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Li A, Swanson M, Sullivan N, Homan Y, Nahas D, Mukhopadhyay S, Li HH, Cao Y, Xu W, Tang H, Vora KA, Chen Z. Phage-derived anti-idiotype and anti-YTE antibodies in development of MK-1654 pharmacokinetic and immune response assays. Bioanalysis 2023; 15:1049-1067. [PMID: 37515532 DOI: 10.4155/bio-2023-0081] [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] [Indexed: 07/31/2023] Open
Abstract
Background: MK-1654 is a fully human monoclonal antibody with YTE mutations currently in phase III clinical trials for prophylactic use in protecting infants from human respiratory syncytial virus infection. Materials & methods: We generated anti-idiotype (anti-ID) and anti-YTE antibodies against MK-1654 by panning with MorphoSys HuCal phage libraries, and used the antibodies in the development of MK-1654 pharmacokinetic (PK) and immune response (IR) assays. Results: Detection of MK-1654 in nonhuman primate and human nasal wash samples showed combined use of anti-ID and anti-YTE antibodies can deliver desired sensitivity and accuracy in PK studies. IR studies showed anti-ID can serve as suitable positive control in neutralizing antibody assays. Conclusion: Phage-derived anti-IDs and anti-YTEs are suitable for PK and IR assays.
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Affiliation(s)
- April Li
- PCD Regulated Immunogenicity and Molecular, Merck and Co., Inc., West Point, PA 19486, USA
| | - Michael Swanson
- PCD Regulated Immunogenicity and Molecular, Merck and Co., Inc., West Point, PA 19486, USA
- Current address: Janssen Pharmaceutical, Ambler, PA 19002, USA
| | - Nicole Sullivan
- Infectious Diseases and Vaccine Research, Merck and Co., Inc., West Point, PA 19486, USA
| | - Ying Homan
- PCD Regulated Immunogenicity and Molecular, Merck and Co., Inc., West Point, PA 19486, USA
| | - Debbie Nahas
- Infectious Diseases and Vaccine Research, Merck and Co., Inc., West Point, PA 19486, USA
| | - Shreya Mukhopadhyay
- Infectious Diseases and Vaccine Research, Merck and Co., Inc., West Point, PA 19486, USA
| | - Hualin Helen Li
- Analytical Research and Development, Merck and Co., Inc., West Point, PA 19486, USA
| | - Yu Cao
- PCD Regulated Immunogenicity and Molecular, Merck and Co., Inc., West Point, PA 19486, USA
| | - Weifeng Xu
- PCD Regulated Immunogenicity and Molecular, Merck and Co., Inc., West Point, PA 19486, USA
| | - Huaping Tang
- PCD Regulated Immunogenicity and Molecular, Merck and Co., Inc., West Point, PA 19486, USA
- Current address: GSK Pharmaceutical, Collegeville, PA 19426, USA
| | - Kalpit A Vora
- Infectious Diseases and Vaccine Research, Merck and Co., Inc., West Point, PA 19486, USA
| | - Zhifeng Chen
- Infectious Diseases and Vaccine Research, Merck and Co., Inc., West Point, PA 19486, USA
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2
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Zhang Y, Li Q, Luo L, Duan C, Shen J, Wang Z. Application of germline antibody features to vaccine development, antibody discovery, antibody optimization and disease diagnosis. Biotechnol Adv 2023; 65:108143. [PMID: 37023966 DOI: 10.1016/j.biotechadv.2023.108143] [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: 01/13/2023] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023]
Abstract
Although the efficacy and commercial success of vaccines and therapeutic antibodies have been tremendous, designing and discovering new drug candidates remains a labor-, time- and cost-intensive endeavor with high risks. The main challenges of vaccine development are inducing a strong immune response in broad populations and providing effective prevention against a group of highly variable pathogens. Meanwhile, antibody discovery faces several great obstacles, especially the blindness in antibody screening and the unpredictability of the developability and druggability of antibody drugs. These challenges are largely due to poorly understanding of germline antibodies and the antibody responses to pathogen invasions. Thanks to the recent developments in high-throughput sequencing and structural biology, we have gained insight into the germline immunoglobulin (Ig) genes and germline antibodies and then the germline antibody features associated with antigens and disease manifestation. In this review, we firstly outline the broad associations between germline antibodies and antigens. Moreover, we comprehensively review the recent applications of antigen-specific germline antibody features, physicochemical properties-associated germline antibody features, and disease manifestation-associated germline antibody features on vaccine development, antibody discovery, antibody optimization, and disease diagnosis. Lastly, we discuss the bottlenecks and perspectives of current and potential applications of germline antibody features in the biotechnology field.
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Affiliation(s)
- Yingjie Zhang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Qing Li
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Liang Luo
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Changfei Duan
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China.
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3
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Pirkalkhoran S, Grabowska WR, Kashkoli HH, Mirhassani R, Guiliano D, Dolphin C, Khalili H. Bioengineering of Antibody Fragments: Challenges and Opportunities. Bioengineering (Basel) 2023; 10:bioengineering10020122. [PMID: 36829616 PMCID: PMC9952581 DOI: 10.3390/bioengineering10020122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Antibody fragments are used in the clinic as important therapeutic proteins for treatment of indications where better tissue penetration and less immunogenic molecules are needed. Several expression platforms have been employed for the production of these recombinant proteins, from which E. coli and CHO cell-based systems have emerged as the most promising hosts for higher expression. Because antibody fragments such as Fabs and scFvs are smaller than traditional antibody structures and do not require specific patterns of glycosylation decoration for therapeutic efficacy, it is possible to express them in systems with reduced post-translational modification capacity and high expression yield, for example, in plant and insect cell-based systems. In this review, we describe different bioengineering technologies along with their opportunities and difficulties to manufacture antibody fragments with consideration of stability, efficacy and safety for humans. There is still potential for a new production technology with a view of being simple, fast and cost-effective while maintaining the stability and efficacy of biotherapeutic fragments.
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Affiliation(s)
- Sama Pirkalkhoran
- School of Biomedical Science, University of West London, London W5 5RF, UK
| | | | | | | | - David Guiliano
- School of Life Science, College of Liberal Arts and Sciences, University of Westminster, London W1W 6UW, UK
| | - Colin Dolphin
- School of Biomedical Science, University of West London, London W5 5RF, UK
| | - Hanieh Khalili
- School of Biomedical Science, University of West London, London W5 5RF, UK
- School of Pharmacy, University College London, London WC1N 1AX, UK
- Correspondence:
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4
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Barber KW, Shrock E, Elledge SJ. CasPlay provides a gRNA-barcoded CRISPR-based display platform for antibody repertoire profiling. CELL REPORTS METHODS 2022; 2:100318. [PMID: 36313802 PMCID: PMC9606310 DOI: 10.1016/j.crmeth.2022.100318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/06/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
Protein display technologies link proteins to distinct nucleic acid sequences (barcodes), enabling multiplexed protein assays via DNA sequencing. Here, we develop Cas9 display (CasPlay) to interrogate customized peptide libraries fused to catalytically inactive Cas9 (dCas9) by sequencing the guide RNA (gRNA) barcodes associated with each peptide. We first confirm the ability of CasPlay to characterize antibody epitopes by recovering a known binding motif for a monoclonal anti-FLAG antibody. We then use a CasPlay library tiling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteome to evaluate vaccine-induced antibody reactivities. Using a peptide library representing the human virome, we demonstrate the ability of CasPlay to identify epitopes across many viruses from microliters of patient serum. Our results suggest that CasPlay is a viable strategy for customized protein interaction studies from highly complex libraries and could provide an alternative to phage display technologies.
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Affiliation(s)
- Karl W. Barber
- Division of Genetics, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen Shrock
- Division of Genetics, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J. Elledge
- Division of Genetics, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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5
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Di Gioacchino A, Procyk J, Molari M, Schreck JS, Zhou Y, Liu Y, Monasson R, Cocco S, Šulc P. Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection. PLoS Comput Biol 2022; 18:e1010561. [PMID: 36174101 PMCID: PMC9553063 DOI: 10.1371/journal.pcbi.1010561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/11/2022] [Accepted: 09/12/2022] [Indexed: 12/03/2022] Open
Abstract
Selection protocols such as SELEX, where molecules are selected over multiple rounds for their ability to bind to a target of interest, are popular methods for obtaining binders for diagnostic and therapeutic purposes. We show that Restricted Boltzmann Machines (RBMs), an unsupervised two-layer neural network architecture, can successfully be trained on sequence ensembles from single rounds of SELEX experiments for thrombin aptamers. RBMs assign scores to sequences that can be directly related to their fitnesses estimated through experimental enrichment ratios. Hence, RBMs trained from sequence data at a given round can be used to predict the effects of selection at later rounds. Moreover, the parameters of the trained RBMs are interpretable and identify functional features contributing most to sequence fitness. To exploit the generative capabilities of RBMs, we introduce two different training protocols: one taking into account sequence counts, capable of identifying the few best binders, and another based on unique sequences only, generating more diverse binders. We then use RBMs model to generate novel aptamers with putative disruptive mutations or good binding properties, and validate the generated sequences with gel shift assay experiments. Finally, we compare the RBM’s performance with different supervised learning approaches that include random forests and several deep neural network architectures. We show that two-layer neural networks, Restricted Boltzmann Machines (RBM), can be successfully trained on sequence ensemble datasets from selection-amplification experiments. We train the RBM using datasets from aptamer selection experiments on thrombin protein, and show that the model can successfully generalize to the test set to predict binders and non-binders. The log-likelihood assigned to a sequence by the RBM is correlated with the sequence fitness as quantified by the amplification between different rounds of selection. We further show that that the model is interpretable and by inspecting the weights of the model, we can identify structural motifs that are characteristic of the good binders. We explore the usage of the RBMs to identify which of the possible protein exosites the aptamers bind to. We show that the RBM can also be used for unsupervised clustering. Finally, we use RBMs to generate novel aptamers, and we experimentally verify predicted binding and non-binding sequences generated from the RBM.
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Affiliation(s)
- Andrea Di Gioacchino
- Laboratoire de Physique de l’Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, Paris, France
| | - Jonah Procyk
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Marco Molari
- Laboratoire de Physique de l’Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, Paris, France
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - John S. Schreck
- National Center for Atmospheric Research, Computational and Information Systems Laboratory, Boulder, Colorado, United States of America
| | - Yu Zhou
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Yan Liu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Rémi Monasson
- Laboratoire de Physique de l’Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, Paris, France
- * E-mail: (RM); (SC); (PŠ)
| | - Simona Cocco
- Laboratoire de Physique de l’Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, Paris, France
- * E-mail: (RM); (SC); (PŠ)
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- * E-mail: (RM); (SC); (PŠ)
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6
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Sun H, Hu N, Wang J. Application of Microfluidic Technology in Antibody Screening. Biotechnol J 2022; 17:e2100623. [PMID: 35481726 DOI: 10.1002/biot.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 11/07/2022]
Abstract
Specific antibodies are widely used in the biomedical field. Current screening methods for specific antibodies mainly involve hybridoma technology and antibody engineering techniques. However, these technologies suffer from tedious screening processes, long preparation periods, high costs, low efficiency, and a degree of automation, which have become a bottleneck for the screening of specific antibodies. To overcome these difficulties, microfluidics has been developed as a promising technology for high-throughput screening and high purity of antibody. In this review, we provide an overview of the recent advances in microfluidic applications for specific antibody screening. In particular, hybridoma technology and four antibody engineering techniques (including phage display, single B cell antibody screening, antibody expression, and cell-free protein synthesis) based on microfluidics have been introduced, challenges, and the future outlook of these technologies are also discussed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Ning Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
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7
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Van Lent J, Breukers J, Ven K, Ampofo L, Horta S, Pollet F, Imbrechts M, Geukens N, Vanhoorelbeke K, Declerck P, Lammertyn J. Miniaturized single-cell technologies for monoclonal antibody discovery. LAB ON A CHIP 2021; 21:3627-3654. [PMID: 34505611 DOI: 10.1039/d1lc00243k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibodies (Abs) are among the most important class of biologicals, showcasing a high therapeutic and diagnostic value. In the global therapeutic Ab market, fully-human monoclonal Abs (FH-mAbs) are flourishing thanks to their low immunogenicity and high specificity. The rapidly emerging field of single-cell technologies has paved the way to efficiently discover mAbs by facilitating a fast screening of the antigen (Ag)-specificity and functionality of Abs expressed by B cells. This review summarizes the principles and challenges of the four key concepts to discover mAbs using these technologies, being confinement of single cells using either droplet microfluidics or microstructure arrays, identification of the cells of interest, retrieval of those cells and single-cell sequence determination required for mAb production. This review reveals the enormous potential for mix-and-matching of the above-mentioned strategies, which is illustrated by the plethora of established, highly integrated devices. Lastly, an outlook is given on the many opportunities and challenges that still lie ahead to fully exploit miniaturized single-cell technologies for mAb discovery.
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Affiliation(s)
- Julie Van Lent
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Karen Ven
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Louanne Ampofo
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
| | - Sara Horta
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
| | - Francesca Pollet
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Maya Imbrechts
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Paul Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
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8
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Bertoglio F, Fühner V, Ruschig M, Heine PA, Abassi L, Klünemann T, Rand U, Meier D, Langreder N, Steinke S, Ballmann R, Schneider KT, Roth KDR, Kuhn P, Riese P, Schäckermann D, Korn J, Koch A, Chaudhry MZ, Eschke K, Kim Y, Zock-Emmenthal S, Becker M, Scholz M, Moreira GMSG, Wenzel EV, Russo G, Garritsen HSP, Casu S, Gerstner A, Roth G, Adler J, Trimpert J, Hermann A, Schirrmann T, Dübel S, Frenzel A, Van den Heuvel J, Čičin-Šain L, Schubert M, Hust M. A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients binds to the ACE2-RBD interface and is tolerant to most known RBD mutations. Cell Rep 2021; 36:109433. [PMID: 34273271 PMCID: PMC8260561 DOI: 10.1016/j.celrep.2021.109433] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 05/20/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
The novel betacoronavirus severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) causes a form of severe pneumonia disease called coronavirus disease 2019 (COVID-19). To develop human neutralizing anti-SARS-CoV-2 antibodies, antibody gene libraries from convalescent COVID-19 patients were constructed and recombinant antibody fragments (scFv) against the receptor-binding domain (RBD) of the spike protein were selected by phage display. The antibody STE90-C11 shows a subnanometer IC50 in a plaque-based live SARS-CoV-2 neutralization assay. The in vivo efficacy of the antibody is demonstrated in the Syrian hamster and in the human angiotensin-converting enzyme 2 (hACE2) mice model. The crystal structure of STE90-C11 Fab in complex with SARS-CoV-2-RBD is solved at 2.0 Å resolution showing that the antibody binds at the same region as ACE2 to RBD. The binding and inhibition of STE90-C11 is not blocked by many known emerging RBD mutations. STE90-C11-derived human IgG1 with FcγR-silenced Fc (COR-101) is undergoing Phase Ib/II clinical trials for the treatment of moderate to severe COVID-19.
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Affiliation(s)
- Federico Bertoglio
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Viola Fühner
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Maximilian Ruschig
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Philip Alexander Heine
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Leila Abassi
- Helmholtz Centre for Infection Research, Department of Vaccinology and Applied Microbiology, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Thomas Klünemann
- Helmholtz Centre for Infection Research, Department of Structure and Function of Proteins, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Ulfert Rand
- Helmholtz Centre for Infection Research, Department of Vaccinology and Applied Microbiology, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Doris Meier
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Nora Langreder
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Stephan Steinke
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Rico Ballmann
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Kai-Thomas Schneider
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Philipp Kuhn
- YUMAB GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Peggy Riese
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany; Helmholtz Centre for Infection Research, Department of Vaccinology and Applied Microbiology, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Dorina Schäckermann
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Janin Korn
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Allan Koch
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - M Zeeshan Chaudhry
- Helmholtz Centre for Infection Research, Department of Vaccinology and Applied Microbiology, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Kathrin Eschke
- Helmholtz Centre for Infection Research, Department of Vaccinology and Applied Microbiology, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Yeonsu Kim
- Helmholtz Centre for Infection Research, Department of Vaccinology and Applied Microbiology, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Susanne Zock-Emmenthal
- Technische Universität Braunschweig, Institut für Genetik, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Marlies Becker
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Margitta Scholz
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Gustavo Marçal Schmidt Garcia Moreira
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Esther Veronika Wenzel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Giulio Russo
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Hendrikus S P Garritsen
- Städtisches Klinikum Braunschweig gGmbH, Celler Str. 38, 38114 Braunschweig, Germany; Fraunhofer Institute for Surface Engineering and Thin Films IST, Bienroder Weg 54E, 38108 Braunschweig, Germany
| | - Sebastian Casu
- Helios Klinikum Salzgitter, Kattowitzer Str. 191, 38226 Salzgitter, Germany
| | - Andreas Gerstner
- Städtisches Klinikum Braunschweig gGmbH, Holwedestraße 16, 38118 Braunschweig, Germany
| | - Günter Roth
- BioCopy GmbH, Elzstrasse 27, 79312 Emmendingen, Germany
| | - Julia Adler
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Andreas Hermann
- CORAT Therapeutics GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Thomas Schirrmann
- YUMAB GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany; CORAT Therapeutics GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Stefan Dübel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - André Frenzel
- YUMAB GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany; Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Joop Van den Heuvel
- Helmholtz Centre for Infection Research, Department of Structure and Function of Proteins, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Luka Čičin-Šain
- Helmholtz Centre for Infection Research, Department of Vaccinology and Applied Microbiology, Inhoffenstr. 7, 38124 Braunschweig, Germany; Centre for Individualised Infection Medicine (CIIM), a joint venture of Helmholtz Centre for Infection Research and Medical School, Hannover, Germany
| | - Maren Schubert
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany.
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9
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Seidel-Greven M, Addai-Mensah O, Spiegel H, Chiegoua Dipah GN, Schmitz S, Breuer G, Frempong M, Reimann A, Klockenbring T, Fischer R, Barth S, Fendel R. Isolation and light chain shuffling of a Plasmodium falciparum AMA1-specific human monoclonal antibody with growth inhibitory activity. Malar J 2021; 20:37. [PMID: 33430886 PMCID: PMC7798374 DOI: 10.1186/s12936-020-03548-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/12/2020] [Indexed: 11/25/2022] Open
Abstract
Background Plasmodium falciparum, the parasite causing malaria, affects populations in many endemic countries threatening mainly individuals with low malaria immunity, especially children. Despite the approval of the first malaria vaccine Mosquirix™ and very promising data using cryopreserved P. falciparum sporozoites (PfSPZ), further research is needed to elucidate the mechanisms of humoral immunity for the development of next-generation vaccines and alternative malaria therapies including antibody therapy. A high prevalence of antibodies against AMA1 in immune individuals has made this antigen one of the major blood-stage vaccine candidates. Material and methods Using antibody phage display, an AMA1-specific growth inhibitory human monoclonal antibody from a malaria-immune Fab library using a set of three AMA1 diversity covering variants (DiCo 1–3), which represents a wide range of AMA1 antigen sequences, was selected. The functionality of the selected clone was tested in vitro using a growth inhibition assay with P. falciparum strain 3D7. To potentially improve affinity and functional activity of the isolated antibody, a phage display mediated light chain shuffling was employed. The parental light chain was replaced with a light chain repertoire derived from the same population of human V genes, these selected antibodies were tested in binding tests and in functionality assays. Results The selected parental antibody achieved a 50% effective concentration (EC50) of 1.25 mg/mL. The subsequent light chain shuffling led to the generation of four derivatives of the parental clone with higher expression levels, similar or increased affinity and improved EC50 against 3D7 of 0.29 mg/mL. Pairwise epitope mapping gave evidence for binding to AMA1 domain II without competing with RON2. Conclusion We have thus shown that a compact immune human phage display library is sufficient for the isolation of potent inhibitory monoclonal antibodies and that minor sequence mutations dramatically increase expression levels in Nicotiana benthamiana. Interestingly, the antibody blocks parasite inhibition independently of binding to RON2, thus having a yet undescribed mode of action.
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Affiliation(s)
- Melanie Seidel-Greven
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Otchere Addai-Mensah
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany.,Department of Medical Diagnostics, Faculty of Allied Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Holger Spiegel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Gwladys Nina Chiegoua Dipah
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Stefan Schmitz
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Gudrun Breuer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Margaret Frempong
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Andreas Reimann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Torsten Klockenbring
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany.,Institute of Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.,Purdue University, West Lafayette, IN, 47907, USA
| | - Stefan Barth
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany.,Department of Experimental Medicine and Immunotherapy, Institute of Applied Medical Engineering, RWTH Aachen University Clinic, Pauwelsstraße 20, 52074, Aachen, Germany.,South African Research Chair in Cancer Biotechnology, Department of Integrative Biomedical Sciences, and Medical Biotechnology & Immunotherapy Research Unit, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Rolf Fendel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany. .,Institute of Tropical Medicine, University of Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany.
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10
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Fernandez-Garcia L, Pacios O, González-Bardanca M, Blasco L, Bleriot I, Ambroa A, López M, Bou G, Tomás M. Viral Related Tools against SARS-CoV-2. Viruses 2020; 12:E1172. [PMID: 33081350 PMCID: PMC7589879 DOI: 10.3390/v12101172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
At the end of 2019, a new disease appeared and spread all over the world, the COVID-19, produced by the coronavirus SARS-CoV-2. As a consequence of this worldwide health crisis, the scientific community began to redirect their knowledge and resources to fight against it. Here we summarize the recent research on viruses employed as therapy and diagnostic of COVID-19: (i) viral-vector vaccines both in clinical trials and pre-clinical phases; (ii) the use of bacteriophages to find antibodies specific to this virus and some studies of how to use the bacteriophages themselves as a treatment against viral diseases; and finally, (iii) the use of CRISPR-Cas technology both to obtain a fast precise diagnose of the patient and also the possible use of this technology as a cure.
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Affiliation(s)
- Laura Fernandez-Garcia
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Olga Pacios
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Mónica González-Bardanca
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Lucia Blasco
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Inés Bleriot
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Antón Ambroa
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - María López
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - German Bou
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for the Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
| | - Maria Tomás
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for the Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
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11
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Zhao X, Cebrián R, Fu Y, Rink R, Bosma T, Moll GN, Kuipers OP. High-Throughput Screening for Substrate Specificity-Adapted Mutants of the Nisin Dehydratase NisB. ACS Synth Biol 2020; 9:1468-1478. [PMID: 32374981 PMCID: PMC7309312 DOI: 10.1021/acssynbio.0c00130] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Microbial
lanthipeptides are formed by a two-step enzymatic introduction
of (methyl)lanthionine rings. A dehydratase catalyzes the dehydration
of serine and threonine residues, yielding dehydroalanine and dehydrobutyrine,
respectively. Cyclase-catalyzed coupling of the formed dehydroresidues
to cysteines forms (methyl)lanthionine rings in a peptide. Lanthipeptide
biosynthetic systems allow discovery of target-specific, lanthionine-stabilized
therapeutic peptides. However, the substrate specificity of existing
modification enzymes impose limitations on installing lanthionines
in non-natural substrates. The goal of the present study was to obtain
a lanthipeptide dehydratase with the capacity to dehydrate substrates
that are unsuitable for the nisin dehydratase NisB. We report high-throughput
screening for tailored specificity of intracellular, genetically encoded
NisB dehydratases. The principle is based on the screening of bacterially
displayed lanthionine-constrained streptavidin ligands, which have
a much higher affinity for streptavidin than linear ligands. The designed
NisC-cyclizable high-affinity ligands can be formed via mutant NisB-catalyzed
dehydration but less effectively via wild-type NisB activity. In Lactococcus lactis, a cell surface display precursor was
designed comprising DSHPQFC. The Asp residue preceding the serine
in this sequence disfavors its dehydration by wild-type NisB. The
cell surface display vector was coexpressed with a mutant NisB library
and NisTC. Subsequently, mutant NisB-containing bacteria that display
cyclized strep ligands on the cell surface were selected via panning
rounds with streptavidin-coupled magnetic beads. In this way, a NisB
variant with a tailored capacity of dehydration was obtained, which
was further evaluated with respect to its capacity to dehydrate nisin
mutants. These results demonstrate a powerful method for selecting
lanthipeptide modification enzymes with adapted substrate specificity.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Yuxin Fu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Rick Rink
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Tjibbe Bosma
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Gert N. Moll
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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12
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Vaughan HJ, Green JJ, Tzeng SY. Cancer-Targeting Nanoparticles for Combinatorial Nucleic Acid Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901081. [PMID: 31222852 PMCID: PMC6923623 DOI: 10.1002/adma.201901081] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/13/2019] [Indexed: 05/03/2023]
Abstract
Nucleic acids are a promising type of therapeutic for the treatment of a wide range of conditions, including cancer, but they also pose many delivery challenges. For efficient and safe delivery to cancer cells, nucleic acids must generally be packaged into a vehicle, such as a nanoparticle, that will allow them to be taken up by the target cells and then released in the appropriate cellular compartment to function. As with other types of therapeutics, delivery vehicles for nucleic acids must also be designed to avoid unwanted side effects; thus, the ability of such carriers to target their cargo to cancer cells is crucial. Classes of nucleic acids, hurdles that must be overcome for effective intracellular delivery, types of nonviral nanomaterials used as delivery vehicles, and the different strategies that can be employed to target nucleic acid delivery specifically to tumor cells are discussed. Additonally, nanoparticle designs that facilitate multiplexed delivery of combinations of nucleic acids are reviewed.
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Affiliation(s)
- Hannah J Vaughan
- Department of Biomedical Engineering, Translational Tissue Engineering Center and Institute for NanoBioTechnology, Johns Hopkins University School of Medicine, 400 North Broadway, Smith Building 5001, Baltimore, MD, 21231, USA
| | - Jordan J Green
- Department of Biomedical Engineering, Translational Tissue Engineering Center and Institute for NanoBioTechnology, Johns Hopkins University School of Medicine, 400 North Broadway, Smith Building 5001, Baltimore, MD, 21231, USA
| | - Stephany Y Tzeng
- Department of Biomedical Engineering, Translational Tissue Engineering Center and Institute for NanoBioTechnology, Johns Hopkins University School of Medicine, 400 North Broadway, Smith Building 5001, Baltimore, MD, 21231, USA
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13
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Sanchez-Lockhart M, Reyes DS, Gonzalez JC, Garcia KY, Villa EC, Pfeffer BP, Trefry JC, Kugelman JR, Pitt ML, Palacios GF. Qualitative Profiling of the Humoral Immune Response Elicited by rVSV-ΔG-EBOV-GP Using a Systems Serology Assay, Domain Programmable Arrays. Cell Rep 2020; 24:1050-1059.e5. [PMID: 30044972 DOI: 10.1016/j.celrep.2018.06.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/20/2018] [Accepted: 06/18/2018] [Indexed: 01/02/2023] Open
Abstract
Development of an effective vaccine became a worldwide priority after the devastating 2013-2016 Ebola disease outbreak. To qualitatively profile the humoral response against advanced filovirus vaccine candidates, we developed Domain Programmable Arrays (DPA), a systems serology platform to identify epitopes targeted after vaccination or filovirus infection. We optimized the assay using a panel of well-characterized monoclonal antibodies. After optimization, we utilized the system to longitudinally characterize the immunoglobulin (Ig) isotype-specific responses in non-human primates vaccinated with rVSV-ΔG-EBOV-glycoprotein (GP). Strikingly, we observed that, although the IgM response was directed against epitopes over the whole GP, the IgG and IgA responses were almost exclusively directed against the mucin-like domain (MLD) of the glycan cap. Further research will be needed to characterize this possible biased IgG and IgA response toward the MLD, but the results corroborate that DPA is a valuable tool to qualitatively measure the humoral response after vaccination.
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Affiliation(s)
- Mariano Sanchez-Lockhart
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Daniel S Reyes
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jeanette C Gonzalez
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - Karla Y Garcia
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Erika C Villa
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bradley P Pfeffer
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - John C Trefry
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - Jeffrey R Kugelman
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - Margaret L Pitt
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - Gustavo F Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA.
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14
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Norbury LJ, Basałaj K, Bąska P, Zawistowska-Deniziak A, Kalinowska A, Wilkowski P, Wesołowska A, Wędrychowicz H. Generation of a single-chain variable fragment phage display antibody library from naïve mice panned against Fasciola hepatica antigens. Exp Parasitol 2019; 205:107737. [PMID: 31401060 DOI: 10.1016/j.exppara.2019.107737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 12/18/2022]
Abstract
Monoclonal antibodies have a wide range of applications in basic and applied research as well as in the medical and pharmaceutical industries. Phage display antibody libraries offer an alternative to hybridoma technology for the generation of monoclonal antibodies and can be applied to high-throughput screening and facilitate the generation of novel antibodies. Despite their utility in several fields of research there has been limited application of antibody libraries in the study of trematode parasites. Fasciola hepatica causes considerable loss to the agriculture sector and is also a human pathogen. The parasite's excretory/secretory material contains numerous molecules that facilitate its invasion and survival within the mammalian host, including cathepsin B and L proteases. F. hepatica cathepsin B2 is expressed during the initial weeks of infection and has suspected roles in immune evasion and as a digestive enzyme in the parasite's gut; it is considered a good target for vaccination or therapeutic inhibitors. In this study, we produced a single-chain variable fragment (scFv) phage display library from naïve mice. The library was used to identify several scFv that can bind to antigens from adult F. hepatica homogenate, and a scFv that can bind to F. hepatica cathepsin B2. The results highlight the potential applicability of such a library to facilitate the study of F. hepatica and other parasites. This is the first report of the application of a naïve phage display antibody library to the study of F. hepatica.
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Affiliation(s)
- Luke J Norbury
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland.
| | - Katarzyna Basałaj
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland
| | - Piotr Bąska
- Division of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Anna Zawistowska-Deniziak
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland
| | - Alicja Kalinowska
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland
| | - Przemysław Wilkowski
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland
| | - Agnieszka Wesołowska
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland
| | - Halina Wędrychowicz
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland
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15
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Vostakolaei MA, Molavi O, Hejazi MS, Kordi S, Rahmati S, Barzegari A, Abdolalizadeh J. Isolation and characterization of a novel scFv antibody fragments specific for Hsp70 as a tumor biomarker. J Cell Biochem 2019; 120:14711-14724. [DOI: 10.1002/jcb.28732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/12/2019] [Accepted: 03/22/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Mehdi Asghari Vostakolaei
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy Tabriz University of Medical Sciences Tabriz Iran
| | - Ommoleila Molavi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy Tabriz University of Medical Sciences Tabriz Iran
- Biotechnology Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Mohammad Saeid Hejazi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy Tabriz University of Medical Sciences Tabriz Iran
| | - Shirafkan Kordi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences Tabriz University of Medical Sciences Tabriz Iran
| | - Saman Rahmati
- Medical Biotechnology Department Biotechnology Research Center, Pasteur Institute of Iran Tehran Iran
| | - Abolfazl Barzegari
- Research Centre for Pharmaceutical Nanotechnology Tabriz University of Medical Sciences Tabriz Iran
| | - Jalal Abdolalizadeh
- Drug Applied Research Center Tabriz University of Medical Sciences Tabriz Iran
- Paramedical Faculty Tabriz University of Medical Sciences Tabriz Iran
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16
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Construction of a novel phage display antibody library against Fasciola hepatica, and generation of a single-chain variable fragment specific for F. hepatica cathepsin L1. Exp Parasitol 2019; 198:87-94. [DOI: 10.1016/j.exppara.2019.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 12/02/2018] [Accepted: 02/10/2019] [Indexed: 12/30/2022]
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17
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Construction of an immunized rabbit phage display antibody library for screening microcystin-LR high sensitive single-chain antibody. Int J Biol Macromol 2019; 123:369-378. [DOI: 10.1016/j.ijbiomac.2018.11.122] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/13/2018] [Accepted: 11/13/2018] [Indexed: 01/19/2023]
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18
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Screening and Preliminary Verification of a Phage Display Single-Chain Antibody Library Against Coal Workers' Pneumoconiosis. J Occup Environ Med 2018; 58:1264-1269. [PMID: 27930489 DOI: 10.1097/jom.0000000000000907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVES To construct a phage display human antibody library (PDHAL) against pneumoconiosis for the diagnosis and treatment of coal worker pneumoconiosis (CWP). METHODS The PDHAL was established via CWP blood and six positive antibodies were discovered. 867 coal workers (558 CWP and 309 without CWP) and 393 controls were recruited to validate the results. RESULTS A PDHAL against CWP was established, from which six strong positive clones were selected, sequenced and identified as VEGF, interleukin-18, HSP70, HER3, Gz-B and RF. Logistic regression analysis revealed that VEGF (OR (95% CI), 0.02 (0.01to 0.07), P < 0.05), RF-Ab (OR (95% CI): 0.46 (0.28 to 0.73), P < 0.05) and HSP70/HSP-70-Ab (OR (95% CI): 0.71 (0.53 to 0.95), P < 0.05) were protective factors for CWP after adjustment of confounding factors. CONCLUSION The serum VEGF, RF-Ab and HSP-70/HSP-70 antibodies were potential biomarkers for diagnosis and treatment of CWP.
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19
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Lee J, Shin YJ, Lee K, Cho HJ, Sa JK, Lee SY, Kim SH, Lee J, Yoon Y, Nam DH. Anti-SEMA3A Antibody: A Novel Therapeutic Agent to Suppress Glioblastoma Tumor Growth. Cancer Res Treat 2017; 50:1009-1022. [PMID: 29129044 PMCID: PMC6056981 DOI: 10.4143/crt.2017.315] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/30/2017] [Indexed: 11/21/2022] Open
Abstract
Purpose Glioblastoma (GBM) is classified as one of the most aggressive and lethal brain tumor. Great strides have been made in understanding the genomic and molecular underpinnings of GBM, which translated into development of new therapeutic approaches to combat such deadly disease. However, there are only few therapeutic agents that can effectively inhibit GBM invasion in a clinical framework. In an effort to address such challenges, we have generated anti-SEMA3A monoclonal antibody as a potential therapeutic antibody against GBM progression. Materials and Methods We employed public glioma datasets, Repository of Molecular Brain Neoplasia Data and The Cancer Genome Atlas, to analyze SEMA3AmRNA expression in human GBM specimens. We also evaluated for protein expression level of SEMA3A via tissue microarray (TMA) analysis. Cell migration and proliferation kinetics were assessed in various GBM patient-derived cells (PDCs) and U87-MG cell-line for SEMA3A antibody efficacy. GBM patient-derived xenograft (PDX) models were generated to evaluate tumor inhibitory effect of anti-SEMA3A antibody in vivo. Results By combining bioinformatics and TMA analysis, we discovered that SEMA3A is highly expressed in human GBM specimens compared to non-neoplastic tissues. We developed three different anti-SEMA3A antibodies, in fully human IgG form, through screening phage-displayed synthetic antibody library using a classical panning method. Neutralization of SEMA3A significantly reduced migration and proliferation capabilities of PDCs and U87-MG cell line in vitro. In PDX models, treatment with anti-SEMA3A antibody exhibited notable tumor inhibitory effect through down-regulation of cellular proliferative kinetics and tumor-associated macrophages recruitment. Conclusion In present study, we demonstrated tumor inhibitory effect of SEMA3A antibody in GBM progression and present its potential relevance as a therapeutic agent in a clinical framework.
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Affiliation(s)
- Jaehyun Lee
- Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, Korea
| | - Yong Jae Shin
- Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyoungmin Lee
- Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, Korea
| | - Hee Jin Cho
- Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jason K Sa
- Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sang-Yun Lee
- Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, Korea
| | - Seok-Hyung Kim
- Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, Korea.,Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeongwu Lee
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yeup Yoon
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, Korea
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, Korea.,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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20
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Parola C, Neumeier D, Reddy ST. Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering. Immunology 2017; 153:31-41. [PMID: 28898398 DOI: 10.1111/imm.12838] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022] Open
Abstract
Monoclonal antibody discovery and engineering is a field that has traditionally been dominated by high-throughput screening platforms (e.g. hybridomas and surface display). In recent years the emergence of high-throughput sequencing has made it possible to obtain large-scale information on antibody repertoire diversity. Additionally, it has now become more routine to perform high-throughput sequencing on antibody repertoires to also directly discover antibodies. In this review, we provide an overview of the progress in this field to date and show how high-throughput screening and sequencing are converging to deliver powerful new workflows for monoclonal antibody discovery and engineering.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Life Science Zurich Graduate School, Systems Biology, ETH Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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21
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Tiller KE, Chowdhury R, Li T, Ludwig SD, Sen S, Maranas CD, Tessier PM. Facile Affinity Maturation of Antibody Variable Domains Using Natural Diversity Mutagenesis. Front Immunol 2017; 8:986. [PMID: 28928732 PMCID: PMC5591402 DOI: 10.3389/fimmu.2017.00986] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/02/2017] [Indexed: 11/13/2022] Open
Abstract
The identification of mutations that enhance antibody affinity while maintaining high antibody specificity and stability is a time-consuming and laborious process. Here, we report an efficient methodology for systematically and rapidly enhancing the affinity of antibody variable domains while maximizing specificity and stability using novel synthetic antibody libraries. Our approach first uses computational and experimental alanine scanning mutagenesis to identify sites in the complementarity-determining regions (CDRs) that are permissive to mutagenesis while maintaining antigen binding. Next, we mutagenize the most permissive CDR positions using degenerate codons to encode wild-type residues and a small number of the most frequently occurring residues at each CDR position based on natural antibody diversity. This mutagenesis approach results in antibody libraries with variants that have a wide range of numbers of CDR mutations, including antibody domains with single mutations and others with tens of mutations. Finally, we sort the modest size libraries (~10 million variants) displayed on the surface of yeast to identify CDR mutations with the greatest increases in affinity. Importantly, we find that single-domain (VHH) antibodies specific for the α-synuclein protein (whose aggregation is associated with Parkinson’s disease) with the greatest gains in affinity (>5-fold) have several (four to six) CDR mutations. This finding highlights the importance of sampling combinations of CDR mutations during the first step of affinity maturation to maximize the efficiency of the process. Interestingly, we find that some natural diversity mutations simultaneously enhance all three key antibody properties (affinity, specificity, and stability) while other mutations enhance some of these properties (e.g., increased specificity) and display trade-offs in others (e.g., reduced affinity and/or stability). Computational modeling reveals that improvements in affinity are generally not due to direct interactions involving CDR mutations but rather due to indirect effects that enhance existing interactions and/or promote new interactions between the antigen and wild-type CDR residues. We expect that natural diversity mutagenesis will be useful for efficient affinity maturation of a wide range of antibody fragments and full-length antibodies.
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Affiliation(s)
- Kathryn E Tiller
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Tong Li
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Seth D Ludwig
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Sabyasachi Sen
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Peter M Tessier
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
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22
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He L, Lin X, de Val N, Saye-Francisco KL, Mann CJ, Augst R, Morris CD, Azadnia P, Zhou B, Sok D, Ozorowski G, Ward AB, Burton DR, Zhu J. Hidden Lineage Complexity of Glycan-Dependent HIV-1 Broadly Neutralizing Antibodies Uncovered by Digital Panning and Native-Like gp140 Trimer. Front Immunol 2017; 8:1025. [PMID: 28883821 PMCID: PMC5573810 DOI: 10.3389/fimmu.2017.01025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/08/2017] [Indexed: 11/30/2022] Open
Abstract
Germline precursors and intermediates of broadly neutralizing antibodies (bNAbs) are essential to the understanding of humoral response to HIV-1 infection and B-cell lineage vaccine design. Using a native-like gp140 trimer probe, we examined antibody libraries constructed from donor-17, the source of glycan-dependent PGT121-class bNAbs recognizing the N332 supersite on the HIV-1 envelope glycoprotein. To facilitate this analysis, a digital panning method was devised that combines biopanning of phage-displayed antibody libraries, 900 bp long-read next-generation sequencing, and heavy/light (H/L)-paired antibodyomics. In addition to single-chain variable fragments resembling the wild-type bNAbs, digital panning identified variants of PGT124 (a member of the PGT121 class) with a unique insertion in the heavy chain complementarity-determining region 1, as well as intermediates of PGT124 exhibiting notable affinity for the native-like trimer and broad HIV-1 neutralization. In a competition assay, these bNAb intermediates could effectively compete with mouse sera induced by a scaffolded BG505 gp140.681 trimer for the N332 supersite. Our study thus reveals previously unrecognized lineage complexity of the PGT121-class bNAbs and provides an array of library-derived bNAb intermediates for evaluation of immunogens containing the N332 supersite. Digital panning may prove to be a valuable tool in future studies of bNAb diversity and lineage development.
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Affiliation(s)
- Linling He
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Xiaohe Lin
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Natalia de Val
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Karen L Saye-Francisco
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Colin J Mann
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Ryan Augst
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Charles D Morris
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Parisa Azadnia
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Bin Zhou
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, United States
| | - Devin Sok
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jiang Zhu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
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23
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Schmitt MG, Rajendra Y, Hougland MD, Boyles JS, Barnard GC. Polymer-mediated flocculation of transient CHO cultures as a simple, high throughput method to facilitate antibody discovery. Biotechnol Prog 2017; 33:1393-1400. [PMID: 28722325 DOI: 10.1002/btpr.2527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/16/2017] [Indexed: 11/10/2022]
Abstract
Most biopharmaceutical drugs, especially monoclonal antibodies (mAbs), bispecific antibodies (BsAbs) and Fc-fusion proteins, are expressed using Chinese Hamster Ovary (CHO) cell lines. CHO cells typically yield high product titers and high product quality. Unfortunately, CHO cell lines also generate high molecular weight (HMW) aggregates of the desired product during cell culture along with CHO host cell protein (HCP) and CHO DNA. These immunogenic species, co-purified during Protein A purification, must be removed in a multi-step purification process. Our colleagues have reported the use of a novel polymer-mediated flocculation step to simultaneously reduce HMW, HCP and DNA from stable CHO cell cultures prior to Protein A purification. The objective of this study was to evaluate this novel "smart polymer" (SmP) in a high throughput antibody discovery workflow using transiently transfected CHO cultures. SmP treatment of 19 different molecules from four distinct molecular categories (human mAbs, murine mAbs, BsAbs and Fabs) with 0.1% SmP and 25 mM stimulus resulted in minimal loss of monomeric protein. Treatment with SmP also demonstrated a variable, concentration-dependent removal of HMW aggregates after Protein A purification. SmP treatment also effectively reduced HCP levels at each step of mAb purification with final HCP levels being several fold lower than the untreated control. Interestingly, SmP treatment was able to significantly reduce high concentrations of artificially spiked levels of endotoxin in the cultures. In summary, adding a simple flocculation step to our existing transient CHO process reduced the downstream purification burden to remove impurities and improved final product quality. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1393-1400, 2017.
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Affiliation(s)
- Matthew G Schmitt
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285
| | - Yashas Rajendra
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285
| | - Maria D Hougland
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285
| | - Jeffrey S Boyles
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285
| | - Gavin C Barnard
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285
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24
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Abstract
Antibodies are a group of proteins responsible for mediating immune reactions in vertebrates. They are able to bind a variety of structural motifs on noxious molecules tagging them for elimination from the organism. As a result of their versatile binding properties, antibodies are currently one of the most important classes of biopharmaceuticals. In this chapter, we discuss how knowledge-based computational methods can aid experimentalists in the development of potent antibodies. When using common experimental methods for antibody development, we often know the sequence of an antibody that binds to our molecule, antigen, of interest. We may also have a structure or model of the antigen. In these cases, computational methods can help by both modeling the antibody and identifying the antibody-antigen contact residues. This information can then play a key role in the rational design of more potent antibodies.
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Affiliation(s)
| | - James Dunbar
- Department of Statistics, University of Oxford, Oxford, UK
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25
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Solution Equilibrium Titration for High-Throughput Affinity Estimation of Unpurified Antibodies and Antibody Fragments. ACTA ACUST UNITED AC 2015; 20:1256-67. [DOI: 10.1177/1087057115595002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/14/2015] [Indexed: 01/14/2023]
Abstract
The generation of therapeutic antibodies with extremely high affinities down to the low picomolar range is today feasible with state-of-the art recombinant technologies. However, reliable and efficient identification of lead candidates with the desired affinity from a pool of thousands of antibody clones remains a challenge. Here, we describe a high-throughput procedure that allows reliable affinity screening of unpurified immunoglobulin G or antibody fragments. The method is based on the principle of solution equilibrium titration (SET) using highly sensitive electrochemiluminescence as a readout system. Because the binding partners are not labeled, the resulting KD represents a sound approximation of the real affinity. For screening, diluted bacterial lysates or cell culture supernatants are equilibrated with four different concentrations of a soluble target molecule, and unbound antibodies are subsequently quantified on 384-well Meso Scale Discovery (MSD) plates coated with the respective antigen. For determination of KD values from the resulting titration curves, fit models deduced from the law of mass action for 1:1 and 2:1 binding modes are applied to assess hundreds of interactions simultaneously. The accuracy of the method is demonstrated by comparing results from different screening campaigns from affinity optimization projects with results from detailed affinity characterization.
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26
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Barnard GC, Hougland MD, Rajendra Y. High-throughput mAb expression and purification platform based on transient CHO. Biotechnol Prog 2014; 31:239-47. [DOI: 10.1002/btpr.2012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/10/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Gavin C. Barnard
- Biotechnology Discovery Research; Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center; Indianapolis IN 46285
| | - Maria D. Hougland
- Biotechnology Discovery Research; Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center; Indianapolis IN 46285
| | - Yashas Rajendra
- Biotechnology Discovery Research; Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center; Indianapolis IN 46285
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27
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Mohammadzadeh S, Rajabibazl M, Fourozandeh M, Rasaee MJ, Rahbarizadeh F, Mohammadi M. Production of recombinant scFv against p24 of human immunodeficiency virus type 1 by phage display technology. Monoclon Antib Immunodiagn Immunother 2014; 33:28-33. [PMID: 24555933 DOI: 10.1089/mab.2013.0059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Phage display has a fundamental role in protein isolation and engineering. Isolated proteins produced with this method can be modified for specific binding and affinity. P24 is the most produced protein during human immune deficiency virus (HIV) replication; especially in the early steps of HIV-1 infection, its evaluation may have diagnostic values. To test the HIV-1 infection, p24 antigen assay appears to be a very promising alternative to RNA assays. In this study, we have generated a recombinant mouse single chain antibody fragment against p24 of the HIV-1 with the use of phage display technology. After isolation of antibody variable-region (V) gene of B cells extracted from the spleen of an immunized mouse, a library of single chain Fv fragments (scFv) was constructed. The library was used in a series of bio-panning processes against recombinant p24 protein expressed from Escherichia coli. The isolated scFv antibody specifically recognizes the HIV-1 capsid protein p24. The affinity constant of the isolated scFv antibody (MF85) was found to be 2×10(-9) M. Our studies showed that the MF85 scFV antibody has similar properties as that of monoclonal antibodies produced by the hybridoma technology.
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Affiliation(s)
- Sara Mohammadzadeh
- 1 Medical Biotechnology Department, Faculty of Medical Sciences, Tarbiat Modares University , Tehran, Iran
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28
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Production of Nanobodies against Prostate-Specific Membrane Antigen (PSMA) Recognizing LnCaP Cells. Int J Biol Markers 2014; 29:e169-79. [PMID: 24425321 DOI: 10.5301/jbm.5000063] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2013] [Indexed: 12/17/2022]
Abstract
Prostate cancer is the most common type of cancer in men. The antibody-mediated therapy for cancer treatment depends on the identification of selected molecular targets. The prostate-specific membrane antigen (PSMA) is a potential molecular target in prostate cancer and is abundantly expressed in this type of cancer. This study is aimed at designing and producing a recombinant PSMA epitope and a monoclonal nanobody with a high affinity toward the PSMA protein. A DNA fragment encoding the dominant epitopes of PSMA was designed, synthesized, and expressed in E. coli BL21 (DE3). A camel was immunized with the purified recombinant PSMA (rPSMA). Following mRNA isolation and cDNA synthesis, the variable fragment of heavy-chain antibodies (VHH) fragments were cloned and displayed on the surface of an M13 phage and used in sequential panning rounds. After phage ELISA and selection of colonies with the highest affinity, soluble nanobodies were produced and evaluated. Affinity of the nanobodies to rPSMA was estimated to be 3.5 × 10−7. Adherence of the purified anti-PSMA VHH was tested in cell-ELISA in the LnCaP and PC3 cell lines. VHH efficiently bound to LnCaP cells. The high specificity and affinity of this nanobody suggests its possible application as an effective tool in the diagnosis and treatment of prostate cancer.
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29
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Picha K, Huang C, Bugelski P, O'Neil K. Engineering peptide therapeutics using MIMETIBODY™ technology. Methods Mol Biol 2014; 1088:125-45. [PMID: 24146401 DOI: 10.1007/978-1-62703-673-3_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The MIMETIBODY™ platform was developed to expand the opportunities for application of biotherapeutics. While the utility of antibodies as antagonists has been well demonstrated, their application as agonists has been more challenging. For steric reasons, antibodies may be less well suited to perform as agonists or as inhibitors of GPCRs. In contrast, many bioactive peptides function as agonists or by interaction with GPCRs but their development as therapeutics has been challenging due to their small size and metabolic lability. The MIMETIBODY™ platform has been used to develop a variety of stable, long-lived molecules with intrinsic activities similar to that of their parent peptides. This chapter describes methods for construction of expression plasmids, expression and purification strategies, and methods for characterizing the activity of these novel proteins.
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Affiliation(s)
- Kristen Picha
- Centocor Research and Development, Inc., A Division of Johnson & Johnson Company, Radnor, PA, USA
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30
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Pointer KB, Clark PA, Zorniak M, Alrfaei BM, Kuo JS. Glioblastoma cancer stem cells: Biomarker and therapeutic advances. Neurochem Int 2014; 71:1-7. [PMID: 24657832 DOI: 10.1016/j.neuint.2014.03.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 02/28/2014] [Accepted: 03/08/2014] [Indexed: 02/08/2023]
Abstract
Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumor in humans. It accounts for fifty-two percent of primary brain malignancies in the United States and twenty percent of all primary intracranial tumors. Despite the current standard therapies of maximal safe surgical resection followed by temozolomide and radiotherapy, the median patient survival is still less than 2 years due to inevitable tumor recurrence. Glioblastoma cancer stem cells (GSCs) are a subgroup of tumor cells that are radiation and chemotherapy resistant and likely contribute to rapid tumor recurrence. In order to gain a better understanding of the many GBM-associated mutations, analysis of the GBM cancer genome is on-going; however, innovative strategies to target GSCs and overcome tumor resistance are needed to improve patient survival. Cancer stem cell biology studies reveal basic understandings of GSC resistance patterns and therapeutic responses. Membrane proteomics using phage and yeast display libraries provides a method to identify novel antibodies and surface antigens to better recognize, isolate, and target GSCs. Altogether, basic GBM and GSC genetics and proteomics studies combined with strategies to discover GSC-targeting agents could lead to novel treatments that significantly improve patient survival and quality of life.
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Affiliation(s)
- Kelli B Pointer
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Department of Neurological Surgery, Madison, WI, United States; Cellular and Molecular Biology, Madison, WI, United States
| | - Paul A Clark
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Department of Neurological Surgery, Madison, WI, United States
| | - Michael Zorniak
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Department of Neurological Surgery, Madison, WI, United States; Neuroscience Training Program, Madison, WI, United States
| | - Bahauddeen M Alrfaei
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Department of Neurological Surgery, Madison, WI, United States; Cellular and Molecular Pathology Training Program, Madison, WI, United States; Human Oncology, Madison, WI, United States
| | - John S Kuo
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Department of Neurological Surgery, Madison, WI, United States; Cellular and Molecular Biology, Madison, WI, United States; Neuroscience Training Program, Madison, WI, United States; Cellular and Molecular Pathology Training Program, Madison, WI, United States; Human Oncology, Madison, WI, United States; Carbone Cancer Center, Madison, WI, United States.
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31
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Ebrahimizadeh W, Rajabibazl M. Bacteriophage vehicles for phage display: biology, mechanism, and application. Curr Microbiol 2014; 69:109-20. [PMID: 24638925 DOI: 10.1007/s00284-014-0557-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/26/2014] [Indexed: 11/29/2022]
Abstract
The phage display technique is a powerful tool for selection of various biological agents. This technique allows construction of large libraries from the antibody repertoire of different hosts and provides a fast and high-throughput selection method. Specific antibodies can be isolated based on distinctive characteristics from a library consisting of millions of members. These features made phage display technology preferred method for antibody selection and engineering. There are several phage display methods available and each has its unique merits and application. Selection of appropriate display technique requires basic knowledge of available methods and their mechanism. In this review, we describe different phage display techniques, available bacteriophage vehicles, and their mechanism.
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Affiliation(s)
- Walead Ebrahimizadeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran,
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32
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Baral TN, MacKenzie R, Arbabi Ghahroudi M. Single-domain antibodies and their utility. ACTA ACUST UNITED AC 2013; 103:2.17.1-2.17.57. [PMID: 24510545 DOI: 10.1002/0471142735.im0217s103] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Engineered monoclonal antibody fragments have gained market attention due to their versatility and tailor-made potential and are now considered to be an important part of future immunobiotherapeutics. Single-domain antibodies (sdAbs), also known as nanobodies, are derived from VHHs [variable domains (V) of heavy-chain-only antibodies (HCAb)] of camelid heavy-chain antibodies. These nature-made sdAbs are well suited for various applications due to their favorable characteristics such as small size, ease of genetic manipulation, high affinity and solubility, overall stability, resistance to harsh conditions (e.g., low pH, high temperature), and low immunogenicity. Most importantly, sdAbs have the feature of penetrating into cavities and recognizing hidden epitopes normally inaccessible to conventional antibodies, mainly due to their protruding CDR3/H3 loops. In this unit, we will present and discuss comprehensive and step-by-step protocols routinely practiced in our laboratory for isolating sdAbs from immunized llamas (or other members of the Camelidae family) against target antigens using phage-display technology. Expression, purification, and characterization of the isolated sdAbs will then be described, followed by presentation of several examples of applications of sdAbs previously characterized in our laboratory and elsewhere.
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Affiliation(s)
- Toya Nath Baral
- Human Health Therapeutics, Life Sciences Division, National Research Council Canada, Ottawa, Ontario, Canada
| | - Roger MacKenzie
- Human Health Therapeutics, Life Sciences Division, National Research Council Canada, Ottawa, Ontario, Canada.,University of Guelph, Guelph, Ontario, Canada
| | - Mehdi Arbabi Ghahroudi
- Human Health Therapeutics, Life Sciences Division, National Research Council Canada, Ottawa, Ontario, Canada.,University of Guelph, Guelph, Ontario, Canada.,Department of Biology, Carleton University, Ottawa, Ontario, Canada
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33
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Phage display antibodies for diagnostic applications. Biologicals 2013; 41:209-16. [DOI: 10.1016/j.biologicals.2013.04.001] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/29/2013] [Accepted: 04/02/2013] [Indexed: 11/23/2022] Open
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Bodelón G, Palomino C, Fernández LÁ. Immunoglobulin domains inEscherichia coliand other enterobacteria: from pathogenesis to applications in antibody technologies. FEMS Microbiol Rev 2013; 37:204-50. [DOI: 10.1111/j.1574-6976.2012.00347.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 06/07/2012] [Accepted: 06/14/2012] [Indexed: 11/28/2022] Open
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Sayer JM, Aniana A, Louis JM. Mechanism of dissociative inhibition of HIV protease and its autoprocessing from a precursor. J Mol Biol 2012; 422:230-44. [PMID: 22659320 PMCID: PMC3418415 DOI: 10.1016/j.jmb.2012.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/15/2012] [Accepted: 05/15/2012] [Indexed: 11/17/2022]
Abstract
Dimerization is indispensible for release of the human immunodeficiency virus protease (PR) from its precursor (Gag-Pol) and ensuing mature-like catalytic activity that is crucial for virus maturation. We show that a single-chain Fv fragment (scFv) of a previously reported monoclonal antibody (mAb1696), which recognizes the N-terminus of PR, dissociates a dimeric mature D25N PR mutant with an enhanced dimer dissociation constant (K(d)) in the sub-micromolar range to form predominantly a monomer-scFv complex at a 1:1 ratio, along with small (5-10%) amounts of a dimer-scFv complex. Enzyme kinetics indicate a mixed mechanism of inhibition of the wild-type PR, which exhibits a K(d)<10nM, with effects both on K(m) and k(cat) at an scFv-to-PR ratio of 10:1. ScFv binds to the N-terminal peptide P(1)QITLW(6) of PR and to PR monomers with dissociation constants of ≤30 nM and ~100 nM, respectively. Consistent with an ~400-fold increase in the dissociation of the antibody (K(Ab)) on even addition of an acetyl group to P(1) of the peptide, the antibody fails to inhibit N-terminal autoprocessing of the PR from a model precursor (at ~5 μM). However, subsequent to this cleavage, it sequesters the PR, thus blocking autoprocessing at its C-terminus. A second monoclonal antibody [PRM1 (human monoclonal antibody to PR)], which recognizes part of the flap region (residues 41-47) of the mature PR and its precursor, does not inhibit autoprocessing and ensuing catalytic activity. However, its failure to recognize drug-resistant clinical mutants of PR may be beneficial to monitor the selection of mutations in this region under drug pressure.
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Affiliation(s)
| | | | - John M. Louis
- Corresponding author: John M. Louis, Building 5, Room B2-29, LCP, NIDDK, NIH, Bethesda, MD 20892-0520, Tel. 301 594-3122; Fax. 301 480-4001;
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Abstract
In this chapter we describe in detail the current protocols that are used to express single-domain antibodies in bacteria. Bacteria are among the most common expression systems for expressing recombinant proteins. We present different approaches for carrying out periplasmic and cytoplasmic expression, as well as small-scale and large-scale expression. In addition, we discuss the advantages and possible drawbacks of each protocol. We present data related to expression vectors, expression conditions, methods of protein extraction and purification, and yield and purity analysis of sdAbs. We also highlight important points that need to be considered before sdAbs that have been expressed in bacteria are used either in vitro or in vivo.
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Ullman CG, Frigotto L, Cooley RN. In vitro methods for peptide display and their applications. Brief Funct Genomics 2011; 10:125-34. [PMID: 21628313 DOI: 10.1093/bfgp/elr010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The presentation of recombinant peptide libraries linked to their coding sequence can be referred to as 'peptide display'. Phage display is the most widely practiced peptide display technology but more recent alternatives such as CIS display, ribosome display and mRNA display offer advantages over phage for speed, library size and the display of unnatural amino acids. These have provided researchers with tools to address some of the failings of peptides such as their low affinity, low stability and inability to cross biological membranes. In this review, we assess some of the recent advances in peptide display and its application.
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Affiliation(s)
- Christopher G Ullman
- Isogenica Ltd., The Mansion, Chesterford Research Park, Little Chesterford, Essex, UK.
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Bullous AJ, Alonso CMA, Boyle RW. Photosensitiser–antibody conjugates for photodynamic therapy. Photochem Photobiol Sci 2011; 10:721-50. [DOI: 10.1039/c0pp00266f] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kiss E, Kuluncsics Z, Kiss Z, Poór G. [Biotechnological advances in monoclonal antibody therapy: the RANK ligand inhibitor antibody]. Orv Hetil 2010; 151:2137-44. [PMID: 21147699 DOI: 10.1556/oh.2010.29010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Biological drugs have been used since the middle of the last century in medicine. Nowadays we are witnesses of the intensive development and wider administration of these drugs in clinical practice. Around 250 biological drugs are available and more than 350 million patients have been treated since their marketed authorization. Among the biologics there are protein based macromolecules, which mass production can be performed with the help of biotechnology. This term referring to the use of living organisms for production of molecules, was introduced by the Hungarian engineer, Károly Ereky. The present review focuses on the research, production and development of monoclonal antibodies manufactured by biotechnology. Some steps of this development have changed our immunological knowledge and the outcome of several diseases. The development of antibodies was highly recognized by two Nobel prizes. Authors detail the structure and functions of immunoglobulins, and their development, including fully human monoclonal antibodies. The RANKL inhibitor denosumab, a fully human IgG2 monoclonal antibody belongs to this latter group and it is available for treatment of osteoporosis. Authors also summarize the basic process of bone metabolism and the benefits of RANK ligand inhibition.
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Affiliation(s)
- Emese Kiss
- Semmelweis Egyetem, Általános Orvostudományi Kar III, Belgyógyászati Klinika Reumatológiai és Fizioterápiás Tanszéki Csoport II, Kihelyezett Részleg, Frankel Leó út 38-40, Budapest.
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Vielemeyer O, Nizak C, Jimenez AJ, Echard A, Goud B, Camonis J, Rain JC, Perez F. Characterization of single chain antibody targets through yeast two hybrid. BMC Biotechnol 2010; 10:59. [PMID: 20727208 PMCID: PMC2936416 DOI: 10.1186/1472-6750-10-59] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 08/22/2010] [Indexed: 05/12/2023] Open
Abstract
Background Due to their unique ability to bind their targets with high fidelity, antibodies are used widely not only in biomedical research, but also in many clinical applications. Recombinant antibodies, including single chain variable fragments (scFv), are gaining momentum because they allow powerful in vitro selection and manipulation without loss of function. Regardless of the ultimate application or type of antibody used, precise understanding of the interaction between the antibody's binding site and its specific target epitope(s) is of great importance. However, such data is frequently difficult to obtain. Results We describe an approach that allows detailed characterization of a given antibody's target(s) using the yeast two-hybrid system. Several recombinant scFv were used as bait and screened against highly complex cDNA libraries. Systematic sequencing of all retained clones and statistical analysis allowed efficient ranking of the prey fragments. Multiple alignment of the obtained cDNA fragments provided a selected interacting domain (SID), efficiently narrowing the epitope-containing region. Interactions between antibodies and their respective targets were characterized for several scFv. For AA2 and ROF7, two conformation-specific sensors that exclusively bind the activated forms of the small GTPases Rab6 and Rab1 respectively, only fragments expressing the entire target protein's core region were retained. This strongly suggested interaction with a non-linear epitope. For two other scFv, TA10 and SF9, which recognize the large proteins giantin and non-muscle myosin IIA, respectively, precise antibody-binding regions within the target were defined. Finally, for some antibodies, secondary targets within and across species could be revealed. Conclusions Our method, utilizing the yeast two-hybrid technology and scFv as bait, is a simple yet powerful approach for the detailed characterization of antibody targets. It allows precise domain mapping for linear epitopes, confirmation of non-linear epitopes for conformational sensors, and detection of secondary binding partners. This approach may thus prove to be an elegant and rapid method for the target characterization of newly obtained scFv antibodies. It may be considered prior to any research application and particularly before any use of such recombinant antibodies in clinical medicine.
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Affiliation(s)
- Ole Vielemeyer
- Institut Curie-Research Center, 26 rue d'Ulm, Paris cedex 05, France
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Isolation and characterization of selective and potent human Fab inhibitors directed to the active-site region of the two-component NS2B-NS3 proteinase of West Nile virus. Biochem J 2010; 427:369-76. [PMID: 20156198 DOI: 10.1042/bj20100074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
There is a need to develop inhibitors of mosquito-borne flaviviruses, including WNV (West Nile virus). In the present paper, we describe a novel and efficient recombinant-antibody technology that led us to the isolation of inhibitory high-affinity human antibodies to the active-site region of a viral proteinase. As a proof-of-principal, we have successfully used this technology and the synthetic naive human combinatorial antibody library HuCAL GOLD(R) to isolate selective and potent function-blocking active-site-targeting antibodies to the two-component WNV NS (non-structural protein) 2B-NS3 serine proteinase, the only proteinase encoded by the flaviviral genome. First, we used the wild-type enzyme in antibody screens. Next, the positive antibody clones were counter-screened using an NS2B-NS3 mutant with a single mutation of the catalytically essential active-site histidine residue. The specificity of the antibodies to the active site was confirmed by substrate-cleavage reactions and also by using proteinase mutants with additional single amino-acid substitutions in the active-site region. The selected WNV antibodies did not recognize the structurally similar viral proteinases from Dengue virus type 2 and hepatitis C virus, and human serine proteinases. Because of their high selectivity and affinity, the identified human antibodies are attractive reagents for both further mutagenesis and structure-based optimization and, in addition, for studies of NS2B-NS3 activity. Conceptually, it is likely that the generic technology reported in the present paper will be useful for the generation of active-site-specific antibody probes for multiple enzymes.
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Combinatorial libraries against libraries for selecting neoepitope activation-specific antibodies. Proc Natl Acad Sci U S A 2010; 107:6252-7. [PMID: 20308586 DOI: 10.1073/pnas.0914358107] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A systematic approach to the discovery of conformation-specific antibodies or those that recognize activation-induced neoepitopes in signaling molecules and enzymes will be a powerful tool in developing antibodies for basic science and therapy. Here, we report the isolation of antibody antagonists that preferentially bind activated integrin Mac-1 (alpha(M)beta(2)) and are potent in blocking neutrophil adhesion and migration. A novel strategy was developed for this task, consisting of yeast surface display of Mac-1 inserted (I) domain library, directed evolution to isolate active mutants of the I domain, and screening of phage display of human antibody library against the active I domain in yeast. Enriched antibody library was then introduced into yeast surface two-hybrid system for final quantitative selection of antibodies from monomeric antigen-antibody interaction. This led to highly efficient isolation of intermediate to high affinity antibodies, which preferentially reacted with the active I domain, antagonized the I domain binding to intercellular adhesion molecule (ICAM)-1, complement C3 fragment iC3b, and fibronectin, and potently inhibited neutrophil migration on fibrinogen. The strategy demonstrated herein can be broadly applicable to developing antibodies against modular domains that switch between inactive and active conformations, particularly toward the discovery of antibody antagonists in therapeutic and diagnostic applications.
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43
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Cloning antifungal single chain fragment variable antibodies by phage display and competitive panning elution. Anal Biochem 2009; 395:16-24. [DOI: 10.1016/j.ab.2009.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 07/08/2009] [Accepted: 08/02/2009] [Indexed: 11/19/2022]
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44
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Gustchina E, Louis JM, Frisch C, Ylera F, Lechner A, Bewley CA, Clore GM. Affinity maturation by targeted diversification of the CDR-H2 loop of a monoclonal Fab derived from a synthetic naïve human antibody library and directed against the internal trimeric coiled-coil of gp41 yields a set of Fabs with improved HIV-1 neutralization potency and breadth. Virology 2009; 393:112-9. [PMID: 19695655 DOI: 10.1016/j.virol.2009.07.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 06/28/2009] [Accepted: 07/19/2009] [Indexed: 10/20/2022]
Abstract
Previously we reported a broadly HIV-1 neutralizing mini-antibody (Fab 3674) of modest potency that was derived from a human non-immune phage library by panning against the chimeric gp41-derived construct N(CCG)-gp41. This construct presents the N-heptad repeat of the gp41 ectodomain as a stable, helical, disulfide-linked trimer that extends in helical phase from the six-helix bundle of gp41. In this paper, Fab 3674 was subjected to affinity maturation against the N(CCG)-gp41 antigen by targeted diversification of the CDR-H2 loop to generate a panel of Fabs with diverse neutralization activity. Three affinity-matured Fabs selected for further study, Fabs 8060, 8066 and 8068, showed significant increases in both potency and breadth of neutralization against HIV-1 pseudotyped with envelopes of primary isolates from the standard subtype B and C HIV-1 reference panels. The parental Fab 3674 is 10-20-fold less potent in monovalent than bivalent format over the entire B and C panels of HIV-1 pseudotypes. Of note is that the improved neutralization activity of the affinity-matured Fabs relative to the parental Fab 3674 was, on average, significantly greater for the Fabs in monovalent than bivalent format. This suggests that the increased avidity of the Fabs for the target antigen in bivalent format can be partially offset by kinetic and/or steric advantages afforded by the smaller monovalent Fabs. Indeed, the best affinity-matured Fab (8066) in monovalent format ( approximately 50 kDa) was comparable in HIV-1 neutralization potency to the parental Fab 3674 in bivalent format ( approximately 120 kDa) across the subtype B and C reference panels.
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Affiliation(s)
- Elena Gustchina
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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Jung SM, Tsuji K, Moroi M. Glycoprotein (GP) VI dimer as a major collagen-binding site of native platelets: direct evidence obtained with dimeric GPVI-specific Fabs. J Thromb Haemost 2009; 7:1347-55. [PMID: 19486274 DOI: 10.1111/j.1538-7836.2009.03496.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND The platelet collagen receptor glycoprotein (GP) VI is suggested to exist as a dimer on the platelet surface, but no direct proof of the functional importance of dimer formation has been provided. OBJECTIVES To obtain direct evidence for GPVI dimers on the platelet membrane and their functional importance, Fab antibodies were developed that bind to GPVI dimer (GPVI-Fc2) but not to GPVI monomer (GPVIex) through a phage display method. RESULTS Six Fabs were found: B-F, only reactive with GPVI-Fc2, and A, mainly reactive with GPVI-Fc2, with some reactivity towards GPVIex; each Fab (Fab-dHLX-MH) forms a bivalent dimer (b-Fab) by dimerizing the dHLX domains from two Fab molecules. Fab F was subcloned to a monovalent format by deleting its dHLX domain. All b-Fabs induced platelet aggregation, but the monomeric form of Fab F (m-Fab-F) specifically inhibited collagen-induced aggregation. All b-Fabs and m-Fab-F inhibited GPVI-Fc2 binding to fibrous collagen. Immunoblotting showed that b-Fab-F and m-Fab-F bound weakly to GPVI-Fc2. Adding the anti-GPVI monoclonal antibody 204-11 increased the B(max) of m-Fab-F binding to GPVI-Fc2, suggesting that 204-11 binds to GPVI-Fc2 molecules not already in the appropriate conformation to recognize the Fab, converting them to a conformation reactive to the Fab. CONCLUSIONS GPVI forms a specific structure by dimerization that is necessary for the binding of this receptor to collagen fibrils. The binding of m-Fab-F to platelets directly demonstrates that GPVI is present as a functionally relevant dimer on the platelet surface.
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Affiliation(s)
- S M Jung
- Department of Protein Biochemistry, Institute of Life Science, Kurume University, Kurume-shi, Fukuoka-ken, Japan.
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Chen W, Zhang J, Zhang T, Li H, Wang W, Xia Z, Wang M. Improved isolation of anti-rhTNF-alpha scFvs from phage display library by bioinformatics. Mol Biotechnol 2009; 43:20-8. [PMID: 19412671 DOI: 10.1007/s12033-009-9172-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 04/07/2009] [Indexed: 11/30/2022]
Abstract
Phage display technology has been widely used to isolate antibodies with specific properties. The objective of this study was to isolate anti-rhTNF-alpha scFvs from phage display library. However, the inserted genes of eluted phages were either incorrect or truncated. In order to address this issue, bioinformatics was applied to facilitate the screening of the eluted phages. The alignment of the sequencing results was performed with the software ClustalW. The gene of scFv (F6) was assembled by ligating together the identical VH and VL fragments and then analyzed by using program BLASTX. F6 was identified to share 80% sequence identity with a human anti-TNF-alpha scFv. Subsequently, the conformation of F6 binding to hTNF-alpha predicted by docking assay showed that F6 could bind to hTNF-alpha via the six CDRs. Finally, ELISA assay and Western blot analysis indicated that F6 might bind to rhTNF-alpha specifically. Biological assay demonstrated that F6 might neutralize rhTNF-alpha-induced cytotoxicity in L929 cells. In conclusion, F6 could be a candidate for further investigation, based on the experimental data and the prediction by bioinformatics.
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Affiliation(s)
- Wei Chen
- School of Life Science & Technology, China Pharmaceutical University, 153# Tong Jia Xiang 24, Nanjing 210009, People's Republic of China
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Dimitrov AS. Therapeutic antibodies: current state and future trends--is a paradigm change coming soon? Methods Mol Biol 2009; 525:1-27, xiii. [PMID: 19252861 PMCID: PMC3402212 DOI: 10.1007/978-1-59745-554-1_1] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Antibody-based therapeutics currently enjoy unprecedented success, growth in research and revenues, and recognition of their potential. It appears that the promise of the "magic bullet" has largely been realized. There are currently 22 monoclonal antibodies (mAbs) approved by the United States Food and Drug Administration (FDA) for clinical use and hundreds are in clinical trials for treatment of various diseases including cancers, immune disorders, and infections. The revenues from the top five therapeutic antibodies (Rituxan, Remicade, Herceptin, Humira, and Avastin) nearly doubled from $6.4 billion in 2004 to $11.7 billion in 2006. During the last several years major pharmaceutical companies raced to acquire antibody companies, with a recent example of MedImmune being purchased for $15.6 billion by AstraZeneca. These therapeutic and business successes reflect the major advances in antibody engineering which have resulted in the generation of safe, specific, high-affinity, and non-immunogenic antibodies during the last three decades. Currently, second and third generations of antibodies are under development, mostly to improve already existing antibody specificities. However, although the refinement of already known methodologies is certainly of great importance for potential clinical use, there are no conceptually new developments in the last decade comparable, for example, to the development of antibody libraries, phage display, domain antibodies (dAbs), and antibody humanization to name a few. A fundamental question is then whether there will be another change in the paradigm of research as happened 1-2 decades ago or the current trend of gradual improvement of already developed methodologies and therapeutic antibodies will continue. Although any prediction could prove incorrect, it appears that conceptually new methodologies are needed to overcome the fundamental problems of drug (antibody) resistance due to genetic or/and epigenetic alterations in cancer and chronic infections, as well as problems related to access to targets and complexity of biological systems. If new methodologies are not developed, it is likely that gradual saturation will occur in the pipeline of conceptually new antibody therapeutics. In this scenario we will witness an increase in combination of targets and antibodies, and further attempts to personalize targeted treatments by using appropriate biomarkers as well as to develop novel scaffolds with properties that are superior to those of the antibodies now in clinical use.
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49
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Feng B, Dai Y, Wang L, Tao N, Huang S, Zeng H. A novel affinity ligand for polystyrene surface from a phage display random library and its application in anti-HIV-1 ELISA system. Biologicals 2008; 37:48-54. [PMID: 19056299 DOI: 10.1016/j.biologicals.2008.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2008] [Revised: 09/23/2008] [Accepted: 10/24/2008] [Indexed: 12/16/2022] Open
Abstract
In order to develop an affinity ligand for site-directed immobilization of target proteins on polystyrene (PS) surface, a linear 12-mer peptide phage display random library was screened. Phage clones that specifically bound to PS plate were sequenced after three rounds of biopanning. The obtained DNA sequences revealed that there were several aromatic and basic amino acid residues, which may be critical to binding. One of the selected dodecapeptides, named Lig1 (FKFWLYEHVIRG), was genetically fused to the N/C-terminus of recombinant antigen ENV which could be recognized by specific antibodies against human immunodeficiency virus type 1 (HIV-1), to investigate its performance as an affinity ligand. The ligand-fused ENVs overexpressed in Escherichia coli were compared to the original one in terms of the immobilization characteristics on PS plate in enzyme-linked immunosorbent assay (ELISA). The results indicated that the ligand-fused proteins showed a considerably improved affinity to PS surface, and were preferentially adsorbed on PS plate suffering only scarcely from interference by coexisting protein molecules. Anti-HIV-1 ELISA system, which employed Lig1-ENV (Lig1 fused to ENV N-terminus) as immobilization antigen also exhibited sufficiently high sensitivity and specificity in serodiagnosis tests.
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Affiliation(s)
- Bo Feng
- Biological Engineering Department, Xiangtan University, Xiangtan 411105, Hunan Province, China.
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50
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Abstract
The tremendous challenge of inhibiting therapeutically important protein-protein interactions has created the opportunity to extend traditional medicinal chemistry to a new class of targets and to explore nontraditional strategies. Here we review a widely studied system, the interaction between tumor suppressor p53 and its natural antagonist MDM2, for which both traditional and nontraditional approaches have been reported. This system has been a testing ground for novel proteomimetic scaffold-based strategies, i.e., for attempts to mimic the recognition surface displayed by a folded protein with unnatural oligomers. Retroinverso peptides, peptoids, terphenyls, beta-hairpins, p-oligobenzamides, beta-peptides, and miniproteins have all been explored as inhibitors of the p53/MDM2 interaction, and we focus on these oligomer-based efforts. Traditional approaches have been successful as well, and we briefly review small molecule inhibitors along with other strategies for reactivation of the p53 pathway, for comparison with oligomer- based approaches. We close with comments on an emerging dichotomy among protein-protein interaction targets.
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Affiliation(s)
- Justin K Murray
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706, USA
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