luz Del Carmen Alarcón-Romero
- Laboratorio de Investigación en Citopatología e Histoquímica, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Mexico
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Tohari TR, Anshori I, Baroroh U, Nugroho AE, Gumilar G, Kusumawardani S, Syahruni S, Yuliarto B, Arnafia W, Faizal I, Hartati YW, Subroto T, Yusuf M. Development of a Single-Chain Variable Fragment of CR3022 for a Plasmonic-Based Biosensor Targeting the SARS-CoV-2 Spike Protein. BIOSENSORS 2022; 12:1133. [PMID: 36551102 PMCID: PMC9776105 DOI: 10.3390/bios12121133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Two years after SARS-CoV-2 caused the first case of COVID-19, we are now in the "new normal" period, where people's activity has bounced back, followed by the easing of travel policy restrictions. The lesson learned is that the wide availability of accurate and rapid testing procedures is crucial to overcome possible outbreaks in the future. Therefore, many laboratories worldwide have been racing to develop a new point-of-care diagnostic test. To aid continuous innovation, we developed a plasmonic-based biosensor designed explicitly for portable Surface Plasmon Resonance (SPR). In this study, we designed a single chain variable fragment (scFv) from the CR3022 antibody with a particular linker that inserted a cysteine residue at the second position. It caused the linker to have a strong affinity to the gold surface through thiol-coupling and possibly become a ready-to-use bioreceptor toward a portable SPR gold chip without purification steps. The theoretical affinity of this scFv on spike protein was -64.7 kcal/mol, computed using the Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method from the 100 ns molecular dynamics trajectory. Furthermore, the scFv was produced in Escherichia coli BL21 (DE3) as a soluble protein. The binding activity toward Spike Receptor Binding Domain (RBD) SARS-CoV-2 was confirmed with a spot-test, and the experimental binding free energy of -10.82 kcal/mol was determined using portable SPR spectroscopy. We hope this study will be useful in designing specific and low-cost bioreceptors, particularly early in an outbreak when the information on antibody capture is still limited.
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Affiliation(s)
- Taufik Ramdani Tohari
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
| | - Isa Anshori
- Lab-on-Chip Group, Biomedical Engineering Department, Institute of Technology, Bandung 40132, Indonesia
- Research Center for Nanoscience and Nanotechnology (RCNN), Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Umi Baroroh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Biotechnology, Indonesian School of Pharmacy, Bandung 40266, Indonesia
| | - Antonius Eko Nugroho
- Lab-on-Chip Group, Biomedical Engineering Department, Institute of Technology, Bandung 40132, Indonesia
| | - Gilang Gumilar
- Research Center for Nanoscience and Nanotechnology (RCNN), Institut Teknologi Bandung, Bandung 40132, Indonesia
- Advanced Functional Material Research Group, Faculty of Industrial Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
- Research and Development Division, PT. Biostark Analitika Inovasi, Bandung 40375, Indonesia
| | - Shinta Kusumawardani
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
| | - Sari Syahruni
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
| | - Brian Yuliarto
- Research Center for Nanoscience and Nanotechnology (RCNN), Institut Teknologi Bandung, Bandung 40132, Indonesia
- Advanced Functional Material Research Group, Faculty of Industrial Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Wyanda Arnafia
- Research and Development Division, PT. Tekad Mandiri Citra, Bandung 40292, Indonesia
| | - Irvan Faizal
- Centre for Vaccine and Drug Research, National Research and Innovation Agency Republic of Indonesia, Kawasan Puspiptek Serpong, Tangerang Selatan 15314, Indonesia
- Department of Biotechnology, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, BSD Campus, Tangerang 15345, Indonesia
| | - Yeni Wahyuni Hartati
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Toto Subroto
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Muhammad Yusuf
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
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Juengsanguanpornsuk W, Kitisripanya T, Boonsnongcheep P, Yusakul G, Srisongkram T, Sakamoto S, Putalun W. Improvement in the binding specificity of anti-isomiroestrol antibodies by expression as fragments under oxidizing conditions inside the SHuffle T7 E. coli cytoplasm. Biosci Biotechnol Biochem 2022; 86:1368-1377. [PMID: 35876636 DOI: 10.1093/bbb/zbac126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/18/2022] [Indexed: 11/14/2022]
Abstract
Sensitive and specific analysis of isomiroestrol (Iso) is required for the quality control of Pueraria candollei, an herb used to treat menopausal disorders. The anti-isomiroestrol monoclonal antibody (Iso-mAb) exhibits cross-reactivity with miroestrol and deoxymiroestrol, which impacts the analytical results. Here, the active and soluble forms of the single-chain variable fragment (Iso-scFv) and fragment antigen-binding (Iso-Fab) against Iso were expressed using Escherichia coli SHuffle® T7 to alter the binding specificity. The Iso-scFv format exhibited a higher binding activity than the Iso-Fab format. The reactivity of Iso-scFv towards Iso was comparable to that of the parental Iso-mAb. Remarkably, the binding specificity of the scFv structure was improved and cross-reactivity against analogs was reduced from 13.3-21.0% to less than 1%. The structure of recombinant antibodies affects the binding characteristics. Therefore, the immunoassays should improve specificity; these findings can be useful in agricultural processes and for quality monitoring of P. candollei-related materials.
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Affiliation(s)
| | - Tharita Kitisripanya
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | | | - Gorawit Yusakul
- School of Pharmacy, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Tarapong Srisongkram
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Seiichi Sakamoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Waraporn Putalun
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
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6
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Structure-specific amyloid precipitation in biofluids. Nat Chem 2022; 14:1045-1053. [PMID: 35798951 DOI: 10.1038/s41557-022-00976-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/16/2022] [Indexed: 11/08/2022]
Abstract
The composition of soluble toxic protein aggregates formed in vivo is currently unknown in neurodegenerative diseases, due to their ultra-low concentration in human biofluids and their high degree of heterogeneity. Here we report a method to capture amyloid-containing aggregates in human biofluids in an unbiased way, a process we name amyloid precipitation. We use a structure-specific chemical dimer, a Y-shaped, bio-inspired small molecule with two capture groups, for amyloid precipitation to increase affinity. Our capture molecule for amyloid precipitation (CAP-1) consists of a derivative of Pittsburgh Compound B (dimer) to target the cross β-sheets of amyloids and a biotin moiety for surface immobilization. By coupling CAP-1 to magnetic beads, we demonstrate that we can target the amyloid structure of all protein aggregates present in human cerebrospinal fluid, isolate them for analysis and then characterize them using single-molecule fluorescence imaging and mass spectrometry. Amyloid precipitation enables unbiased determination of the molecular composition and structural features of the in vivo aggregates formed in neurodegenerative diseases.
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7
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Zhang Y, Song Y, Ren H, Zeng Q, Yuan Y, Xia L, Wei Z. Preparation of a Single-Chain Antibody against Nucleocapsid Protein of Porcine Deltacoronavirus by Phage Display Technology. Viruses 2022; 14:v14040772. [PMID: 35458502 PMCID: PMC9030028 DOI: 10.3390/v14040772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 11/30/2022] Open
Abstract
Porcine deltacoronavirus (PDCoV) mainly causes severe diarrhea and intestinal pathological damage in piglets and poses a serious threat to pig farms. Currently, no effective reagents or vaccines are available to control PDCoV infection. Single-chain fragment variable (scFv) antibodies can effectively inhibit virus infection and may be a potential therapeutic reagent for PDCoV treatment. In this study, a porcine phage display antibody library from the peripheral blood lymphocytes of piglets infected with PDCoV was constructed and used to select PDCoV-specific scFv. The library was screened with four rounds of biopanning using the PDCoV N protein, and the colony with the highest affinity to the PDCoV N protein was obtained (namely, N53). Then, the N53-scFv gene fragment was cloned into plasmid pFUSE-hIgG-Fc2 and expressed in HEK-293T cells. The scFv-Fc antibody N53 (namely, scFv N53) was purified using Protein A-sepharose. The reactive activity of the purified antibody with the PDCoV N protein was confirmed by indirect enzyme-linked immunosorbent assay (ELISA), western blot and indirect immunofluorescence assay (IFA). Finally, the antigenic epitopes that the scFv N53 recognized were identified by a series of truncated PDCoV N proteins. The amino acid residues 82GELPPNDTPATTRVT96 of the PDCoV N protein were verified as the minimal epitope that can be recognized by the scFv-Fc antibody N53. In addition, the interaction between the scFv-Fc antibody N53 and the PDCoV N protein was further analyzed by molecule docking. In conclusion, our research provides some references for the treatment and prevention of PDCoV.
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Affiliation(s)
- Yixuan Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.S.); (H.R.); (Q.Z.); (Y.Y.)
| | - Yue Song
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.S.); (H.R.); (Q.Z.); (Y.Y.)
- Molecule Biology Laboratory, Zhengzhou Normal University, Zhengzhou 450044, China
| | - Haojie Ren
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.S.); (H.R.); (Q.Z.); (Y.Y.)
| | - Quan Zeng
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.S.); (H.R.); (Q.Z.); (Y.Y.)
| | - Yixin Yuan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.S.); (H.R.); (Q.Z.); (Y.Y.)
| | - Lu Xia
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.S.); (H.R.); (Q.Z.); (Y.Y.)
- Correspondence: (L.X.); (Z.W.)
| | - Zhanyong Wei
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.S.); (H.R.); (Q.Z.); (Y.Y.)
- Key Laboratory for Animal-Derived Food Safety of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
- Correspondence: (L.X.); (Z.W.)
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Frota NF, Rebouças ADS, Fuzo CA, Lourenzoni MR. Alemtuzumab scFv fragments and CD52 interaction study through molecular dynamics simulation and binding free energy. J Mol Graph Model 2021; 107:107949. [PMID: 34089985 DOI: 10.1016/j.jmgm.2021.107949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/14/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022]
Abstract
Specific antibody-antigen recognition is crucial for the immune response. Knowledge of molecular interaction details in the recognition process is fundamental for the rational design of antibodies with improved properties. We used state-of-the-art computer simulation tools to deepen the molecular-level understanding of the interactions between the monoclonal antibody Alemtuzumab and its antigen, the CD52 membrane receptor, of great biotechnological importance. Thus, we seek such responses by modeling the interaction of native and known mutants single-chain fragment variable (scFv) of Alemtuzumab with CD52 inserted in a membrane model to mimic the physiological conditions of antibody-antigen binding. Extensive molecular dynamics simulations of the interaction between Alemtuzumab's scFvs and CD52 promoted greater understanding of the structural and energetic bases, which can be translated into the biological action and affinity of this antibody. The quantification of the scFv-CD52 complexes binding free energy (ΔGbind) by Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) correlated with the experimental binding energies described before. Thus, the mutants D53K, K54D, and K56D resulted in less attractive ΔGbind, therefore lower scFv-CD52 affinity than the native scFv. On the other hand, K56D and K54D/K56D showed lower binding to CD52. These Results revealed that the model system mimicking an environment close to the physiological with the presence of the CD52 in a membrane model proved essential for this system's study. The present study allowed to unveil the molecular mechanisms involved in antigen-antibody interaction and the effects of mutations. Thus, these mechanisms may be explored in the Alemtuzumab variants' rational design with enhanced properties.
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Affiliation(s)
- Natália Fernandes Frota
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, 61760000, Eusébio, Ceara, Brazil; Federal University of Ceara (UFC), Campus do Pici (Bloco 873), 60440-970, Fortaleza, Ceara Brazil
| | - Alison de Sousa Rebouças
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, 61760000, Eusébio, Ceara, Brazil; Federal University of Ceara (UFC), Campus do Pici (Bloco 873), 60440-970, Fortaleza, Ceara Brazil
| | - Carlos Alessandro Fuzo
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marcos Roberto Lourenzoni
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, 61760000, Eusébio, Ceara, Brazil.
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9
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Lim S, Kim DS, Ko K. Expression of a Large Single-Chain 13F6 Antibody with Binding Activity against Ebola Virus-Like Particles in a Plant System. Int J Mol Sci 2020; 21:E7007. [PMID: 32977599 PMCID: PMC7582593 DOI: 10.3390/ijms21197007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/17/2020] [Accepted: 09/20/2020] [Indexed: 11/16/2022] Open
Abstract
Pathogenic animal and human viruses present a growing and persistent threat to humans worldwide. Ebola virus (EBOV) causes zoonosis in humans. Here, two structurally different anti-Ebola 13F6 antibodies, recognizing the heavily glycosylated mucin-like domain (MLD) of the glycoprotein (GP), were expressed in transgenic Nicotiana tabacum plants and designed as inexpensive and effective diagnostic antibodies against Ebola virus disease (EVD). The first was anti-EBOV 13F6 full size antibody with heavy chain (HC) and light chain (LC) (monoclonal antibody, mAb 13F6-FULL), while the second was a large single-chain (LSC) antibody (mAb 13F6-LSC). mAb 13F6-LSC was constructed by linking the 13F6 LC variable region (VL) with the HC of mAb 13F6-FULL using a peptide linker and extended to the C-terminus using the endoplasmic reticulum (ER) retention motif KDEL. Agrobacterium-mediated plant transformation was employed to express the antibodies in N. tabacum. PCR, RT-PCR, and immunoblot analyses confirmed the gene insertion, transcription, and protein expression of these antibodies, respectively. The antibodies tagged with the KDEL motif displayed high-mannose type N-glycan structures and efficient binding to EBOV-like particles (VLPs). Thus, various forms of anti-EBOV plant-derived mAbs 13F6-FULL and LSC with efficient binding affinity to EBOV VLP can be produced in the plant system.
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Affiliation(s)
- Sohee Lim
- Department of Medicine, College of Medicine, Chung-Ang University, Seoul 06974, Korea;
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Korea;
| | - Kisung Ko
- Department of Medicine, College of Medicine, Chung-Ang University, Seoul 06974, Korea;
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10
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Sandomenico A, Sivaccumar JP, Ruvo M. Evolution of Escherichia coli Expression System in Producing Antibody Recombinant Fragments. Int J Mol Sci 2020; 21:ijms21176324. [PMID: 32878291 PMCID: PMC7504322 DOI: 10.3390/ijms21176324] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/12/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
Antibodies and antibody-derived molecules are continuously developed as both therapeutic agents and key reagents for advanced diagnostic investigations. Their application in these fields has indeed greatly expanded the demand of these molecules and the need for their production in high yield and purity. While full-length antibodies require mammalian expression systems due to the occurrence of functionally and structurally important glycosylations, most antibody fragments and antibody-like molecules are non-glycosylated and can be more conveniently prepared in E. coli-based expression platforms. We propose here an updated survey of the most effective and appropriate methods of preparation of antibody fragments that exploit E. coli as an expression background and review the pros and cons of the different platforms available today. Around 250 references accompany and complete the review together with some lists of the most important new antibody-like molecules that are on the market or are being developed as new biotherapeutics or diagnostic agents.
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11
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Vermeulen JG, Burt F, van Heerden E, du Preez LL, Meiring M. Characterization of the inhibition mechanism of a tissuefactor inhibiting single-chain variable fragment: a combined computational approach. J Mol Model 2020; 26:87. [PMID: 32219568 DOI: 10.1007/s00894-020-4350-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
Abstract
The interaction of a single-chain variable fragment (scFv) directed against human tissue factor (TF) was predicted using an in silico approach with the aim to establish a most likely mechanism of inhibition. The structure of the TF inhibiting scFv (TFI-scFv) was predicted using homology modeling, and complementarity-determining regions (CDRs) were identified. The CDR was utilized to direct molecular docking between the homology model of TFI-scFv and the crystal structure of the extracellular domains of human tissue factor. The rigid-body docking model was refined by means of molecular dynamic (MD) simulations, and the most prevalent cluster was identified. MD simulations predicted improved interaction between TFI-scFv and TF and propose the formation of stable complex for duration of the 600-ns simulation. Analysis of the refined docking model suggests that the interactions between TFI-scFv would interfere with the allosterical activation of coagulation factor VII (FVII) by TF. This interaction would prevent the formation of the active TF:VIIa complex and in so doing inhibit the initiation phase of blood coagulation as observers during in vitro testing.
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Affiliation(s)
- Jan-G Vermeulen
- Department of Microbial, Biochemical and Food Biotechnology, Faculty of Agricultural Sciences, University of the Free State, Bloemfontein, South Africa. .,Department of Haematology and Cell Biology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.
| | - Felicity Burt
- Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.,National Health Laboratory Service, Universitas, Bloemfontein, South Africa
| | - Esta van Heerden
- Department of Microbial, Biochemical and Food Biotechnology, Faculty of Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Louis Lategan du Preez
- Department of Microbial, Biochemical and Food Biotechnology, Faculty of Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Muriel Meiring
- Department of Haematology and Cell Biology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.,National Health Laboratory Service, Universitas, Bloemfontein, South Africa
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12
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Mei M, Li J, Wang S, Lee KB, Iverson BL, Zhang G, Ge X, Yi L. Prompting Fab Yeast Surface Display Efficiency by ER Retention and Molecular Chaperon Co-expression. Front Bioeng Biotechnol 2019; 7:362. [PMID: 32039168 PMCID: PMC6988814 DOI: 10.3389/fbioe.2019.00362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/12/2019] [Indexed: 12/15/2022] Open
Abstract
For antibody discovery and engineering, yeast surface display (YSD) of antigen-binding fragments (Fabs) and coupled fluorescence activated cell sorting (FACS) provide intact paratopic conformations and quantitative analysis at the monoclonal level, and thus holding great promises for numerous applications. Using anti-TNFα mAbs Infliximab, Adalimumab, and its variants as model Fabs, this study systematically characterized complementary approaches for the optimization of Fab YSD. Results suggested that by using divergent promoter GAL1-GAL10 and endoplasmic reticulum (ER) signal peptides for co-expression of light chain and heavy chain-Aga2 fusion, assembled Fabs were functionally displayed on yeast cell surface with sigmoidal binding responses toward TNFα. Co-expression of a Hsp70 family molecular chaperone Kar2p and/or protein-disulfide isomerase (Pdi1p) significantly improved efficiency of functional display (defined as the ratio of cells displaying functional Fab over cells displaying assembled Fab). Moreover, fusing ER retention sequences (ERSs) with light chain also enhanced Fab display quality at the expense of display quantity, and the degree of improvements was correlated with the strength of ERSs and was more significant for Infliximab than Adalimumab. The feasibility of affinity maturation was further demonstrated by isolating a high affinity Fab clone from 1:103 or 1:105 spiked libraries.
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Affiliation(s)
- Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Junhong Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Shengchen Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Ki Baek Lee
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, United States
| | - Brent L Iverson
- Department of Chemistry, University of Texas, Austin, TX, United States
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, United States
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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13
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Tadokoro T, Jahan ML, Ito Y, Tahara M, Chen S, Imai A, Sugimura N, Yoshida K, Saito M, Ose T, Hashiguchi T, Takeda M, Fukuhara H, Maenaka K. Biophysical characterization and single-chain Fv construction of a neutralizing antibody to measles virus. FEBS J 2019; 287:145-159. [PMID: 31287622 DOI: 10.1111/febs.14991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 05/01/2019] [Accepted: 07/06/2019] [Indexed: 12/22/2022]
Abstract
The measles virus (MV) is a major cause of childhood morbidity and mortality worldwide. We previously established a mouse monoclonal antibody, 2F4, which shows high neutralizing titers against eight different genotypes of MV. However, the molecular basis for the neutralizing activity of the 2F4 antibody remains incompletely understood. Here, we have evaluated the binding characteristics of a Fab fragment of the 2F4 antibody. Using the MV infectious assay, we demonstrated that 2F4 Fab inhibits viral entry via either of two cellular receptors, SLAM and Nectin4. Surface plasmon resonance (SPR) analysis of recombinant proteins indicated that 2F4 Fab interacts with MV hemagglutinin (MV-H) with a KD value at the nm level. Furthermore, we designed a single-chain Fv fragment of 2F4 antibody as another potential biopharmaceutical to target measles. The stable 2F4 scFv was successfully prepared by the refolding method and shown to interact with MV-H at the μm level. Like 2F4 Fab, scFv inhibited receptor binding and viral entry. This indicates that 2F4 mAb uses the receptor-binding site and/or a neighboring region as an epitope with high affinity. These results provide insight into the neutralizing activity and potential therapeutic use of antibody fragments for MV infection.
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Affiliation(s)
- Takashi Tadokoro
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Mst Lubna Jahan
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Yuri Ito
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Maino Tahara
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Surui Chen
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Atsutoshi Imai
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Natsumi Sugimura
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Koki Yoshida
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Mizuki Saito
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Toyoyuki Ose
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Takao Hashiguchi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideo Fukuhara
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
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14
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Yamashita T. Toward rational antibody design: recent advancements in molecular dynamics simulations. Int Immunol 2019; 30:133-140. [PMID: 29346652 DOI: 10.1093/intimm/dxx077] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 01/11/2018] [Indexed: 01/02/2023] Open
Abstract
Because antibodies have become an important therapeutic tool, rational antibody design is a challenging issue involving various science and technology fields. From the computational aspect, many types of design-assist methods have been developed, but their accuracy is not fully satisfactory. Because of recent advancements in computational power, molecular dynamics (MD) simulation has become a helpful tool to trace the motion of proteins and to characterize their properties. Thus, MD simulation has been applied to various systems involving antigen-antibody complexes and has been shown to provide accurate insight into antigen-antibody interactions and dynamics at an atomic resolution. Therefore, it is highly possible that MD simulation will play several roles complementing the conventional antibody design. In this review, we address several important features of MD simulation in the context of rational antibody design.
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Affiliation(s)
- Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Japan
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15
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Wang Y, Cui P, Zhu S, Meng T, Hao F, Zhu G, Zuo W. Preparation of single-chain antibody against VP3 protein of duck hepatitis virus type 1 by phage display technology. J Virol Methods 2018; 257:73-78. [PMID: 29727718 DOI: 10.1016/j.jviromet.2018.04.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 10/17/2022]
Abstract
To construct phage antibody library for VP3 protein of duck hepatitis virus type 1(DHAV-1) and pan the specific single-chain variable fragment antibody (scFv), total RNA was extracted from the protein VP3- immunized mice spleen., vp3 gene encoding VP3 protein was amplified from the genome of DHAV-1 by RT-PCR method for the following recombinant pET-VP3 construction, immunogenic VP3 expression and purification, and combined with SOE-PCR method to complete the assembly of scFv. The scFv gene was cloned into pCANTAB5E vector for phage antibody library construction. Finally, the library for anti-VP3 scFv was screened by four rounds of adsorption-elution-enrichment with the purified VP3 protein. The characters of binding ability, specificity and neutralization of soluble antibodies expressed were evaluated by ELISA. The results showed 7 VP3-specific scFvs have been screened and identified with high both sensitivity and specificity for binding DHAV-1. To our knowledge, this is the first report for VP3-specific scFv of DHAV-1 and potentially promising application used in prevention and treatment of duck viral hepatitis.
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Affiliation(s)
- Yongjuan Wang
- Jiangsu Agri-animal Husbandry Vocational College, Jiang Su Provincial Key Laboratory of Veterinary Bio-pharmaceutical High tech Research, Taizhou, 225300, China
| | | | - Shanyuan Zhu
- Jiangsu Agri-animal Husbandry Vocational College, Jiang Su Provincial Key Laboratory of Veterinary Bio-pharmaceutical High tech Research, Taizhou, 225300, China
| | - Ting Meng
- Jiangsu Agri-animal Husbandry Vocational College, Jiang Su Provincial Key Laboratory of Veterinary Bio-pharmaceutical High tech Research, Taizhou, 225300, China
| | - Fuxing Hao
- Jiangsu Agri-animal Husbandry Vocational College, Jiang Su Provincial Key Laboratory of Veterinary Bio-pharmaceutical High tech Research, Taizhou, 225300, China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China; Oint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Weiyong Zuo
- Jiangsu Agri-animal Husbandry Vocational College, Jiang Su Provincial Key Laboratory of Veterinary Bio-pharmaceutical High tech Research, Taizhou, 225300, China.
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16
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Luz D, Shiga EA, Chen G, Quintilio W, Andrade FB, Maranhão AQ, Caetano BA, Mitsunari T, Silva MA, Rocha LB, Moro AM, Sidhu SS, Piazza RMF. Structural Changes in Stx1 Engineering Monoclonal Antibody Improves Its Functionality as Diagnostic Tool for a Rapid Latex Agglutination Test. Antibodies (Basel) 2018; 7:antib7010009. [PMID: 31544861 PMCID: PMC6698835 DOI: 10.3390/antib7010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/10/2018] [Accepted: 01/26/2018] [Indexed: 11/16/2022] Open
Abstract
Stx1 toxin is one of the AB5 toxins of Shiga toxin-producing Escherichia coli (STEC) responsible for foodborne intoxication during outbreaks. The single-chain variable fragment (scFv) is the most common recombinant antibody format; it consists of both variable chains connected by a peptide linker with conserved specificity and affinity for antigen. The drawbacks of scFv production in bacteria are the heterologous expression, conformation and stability of the molecule, which could change the affinity for the antigen. In this work, we obtained a stable and functional scFv-Stx1 in bacteria, starting from IgG produced by hybridoma cells. After structural modifications, i.e., change in protein orientation, vector and linker, its solubility for expression in bacteria was increased as well as the affinity for its antigen, demonstrated by a scFv dissociation constant (KD) of 2.26 × 10-7 M. Also, it was able to recognize purified Stx1 and cross-reacted with Stx2 toxin by ELISA (Enzyme-Linked Immunosorbent Assay), and detected 88% of Stx1-producing strains using a rapid latex agglutination test. Thus, the scFv fragment obtained in the present work is a bacteria-produced tool for use in a rapid diagnosis test, providing an alternative for STEC diagnosis.
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Affiliation(s)
- Daniela Luz
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Emerson A Shiga
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Gang Chen
- Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Wagner Quintilio
- Laboratório de Biofármacos em Células Animais, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Fernanda B Andrade
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Andrea Q Maranhão
- Laboratório de Imunologia, Universidade de Brasília, Brasília 70910-900, Brazil.
| | - Bruna A Caetano
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Thaís Mitsunari
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Míriam A Silva
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Letícia B Rocha
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Ana M Moro
- Laboratório de Biofármacos em Células Animais, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Sachdev S Sidhu
- Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Roxane M F Piazza
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
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17
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Erdag B, Balcioglu KB, Bahadir AO, Hinc D, Ibrahimoglu O, Bahar A, Basalp A, Yucel F. Cloning of anti-HBsAg single-chain variable fragments from hybridoma cells for one-step ELISA. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1348256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Berrin Erdag
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Koray Bertan Balcioglu
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Aylin Ozdemir Bahadir
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Duygu Hinc
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Ozlem Ibrahimoglu
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Aydin Bahar
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Aynur Basalp
- Sağlık Yüksekokulu, Mehmet Akif Ersoy Üniversitesi, Department of Health Managment, İstiklal Yerleşkesi, Burdur, Turkey
| | - Fatima Yucel
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
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18
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Paudel MK, Sakamoto S, Tanaka H, Morimoto S. An overview and comparison of a recombinant antigen-binding fragment and an antigen-binding fragment from a monoclonal antibody against wogonin glucuronide. J Nat Med 2017. [PMID: 28623444 DOI: 10.1007/s11418-017-1100-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Wogonin glucuronide (wogonin 7-O-β-D-glucuronide, Wgn) is widely recognized as a constituent of Scutellariae radix, which is used in Kampo medicines. Wgn has been used for both pharmacological (antifebrile uses and in detoxification) and research purposes. A recombinant antigen-binding fragment (rFab) and an antigen-binding fragment from a monoclonal antibody (mFab) against Wgn were constructed and used in an indirect competitive enzyme-linked immunosorbent assay (icELISA) in this study. The rFab and mFab against Wgn showed both activity and recognition against Wgn. The developed icELISA was validated as a quantitative analytical method to detect Wgn by testing both its utility and its reliability using multiple concentrations of Wgn from S. radix. This approach provides a more economic method to analyze and purify Kampo medicines.
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Affiliation(s)
- Madan Kumar Paudel
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Seiichi Sakamoto
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Hiroyuki Tanaka
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Satoshi Morimoto
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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19
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Paudel MK, Sakamoto S, Van Huy L, Tanaka H, Miyamoto T, Morimoto S. The effect of varying the peptide linker length in a single chain variable fragment antibody against wogonin glucuronide. J Biotechnol 2017; 251:47-52. [DOI: 10.1016/j.jbiotec.2017.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/23/2017] [Accepted: 04/03/2017] [Indexed: 12/27/2022]
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20
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Jee PF, Chen FS, Shu MH, Wong WF, Abdul Rahim R, AbuBakar S, Chang LY. Insertion of single-chain variable fragment (scFv) peptide linker improves surface display of influenza hemagglutinin (HA1) on non-recombinant Lactococcus lactis. Biotechnol Prog 2016; 33:154-162. [PMID: 27802566 DOI: 10.1002/btpr.2400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/26/2016] [Indexed: 12/14/2022]
Abstract
Heterologous protein displayed on the surface of Lactococcus lactis using the binding domain of N-acetylmuramidase (AcmA) has a potential application in vaccine delivery. In this study, we developed a non-recombinant L. lactis surface displaying the influenza A (H1N1) 2009 hemagglutinin (HA1). Three recombinant proteins, HA1/L/AcmA, HA1/AcmA, and HA1 were overexpressed in Escherichia coli, and purified. In the binding study using flow cytometry, the HA1/L/AcmA, which contained the single-chain variable fragment (scFv) peptide linker showed significantly higher percentage of binding counts and mean fluorescence binding intensity (MFI) (51.7 ± 1.4% and 3,594.0 ± 675.9, respectively) in comparison to the HA1/AcmA without the scFv peptide linker (41.1 ± 1.5% and 1,652.0 ± 34.1, respectively). Higher amount of HA1/L/AcmA (∼2.9 × 104 molecules per cell) was displayed on L. lactis when compared to HA1/AcmA (∼1.1 × 104 molecules per cell) in the immunoblotting analysis. The HA1/L/AcmA completely agglutinated RBCs at comparable amount of protein to that of HA1/AcmA and HA1. Computational modeling of protein structures suggested that scFv peptide linker in HA1/L/AcmA kept the HA1 and the AcmA domain separated at a much longer distance in comparison to HA1/AcmA. These findings suggest that insertion of the scFv peptide linker between HA1 and AcmA improved binding of recombinant proteins to L. lactis. Hence, insertion of scFv peptide linker can be further investigated as a potential approach for improvement of heterologous proteins displayed on the surface of L. lactis using the AcmA binding domain. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:154-162, 2017.
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Affiliation(s)
- Pui-Fong Jee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Fez-Shin Chen
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Meng-Hooi Shu
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Won Fen Wong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, Kuala Lumpur, Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Sazaly AbuBakar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, Kuala Lumpur, Malaysia
| | - Li-Yen Chang
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, Kuala Lumpur, Malaysia
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21
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Yusakul G, Sakamoto S, Pongkitwitoon B, Tanaka H, Morimoto S. Effect of linker length between variable domains of single chain variable fragment antibody against daidzin on its reactivity. Biosci Biotechnol Biochem 2016; 80:1306-12. [PMID: 27116996 DOI: 10.1080/09168451.2016.1156482] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The peptide linker between variable domains of heavy (VH) and light (VL) chains is one of important factors that influence the characteristics of scFv, including binding activity and specificity against target antigen. The scFvs against daidzin (DZ-scFvs) with different linker lengths were constructed in the format of VH-(GGGGS)n-VL (n = 1, 3, 5, and 7). They were expressed in the hemolymph of silkworm larvae using the Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system, and their reactivity against daidzin and related compounds were evaluated using an indirect competitive enzyme-linked immunosorbent assay (icELISA), which is applicable for quantitative analysis of daidzin. The results showed that the reactivity of scFvs against daidzin was increased, whereas specificity slightly decreased when their peptide linker was lengthened. These results suggested that the linker length of DZ-scFvs contributes to its reactivity. In addition, the results emphasize that the linker length could control the reactivity of DZ-scFvs.
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Affiliation(s)
- Gorawit Yusakul
- a Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences , Kyushu University , Fukuoka , Japan
| | - Seiichi Sakamoto
- a Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences , Kyushu University , Fukuoka , Japan
| | - Benyakan Pongkitwitoon
- b Faculty of Pharmacy, Department of Pharmaceutical Botany , Mahidol University , Bangkok , Thailand
| | - Hiroyuki Tanaka
- a Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences , Kyushu University , Fukuoka , Japan
| | - Satoshi Morimoto
- a Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences , Kyushu University , Fukuoka , Japan
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22
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MacDonald KG, Hoeppli RE, Huang Q, Gillies J, Luciani DS, Orban PC, Broady R, Levings MK. Alloantigen-specific regulatory T cells generated with a chimeric antigen receptor. J Clin Invest 2016; 126:1413-24. [PMID: 26999600 DOI: 10.1172/jci82771] [Citation(s) in RCA: 318] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 02/04/2016] [Indexed: 12/21/2022] Open
Abstract
Adoptive immunotherapy with regulatory T cells (Tregs) is a promising treatment for allograft rejection and graft-versus-host disease (GVHD). Emerging data indicate that, compared with polyclonal Tregs, disease-relevant antigen-specific Tregs may have numerous advantages, such as a need for fewer cells and reduced risk of nonspecific immune suppression. Current methods to generate alloantigen-specific Tregs rely on expansion with allogeneic antigen-presenting cells, which requires access to donor and recipient cells and multiple MHC mismatches. The successful use of chimeric antigen receptors (CARs) for the generation of antigen-specific effector T cells suggests that a similar approach could be used to generate alloantigen-specific Tregs. Here, we have described the creation of an HLA-A2-specific CAR (A2-CAR) and its application in the generation of alloantigen-specific human Tregs. In vitro, A2-CAR-expressing Tregs maintained their expected phenotype and suppressive function before, during, and after A2-CAR-mediated stimulation. In mouse models, human A2-CAR-expressing Tregs were superior to Tregs expressing an irrelevant CAR at preventing xenogeneic GVHD caused by HLA-A2+ T cells. Together, our results demonstrate that use of CAR technology to generate potent, functional, and stable alloantigen-specific human Tregs markedly enhances their therapeutic potential in transplantation and sets the stage for using this approach for making antigen-specific Tregs for therapy of multiple diseases.
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Moradi-Kalbolandi S, Davani D, Golkar M, Habibi-Anbouhi M, Abolhassani M, Shokrgozar MA. Soluble Expression and Characterization of a New scFv Directed to Human CD123. Appl Biochem Biotechnol 2016; 178:1390-406. [DOI: 10.1007/s12010-015-1954-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/07/2015] [Indexed: 12/23/2022]
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Farajnia S, Ahmadzadeh V, Tanomand A, Veisi K, Khosroshahi SA, Rahbarnia L. Development trends for generation of single-chain antibody fragments. Immunopharmacol Immunotoxicol 2014; 36:297-308. [DOI: 10.3109/08923973.2014.945126] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Zhang J, Liu S, Shang Z, Shi L, Yun J. Analysis of the relationship between end-to-end distance and activity of single-chain antibody against colorectal carcinoma. Theor Biol Med Model 2012; 9:38. [PMID: 22913623 PMCID: PMC3582594 DOI: 10.1186/1742-4682-9-38] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 08/17/2012] [Indexed: 01/23/2023] Open
Abstract
We investigated the relationship of End-to-end distance between VH and VL with different peptide linkers and the activity of single-chain antibodies by computer-aided simulation. First, we developed (G4S)n (where n = 1-9) as the linker to connect VH and VL, and estimated the 3D structure of single-chain Fv antibody (scFv) by homologous modeling. After molecular models were evaluated and optimized, the coordinate system of every protein was built and unified into one coordinate system, and End-to-end distances calculated using 3D space coordinates. After expression and purification of scFv-n with (G4S)n as n = 1, 3, 5, 7 or 9, the immunoreactivity of purified ND-1 scFv-n was determined by ELISA. A multi-factorial relationship model was employed to analyze the structural factors affecting scFv: rn=ABn-ABO2+CDn-CDO2+BCn-BCst2. The relationship between immunoreactivity and r-values revealed that fusion protein structure approached the desired state when the r-value = 3. The immunoreactivity declined as the r-value increased, but when the r-value exceeded a certain threshold, it stabilized. We used a linear relationship to analyze structural factors affecting scFv immunoreactivity.
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Affiliation(s)
- Jianhua Zhang
- Faculty of Biomedical Engineering of Zhengzhou University, Zhengzhou, 450001, Henan Province, People's Republic of China
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Detecting CD20-Rituximab interaction forces using AFM single-molecule force spectroscopy. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4789-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Shang GG, Zhang JH, Lü YG, Yun J. Bioinformatics-led design of single-chain antibody molecules targeting DNA sequences for retinoblastoma. Int J Ophthalmol 2011; 4:8-13. [PMID: 22553599 DOI: 10.3980/j.issn.2222-3959.2011.01.02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 01/20/2011] [Indexed: 02/01/2023] Open
Abstract
AIM To analyze the relationship between the structure and function of single-chain Fv antibody (scFv) with bioinformatics methods, so as to provide theoretical basis for retinoblastoma targeted therapy. METHODS Single-chain antibodies are reconstructed for cancer-targeted therapy to provide good penetration into tumor tissue and to improve their pharmacokinetics in vivo, offering a clinically valuable application. The relationship needs to be analyzed that there may be some variations between the structure and function of the fusion proteins, and the relationship between the structure and function of protein molecules was obtained through analyzing relevant literature at home and abroad as well as modeling analysis. RESULTS Through our analysis of the interaction region between the antibody and the antigen, and of the binding sites for molecular conformation, it is clear that existing antibodies need to be modified at the DNA sequence level, enhancing the biological activity of the antibodies. Based on the view that bio-molecular computer models are closely integrated with biological experiments, a bio-molecular structure-activity relationship model can be established in terms of molecular conformation, physical and chemical properties and the biological activity of single-chain antibodies. Two enlightenments are obtained from our analysis. On the one hand, the structure-activity relationship is clear for new immune molecules at the gene expression level. On the other hand, a single-chain antibody molecule can be designed and optimized for the cancer-oriented treatment. CONCLUSION In this article, we provide the theoretical and experimental basis for the development of single-chain antibodies appropriate for retinoblastoma therapy.
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Affiliation(s)
- Guo-Gang Shang
- Department of Radiotherapy, Zhengzhou People's Hospital, Zhengzhou 450052, Henan Province, China
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Detecting CD20-Rituximab specific interactions on lymphoma cells using atomic force microscopy. SCIENCE CHINA-LIFE SCIENCES 2010; 53:1189-95. [DOI: 10.1007/s11427-010-4070-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 07/31/2010] [Indexed: 10/18/2022]
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