1
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Brango-Vanegas J, Leite ML, de Oliveira KBS, da Cunha NB, Franco OL. From exploring cancer and virus targets to discovering active peptides through mRNA display. Pharmacol Ther 2023; 252:108559. [PMID: 37952905 DOI: 10.1016/j.pharmthera.2023.108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
During carcinogenesis, neoplastic cells accumulate mutations in genes important for cellular homeostasis, producing defective proteins. Viral infections occur when viral capsid proteins bind to the host cell receptor, allowing the virus to enter the cells. In both cases, proteins play important roles in cancer development and viral infection, so these targets can be exploited to develop alternative treatments. mRNA display technology is a very powerful tool for the development of peptides capable of acting on specific targets in neoplastic cells or on viral capsid proteins. mRNA display technology allows the selection and evolution of peptides with desired functional properties from libraries of many nucleic acid variants. Among other advantages of this technology, the use of flexizymes allows the production of peptides with unnatural amino acid residues, which can enhance the activity of these molecules. From target immobilization, peptides with greater specificity for the targets of interest are generated during the selection rounds. Herein, we will explore the use of mRNA display technology for the development of active peptides after successive rounds of selection, using proteins present in neoplastic cells and viral particles as targets.
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Affiliation(s)
- José Brango-Vanegas
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Michel Lopes Leite
- Departamento de Biologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Nicolau Brito da Cunha
- Universidade de Brasília, Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
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2
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Lim HT, Kok BH, Leow CY, Leow CH. Exploring shark VNAR antibody against infectious diseases using phage display technology. Fish Shellfish Immunol 2023; 140:108986. [PMID: 37541634 DOI: 10.1016/j.fsi.2023.108986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
Antibody with high affinity and specificity to antigen has widely used as a tool to combat various diseases. The variable domain of immunoglobulin new antigen receptor (VNAR) naturally found in shark contains autonomous function as single-domain antibody. Due to its excellent characteristics, the small, non-complex, and highly stable have made shark VNAR can acquires the antigen-binding capability that might not be reached by conventional antibody. Phage display technology enables shark VNAR to be presented on the surface of phage, allowing the exploration of shark VNAR as an alternative antibody format to target antigens from various infectious diseases. The application of phage-displayed shark VNAR in antibody library and biopanning eventually leads to the discovery and isolation of antigen-specific VNARs with diagnostic and therapeutic potential towards infectious diseases. This review provides an overview of the shark VNAR antibody, the types of phage display technology with comparison to the other types of display system, as well as the application and case studies of phage-displayed shark VNAR antibodies against infectious diseases.
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Affiliation(s)
- Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
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3
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Arbaciauskaite M, Pirhanov A, Ammermann E, Lei Y, Cho YK. Yeast biopanning against site-specific phosphorylations in tau. Protein Eng Des Sel 2023:7192899. [PMID: 37294629 DOI: 10.1093/protein/gzad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/11/2023] [Indexed: 06/11/2023] Open
Abstract
Antibodies that bind to protein phosphorylation sites are a critical tool for detecting the post-translational modification. The detection of site-specific phosphorylation in the microtubule-associated protein tau is emerging as a means to diagnose and monitor the progression of Alzheimer's Disease (AD) as well as other neurodegenerative diseases. However, the need for reliable phospho-site specific antibodies persists due to a lack of approaches for identifying monoclonal antibodies and characterizing non-specific binding. Here, we report a novel approach for yeast biopanning using synthetic peptides containing site-specific phosphorylations as antigens. To readily assess yeast binding and distinguish non-specific binding, we developed bi-directional expression vectors that allow antibody fragment surface display and intracellular fluorescent protein expression. Using yeast cells displaying a previously validated phospho-tau (p-tau) single-chain variable region fragment (scFv), we show that our platform can discriminate yeast cell binding based on the presence of a single phosphate modification on the target peptide. By improving biopanning parameters, we enabled phospho-specific capture of yeast cells displaying scFvs against p-tau with a wide range of affinities (KD = 0.2 to 60 nM). Finally, we demonstrate the capability to screen large yeast libraries against p-tau by performing biopanning in 6-well plates. These results show that yeast biopanning can robustly capture yeast cells based on phospho-site specific antibody binding, opening doors for the facile identification of high-quality monoclonal antibodies.
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Affiliation(s)
- Monika Arbaciauskaite
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA
| | - Azady Pirhanov
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
| | - Erik Ammermann
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA
| | - Yu Lei
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
| | - Yong Ku Cho
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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4
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Yang HJ, Kim MW, Raju CV, Cho CH, Park TJ, Park JP. Highly sensitive and label-free electrochemical detection of C-reactive protein on a peptide receptor-gold nanoparticle-black phosphorous nanocomposite modified electrode. Biosens Bioelectron 2023; 234:115382. [PMID: 37178497 DOI: 10.1016/j.bios.2023.115382] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/21/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
C-reactive protein (CRP) is a phylogenetically highly conserved plasma protein found in blood serum, and an enhanced CRP level is indicative of inflammatory conditions such as infection and cancer, among others. In this work, we developed a novel high CRP-affinity peptide-functionalized label-free electrochemical biosensor for the highly sensitive and selective detection of CRP. Throughout biopanning with random peptide libraries, high affinity peptides for CRP was successfully identified, and then a series of synthetic peptide receptor, of which C-terminus was incorporated to gold binding peptide (GBP) as an anchoring motif was covalently immobilized onto gold nanoparticle (AuNPs) tethered polydopamine (PDA)‒black phosphorus (BP) (AuNPs@BP@PDA) nanocomposite electrode. Interaction between the CRP-binding peptide and CRP was confirmed via enzyme-linked immunosorbent assay along with various physicochemical and electrochemical analyses. Under the optimized experimental conditions, the proposed peptide-based biosensor detects CRP in the range of 0-0.036 μg/mL with a detection limit (LOD) of 0.7 ng/mL. The developed sensor effectively detects CRP in the real samples of serum and plasma of Crohn's disease patients. Thus, the fabricated peptide-based biosensor has potential applications in clinical diagnosis and medical applications.
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Affiliation(s)
- Hyo Jeong Yang
- Basic Research Laboratory, Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Min Woo Kim
- Department of Chemistry, Research Institute of Chem-Bio Diagnostic Technology, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Chikkili Venkateswara Raju
- Basic Research Laboratory, Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chae Hwan Cho
- Basic Research Laboratory, Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Tae Jung Park
- Department of Chemistry, Research Institute of Chem-Bio Diagnostic Technology, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
| | - Jong Pil Park
- Basic Research Laboratory, Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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5
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Spiliotopoulos A, Maurer SK, Tsoumpeli MT, Bonfante JAF, Owen JP, Gough KC, Dreveny I. Next-Generation Phage Display to Identify Peptide Ligands of Deubiquitinases. Methods Mol Biol 2023; 2591:189-218. [PMID: 36350550 DOI: 10.1007/978-1-0716-2803-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phage display (PD) is a powerful method and has been extensively used to generate monoclonal antibodies and identify epitopes, mimotopes, and protein interactions. More recently, the combination of next-generation sequencing (NGS) with PD (NGPD) has revolutionized the capabilities of the method by creating large data sets of sequences from affinity selection-based approaches (biopanning) otherwise challenging to obtain. NGPD can monitor motif enrichment, allow tracking of the selection process over consecutive rounds, and highlight unspecific binders. To tackle the wealth of data obtained, bioinformatics tools have been developed that allow for identifying specific binding sequences (binders) that can then be validated. Here, we provide a detailed account of the use of NGPD experiments to identify ubiquitin-specific protease peptide ligands.
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Affiliation(s)
- Anastasios Spiliotopoulos
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
- Vertex Pharmaceuticals, Abingdon, Oxfordshire, UK
| | - Sigrun K Maurer
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Maria T Tsoumpeli
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
| | - Juan A F Bonfante
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
| | - Jonathan P Owen
- ADAS UK, School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington, Loughborough, Leicestershire, UK
| | - Kevin C Gough
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK.
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK.
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6
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Nur A, Schubert M, Lai JY, Hust M, Choong YS, Isa WYHW, Lim TS. Antibody Phage Display. Methods Mol Biol 2023; 2702:3-12. [PMID: 37679612 DOI: 10.1007/978-1-0716-3381-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The application of antibodies has transcended across many areas of work but mainly as a research tool, for diagnostic and for therapeutic applications. Antibodies are immunoproteins from vertebrates that have the unique property of specifically binding foreign molecules and distinguish target antigens. This property allows antibodies to effectively protect the host from infections. Apart from the hybridoma technology using transgenic animals, antibody phage display is commonly considered the gold standard technique for the isolation of human monoclonal antibodies. The concept of antibody phage display surrounds the ability to display antibody fragments on the surface of M13 bacteriophage particles with the corresponding gene packaged within the particle. A repetitive in vitro affinity based selection process permits the enrichment of target specific binders. This process of recombinant human monoclonal antibody generation also enables additional engineering for various applications. This makes phage display an indispensable technique for antibody development and engineering activities.
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Affiliation(s)
- Alia Nur
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Wan Yus Haniff Wan Isa
- School of Medical Sciences, Department of Medicine, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
- Analytical Biochemistry Research Center, Universiti Sains Malaysia, Penang, Malaysia.
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7
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Li X, Jones KS, Acca FE, Chapados CD, Driscoll HA, Fuller EP, Mendez QM, Mirando G, Weiner MP, Ferguson MR. Epivolve: A Protocol for Site-Directed Antibodies. Methods Mol Biol 2023; 2702:587-601. [PMID: 37679640 PMCID: PMC10568616 DOI: 10.1007/978-1-0716-3381-6_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Researchers can often successfully generate antibodies to predicted epitopes. Especially when the epitopes are on the surface of a protein or in a hydrophilic loop. But it is difficult to direct recombinant antibodies to bind either to- or near a specific amino acid on a protein or peptide. We have developed a unique immune-targeting strategy, that we call "Epivolve," that enables us to make site-specific antibodies (Abs). Epivolve technology leverages a highly immunogenic modified amino acid that acts as a "pseudo-hapten" immuno-target and takes advantage of Ab affinity maturation technologies to make high-affinity site-specific antibodies. Epivolve functions by the evolution of an Ab paratope to either synonymous or especially non-synonymous amino acid (aa) binding. Here we describe the use of Epivolve technology in phage display and the protocols for developing site-specific antibodies.
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Affiliation(s)
| | | | | | | | | | - Emily P Fuller
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
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8
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Tsoumpeli MT, Varghese A, Owen JP, Maddison BC, Daly JM, Gough KC. Mapping Polyclonal Antibody Responses to Infection Using Next-Generation Phage Display. Methods Mol Biol 2023; 2702:467-487. [PMID: 37679636 DOI: 10.1007/978-1-0716-3381-6_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Peptide phage display has historically been used to epitope map monoclonal antibodies. More recently, by coupling this method with next-generation sequencing (so-called next-generation phage display, NGPD) to mass screen peptide binding events, the methodology has been successfully applied to map polyclonal antibody responses to infection. This leads to the identification of panels of mimotopes that represent the pathogen's epitopes. One potential advantage of using such an approach is that the mimotopes can represent not just linear epitopes but also conformational epitopes or those produced from post-translational modifications of proteins or from other non-protein macromolecules. The mapping of such complex immunological recognition of a pathogen can inform novel serological assay development and vaccine design. Here, we provide detailed methods for the application of NGPD to identify panels of mimotopes that are recognized specifically by antibodies from individuals with a particular infection.
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Affiliation(s)
- Maria T Tsoumpeli
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - Anitha Varghese
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | | | | | - Janet M Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - Kevin C Gough
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK.
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9
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Lim TS, Ch'ng ACW, Song BPC, Lai JY. Streptavidin-Coated Solid-Phase Extraction (SPE) Tips for Antibody Phage Display Biopanning. Methods Mol Biol 2023; 2702:275-290. [PMID: 37679625 DOI: 10.1007/978-1-0716-3381-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Phage display is a technique that allows the presentation of unique proteins on the surface of bacteriophages. The phage particles are usually screened via repetitive rounds of antigen-guided selection and phage amplification. The main advantage of this approach lies in the physical linkage between phenotype and genotype. This feature allows the isolation of single unique clones from a panning campaign consisting of a highly diverse population of clones. Due to the high-throughput nature of this technique, different approaches have been developed to assist phage display selections. One of which involves utilizing a streptavidin-coated solid-phase extraction (SPE) tip that is mounted to an electronically controlled motorized multichannel pipette. In this chapter, we will entail the procedures involved in the adaptation of a commercial SPE tip (MSIA™ streptavidin D.A.R.T's®) as the solid phase. This protocol is an updated version of a previous protocol with some minor refinements.
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Affiliation(s)
- Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
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10
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Zhang X, Dong S, Huang Y, Shi H, Chen X, Wang Y, Li Y, Cao D, Wang L. A scFv phage targeting the C. albicans cell wall screened from a bacteriophage-based library of induced immune protection in mice. Infect Genet Evol 2022; 102:105303. [PMID: 35577227 DOI: 10.1016/j.meegid.2022.105303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
C. albicans is the most prevalent opportunistic fungal and can cause life-threatening systemic infections under certain circumstances. The inefficiency and resistance of traditional therapy make the development of novel techniques indispensable. The main components, proteins and glycoproteins, of the C. albicans cell wall are highly immunogenic and very different from those of the host, making it an ideal source of targets for antifungal drug development. This study aimed to screen and identify specific peptides that bind to the C. albicans cell wall using a phage-display peptide library, and to develop a peptide-based therapy targeted to C. albicans. After four rounds of screening, JC-1 ScFv was found to bind to the C. albicans cell wall specifically, inhibit C. albicans growth and viability in vitro, and protect mice from C. albicans infection in vivo. Further study showed that JC-1 could provoke an immune response in C. albicans-infected mice. These results indicated that JC-1 ScFv screened from a phage-display peptide library had the potential to be developed as a vector for targeting C. albicans.
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Affiliation(s)
- Xintong Zhang
- Institute of Cytology and Genetics, School of Life Sciences, Northeast Normal University, Changchun City, Jilin Province 130024, PR China.; The Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun City, Jilin Province 130021, PR China
| | - Shuai Dong
- Institute of Cytology and Genetics, School of Life Sciences, Northeast Normal University, Changchun City, Jilin Province 130024, PR China.; Department of obstetrics and gynecology, The First Hospital of Jilin University, Changchun City, Jilin Province 130021, PR China
| | - Yuanyuan Huang
- Department of pediatric outpatient, First Hospital of Jilin University, Changchun City, Jilin Province 130021, PR China
| | - Hongxi Shi
- Institute of Cytology and Genetics, School of Life Sciences, Northeast Normal University, Changchun City, Jilin Province 130024, PR China
| | - Xi Chen
- Institute of Cytology and Genetics, School of Life Sciences, Northeast Normal University, Changchun City, Jilin Province 130024, PR China
| | - Yicun Wang
- Institute of Cytology and Genetics, School of Life Sciences, Northeast Normal University, Changchun City, Jilin Province 130024, PR China
| | - Yan Li
- Institute of Cytology and Genetics, School of Life Sciences, Northeast Normal University, Changchun City, Jilin Province 130024, PR China
| | - Donghui Cao
- Division of Clinical Research, First Hospital of Jilin University, Changchun City, Jilin Province 130021, PR China..
| | - Li Wang
- Institute of Cytology and Genetics, School of Life Sciences, Northeast Normal University, Changchun City, Jilin Province 130024, PR China..
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11
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Kim JH, Shin JH, Cho CH, Hwang J, Kweon DH, Park TJ, Choi CH, Park JP. Dual synergistic response for the electrochemical detection of H1N1 virus and viral proteins using high affinity peptide receptors. Talanta 2022; 248:123613. [PMID: 35653962 DOI: 10.1016/j.talanta.2022.123613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/19/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022]
Abstract
Identifying alternatives to antibodies as bioreceptors to test samples feasibly is crucial for developing next-generation in vitro diagnostic methods. Here, we aimed to devise an analytical method for detecting H1N1 viral proteins (hemagglutinin [HA] and neuraminidase [NA]) as well as the complete H1N1 virus with high sensitivity and selectivity. By applying biopanning of M13 peptide libraries, high affinity peptides specific for HA or NA were successfully identified. After selection, three different synthetic peptides that incorporated gold-binding motifs were designed and chemically synthesized on the basis of the original sequence identified phage display technique with or without two repeat. Their binding interactions were characterized by enzyme-linked immunosorbent assay (ELISA), square wave voltammetry (SWV), Time of flight-secondary ion mass spectroscopy (ToF-SIMS) and X-ray photoelectron spectroscopy (XPS). The binding constants (Kd) of HA BP1, HA BP2 and NA BP1 peptides were found to be 169.72 nM, 70.02 nM and 224.49 nM for HA or NA proteins by electrochemical measurements (SWV). The single use of HA BP2 peptide enabled the detection of either H1N1 viral proteins or the actual H1N1 virus, while NA BP1 peptide exhibited lower binding for real H1N1 virus particles. Moreover, the use of both HA BP1 and BP2 as a divalent capturing reagent improved sensor performance as well as the strength of the electrochemical signal, thereby exhibiting a dual synergistic effect for the electrochemical detection of H1N1 antigens with satisfactory specificity and sensitivity (limit of detection of 1.52 PFU/mL).
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12
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Zuromski J, Kurtis J, Raj DK. Protocol for Differential Biopanning of P. falciparum Phage Display cDNA Library to Identify Parasite Targets of Protective Antibodies. Methods Mol Biol 2022; 2470:359-366. [PMID: 35881358 DOI: 10.1007/978-1-0716-2189-9_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Malaria remains a significant global health burden, killing hundreds of thousands of children annually (WHO, The world malaria report. WHO, Geneva, 2019). Despite decades of effort, no broadly effective vaccine exists. Differential screening of parasite phage display libraries is a promising approach to identify the targets of human antibodies expressed by resistant but not by susceptible individuals (Raj et al., Nature, 582, 104-108, 2020; Science, 344, 871-877, 2014). Our whole proteome differential screening (WPDS) approach consists of positive selection to capture phage that bind antibodies expressed by malaria-resistant individuals, followed by negative selection to remove phage that bind antibodies expressed by malaria-susceptible individuals, and amplification of differentially recognized clones.
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Affiliation(s)
- Jenna Zuromski
- Department of Pathology and Laboratory Medicine, Brown University Medical School, Providence, RI, USA
| | - Jonathan Kurtis
- Department of Pathology and Laboratory Medicine, Brown University Medical School, Providence, RI, USA
| | - Dipak Kumar Raj
- Department of Pathology and Laboratory Medicine, Brown University Medical School, Providence, RI, USA.
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13
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Panton RA, Stern LA. Ligand Selection by Combination of Recombinant and Cell Panning Selection Techniques. Methods Mol Biol 2022; 2491:217-233. [PMID: 35482193 DOI: 10.1007/978-1-0716-2285-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
High-throughput protein selection methods are a cornerstone for protein engineering and pharmaceutical development. Traditional high-throughput selection strategies rely largely on recombinant antigen to generate target specificity. Though effective, this selection strategy can be limited by soluble target quality, particularly in the case of recombinant extracellular domains of transmembrane proteins. Recent advances in cell-based selection techniques provide new opportunities for improving the outcomes of ligand selection campaigns but can introduce technical challenges in maintaining antigen specificity due to the heterogeneity of biomacromolecule expression on the mammalian cell surface. Here, we describe a combination technique using recombinant antigen to "train" library target specificity followed by cell panning selections to ensure that isolated ligands bind cell-expressed target, as well as a facile microscopy technique for assessing target specificity on a clonal basis without the need to produce soluble ligand.
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Affiliation(s)
- Rojhae A Panton
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Lawrence A Stern
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
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14
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Krohl PJ, Spangler JB. A Hybrid Adherent/Suspension Cell-Based Selection Strategy for Discovery of Antibodies Targeting Membrane Proteins. Methods Mol Biol 2022; 2491:195-216. [PMID: 35482192 PMCID: PMC9667817 DOI: 10.1007/978-1-0716-2285-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Membrane proteins are favored drug targets and antibody therapeutics represent the fastest-growing category of pharmaceuticals. However, there remains a need for rapid and effective approaches for the discovery of antibodies that recognize membrane proteins to develop a robust clinical pipeline for targeted therapeutics. The challenges associated with recombinant expression of membrane proteins make whole cell screening techniques desirable, as these strategies allow presentation of the target membrane proteins in their native conformations. Here, we describe a workflow that employs both adherent cell-based and suspension cell-based whole cell panning methodologies to enrich for specific binders within a yeast-displayed antibody library. The first round of selection consists of an adherent cell-based approach, wherein a diverse library is panned over target-expressing mammalian cell monolayers in order to debulk the naïve library. Subsequent rounds involve the use of suspension cell-based approaches, facilitated with magnetic-activated cell sorting (MACS) or fluorescence-activated cell sorting (FACS), to achieve further library enrichment. Finally, we describe a high-throughput approach to screen target binding and specificity of individual clones isolated from selection campaigns.
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Affiliation(s)
- Patrick J Krohl
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jamie B Spangler
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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15
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Umlauf BJ, Kuo JS, Shusta EV. Identification of Brain ECM Binding Variable Lymphocyte Receptors Using Yeast Surface Display. Methods Mol Biol 2022; 2491:235-248. [PMID: 35482194 DOI: 10.1007/978-1-0716-2285-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Extracellular matrix (ECM) is a rich mixture of proteins and glycans secreted by cells. This includes typical ECM structures such as collagen and heparin as well as glycosylated, secreted proteins such as growth factors and peptidases. Certain components of ECM are ubiquitous among all tissue; however, each biological tissue also displays unique variations that can be identified using biopanning techniques. Here we describe using a variable lymphocyte receptor (VLR) yeast surface display library to identify selective binders to brain ECM by combining ECM biopanning with a rapid ELISA-based screen using clonal VLRs isolated directly from the yeast surface. Finally, potential ECM-binding candidates can be verified by immunostaining murine brain sections with VLRs released from the yeast surface. These methods provide a framework for the identification of tissue-selective ECM-binding VLRs using yeast surface display techniques and could easily be adapted for other binding scaffolds or ECM from other tissues.
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Affiliation(s)
- Benjamin J Umlauf
- Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
- Mulva Clinic for the Neurosciences, The University of Texas at Austin, Austin, TX, USA.
| | - John S Kuo
- Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Mulva Clinic for the Neurosciences, The University of Texas at Austin, Austin, TX, USA
| | - Eric V Shusta
- Departments of Chemical and Biological Engineering and Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA
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16
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Bozovičar K, Molek P, Bizjan BJ, Bratkovič T. Ligand Selection for Affinity Chromatography Using Phage Display. Methods Mol Biol 2022; 2466:159-185. [PMID: 35585318 DOI: 10.1007/978-1-0716-2176-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Phage display coupled with in vitro affinity selection to mimic evolutionary principles has propelled the discovery of specific binding peptides and proteins for diverse applications, including affinity chromatography. By tailoring screening conditions, ligands with desired predefined properties, such as pH- or ion strength-responsive binding, can be identified from phage-displayed combinatorial peptide libraries. Initial hit peptides can be further optimized through directed evolution by focused mutagenesis and rescreening. Quantitative analysis of eluted binders with next-generation sequencing (NGS) assists in reducing enrichment bias and simplifies picking the most promising ligand candidate(s) through enrichment ranking. We describe, in detail, procedures of ligand selection for affinity chromatography using peptide phage display library screening, focused mutagenesis, and NGS. Furthermore, we outline the subsequent workflow for ligand characterization and affinity column construction.
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Affiliation(s)
- Krištof Bozovičar
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Peter Molek
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Barbara Jenko Bizjan
- Clinical Institute of Special Laboratory Diagnostics, University Children's Hospital, University Medical Center, Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia.
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17
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He B, Yang S, Long J, Chen X, Zhang Q, Gao H, Chen H, Huang J. TUPDB: Target-Unrelated Peptide Data Bank. Interdiscip Sci 2021; 13:426-432. [PMID: 33993461 DOI: 10.1007/s12539-021-00436-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/29/2022]
Abstract
The isolation of target-unrelated peptides (TUPs) through biopanning remains as a major problem of phage display selection experiments. These TUPs do not have any actual affinity toward targets of interest, which tend to be mistakenly identified as target-binding peptides. Therefore, an information portal for storing TUP data is urgently needed. Here, we present a TUP data bank (TUPDB), which is a comprehensive, manually curated database of approximately 73 experimentally verified TUPs and 1963 potential TUPs collected from TUPScan, the BDB database, and public research articles. The TUPScan tool has been integrated in TUPDB to facilitate TUP analysis. We believe that TUPDB can help identify and remove TUPs in future reports in the biopanning community. The database is of great importance to improving the quality of phage display-based epitope mapping and promoting the development of vaccines, diagnostics, and therapeutics. The TUPDB database is available at http://i.uestc.edu.cn/tupdb .
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Affiliation(s)
- Bifang He
- School of Medicine, Guizhou University, Guiyang, 550025, China. .,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, China.
| | - Shanshan Yang
- School of Medicine, Guizhou University, Guiyang, 550025, China
| | - Jinjin Long
- School of Medicine, Guizhou University, Guiyang, 550025, China
| | - Xue Chen
- School of Medicine, Guizhou University, Guiyang, 550025, China
| | - Qianyue Zhang
- School of Medicine, Guizhou University, Guiyang, 550025, China
| | - Hui Gao
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Heng Chen
- School of Medicine, Guizhou University, Guiyang, 550025, China.
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, China.
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18
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Qian J, Han Y, Guo J, Zhang J, Hou Y, Song Y, Lu C, Li H. Semi-starvation fluctuation driving rapid partial denitrification granular sludge cultivation in situ by microorganism exudate metabolites feedbacks. Environ Res 2021; 196:110938. [PMID: 33647304 DOI: 10.1016/j.envres.2021.110938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
In this study, semi-starvation fluctuation driving PD granules cultivation in situ by microorganism exudate metabolites feedbacks was firstly investigated. The PD granules of high nitrite production were cultivated with an excellent mean nitrate-to-nitrite transformation rate (NTR) of 56.39% in just 30 days. The granules size was improved from the initial size of 0.09 ± 0.01 mm in diameter to a size above 2 mm when the extracellular polymeric substance (EPS) content increased from 80.21 ± 10.20 mg/g MLVSS to 777.00 ± 22.13 mg/g MLVSS. Acyl-homoserine lactone signals (AHLs) ultimately increased ten-fold more than the initially through 30 days of cultivation. Meanwhile, Thauera had been identified as the main function bacteria of PD, which enriched from 0.47% to 10.67%. Results demonstrated that AHLs, EPS, PD bacteria and the PD granules cultivation were closely associated. Semi-starvation fluctuation produced oligotrophic stress on bacterial community, a part of bacteria would be eliminated on starvation for oligotrophic stress and AHLs of bacteria regarded as distress signals resulted in the rapid formation of PD granules. A mechanism for PD granular cultivation with semi-starvation fluctuation was proposed from the aspect of oligotrophic stress. A better strategy for rapid PD granules cultivation was obtained and it could be useful for the mainstream granule-based PD combined with the anammox process application in the future.
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Affiliation(s)
- Jiuzhou Qian
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China
| | - Yi Han
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China.
| | - Jianbo Guo
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China
| | - Jianbing Zhang
- Tianjin Municipal Engineering Design and Research Institute, Tianjin, 300051, China
| | - Yanan Hou
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China
| | - Yuanyuan Song
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China
| | - Caicai Lu
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China
| | - Haibo Li
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China
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19
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Raynes JM, Tay ML, By SH, Steemson JD, Moreland NJ. Isolation of Monoclonal Antibodies to Group A Streptococcus Antigens Using Phage Display. Methods Mol Biol 2020; 2136:255-68. [PMID: 32430827 DOI: 10.1007/978-1-0716-0467-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
High-affinity monoclonal antibodies are valuable tools for studying the humoral immune response to Group A Streptococcus (GAS) antigens. This protocol describes a method for the selection of monoclonal antibody fragments that bind to GAS antigens using either naïve or immune repertoires displayed on the surface of M13 bacteriophage. Clones that specifically bind to GAS antigens are enriched for during the biopanning process, in which antibody-phage clones bind to an immobilized GAS antigen and are then washed, eluted, and amplified for subsequent rounds of selection. After the final round of biopanning, individual clones are screened by phage enzyme-linked immunosorbent assay (ELISA), and unique clones are identified by DNA fingerprinting and sequencing. The isolated monoclonal antibodies can be used to explore antibody-antigen interactions in molecular detail and provide insight into the protective mechanisms from GAS infection.
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20
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Yuan AQ. Isolation of Antibody Binders to MISIIR from a Phage Display Library by Sorting. Methods Mol Biol 2020; 2108:147-57. [PMID: 31939178 DOI: 10.1007/978-1-0716-0247-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cell surface antigens represent the most common targets for antibody-based cancer therapy. Isolation of lead antibodies to these membrane targets from antibody repertoires, such as immunized or naïve phage display libraries, has been a challenging task, which is an outstanding issue when soluble portion of the target(s) is not available, and/or a naïve phage display library is used. Common cell-based panning methods often encounter numerous difficulties, including high background and loss of cells during repeated washes. Here we described a novel FACS sorter-based protocol to isolate single-chain Fv molecules specific for defined antigen MSIIR expressed on stably transformed mammalian cells, and screening of unique binders to the tumor target.
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21
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Kumada Y, Hasegawa Y, Horiuchi JI. Efficient and robust isolation of rabbit scFv antibodies using antigen-coupled multilamellar vesicles. J Biosci Bioeng 2020; 131:299-304. [PMID: 33221176 DOI: 10.1016/j.jbiosc.2020.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/07/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022]
Abstract
We demonstrated an efficient screening method for rabbit scFv antibodies using antigen-coupled multi-lamellar vesicles (Ag-MLVs) as solid supports. Model phages displaying mouse anti-human IgG scFv at a probability of 10-4-10-5% were successfully isolated by Ag-MLVs after 3 or less rounds of biopanning, whereas they could not be isolated using conventional antigen-coated immunotubes. This screening method was applied to isolate rabbit antigen-specific scFvs from 4 different phage libraries. Biopanning procedures employing Ag-MLVs yielded positive phages in the 3rd round or earlier, and specific antigen-binding of scFvs was observed after the 1st round in two biopanning selections. The dissociation rate constants (koff) of isolated scFv clones tended to decrease with progressing biopanning rounds. The average dissociation constants (KD) of the isolated scFvs ranged between 1.7 and 87 nM, whereas the lowest KD of 12 pM was recorded for anti-CRP scFv. Comprehensive characterization of 355 different clones of the isolated rabbit scFvs presented a relatively low isoelectric point, and most of these were more thermo-stable than the conventional mouse scFvs, based on their instability and aliphatic indices. These results clearly indicate the advantages and potential of a combination of rabbit scFv-displaying phage library and biopanning using Ag-MLVs for antibody discovery. In addition, the results obtained in this study support the suitability of rabbit scFvs for several applications, including the development of diagnostic agents and affinity ligands for molecular diagnosis and bioseparation.
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Affiliation(s)
- Yoichi Kumada
- Department of Functional Chemistry and Engineering, Kyoto Institute of Technology, 1 Matsugasaki-Hashikami-Cho, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Yuya Hasegawa
- Department of Functional Chemistry and Engineering, Kyoto Institute of Technology, 1 Matsugasaki-Hashikami-Cho, Sakyo-ku, Kyoto 606-8585, Japan
| | - Jun-Ichi Horiuchi
- Department of Functional Chemistry and Engineering, Kyoto Institute of Technology, 1 Matsugasaki-Hashikami-Cho, Sakyo-ku, Kyoto 606-8585, Japan
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22
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Jin H, Gao X, Xiao L, He H, Cheng S, Zhang C, Hou Y, Song F, Su X, Gao Q, Lu Z, Yang R, Song X, Yang J, Duan W, Hou Y. Screening and identification of a specific peptide binding to breast cancer cells from a phage-displayed peptide library. Biotechnol Lett 2020; 43:153-164. [PMID: 33145670 DOI: 10.1007/s10529-020-03044-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Breast cancer is a popular fatal malignant tumor for women with high of rates incidence and mortality. Development of the new approaches for breast cancer targeted diagnosis and chemotherapy is emergently needed by the current clinical practice, the important first step is finding a breast cancer specifically binding molecule or fragment as early clinical indicators. RESULTS By a phage-displayed peptide library, a 12-mer peptide, CSB1 was screened out using MCF-7 cells as the target. The consequently results under immunofluorescence and laser scanning confocal microscope (LSCM) indicated that CSB1 bound MCF-7 cells and breast cancer tissues specifically and sensitively with high affinity. Bioinformatics analysis suggested that the peptide CSB1 targets the 5-Lipoxygenase-Activating Protein (FLAP), which has been implicated in breast cancer progression and prognosis. CONCLUSIONS The peptide, CSB1 is of the potential as a candidate to be used for developing the new approaches of molecular imaging detection and targeting chemotherapy of breast cancer in the future.
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Affiliation(s)
- Huijuan Jin
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Xiaojie Gao
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Li Xiao
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Huimin He
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Sinan Cheng
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Caixia Zhang
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Yifan Hou
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Fengying Song
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Xiaorong Su
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Qian Gao
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Zheng Lu
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Ruina Yang
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Xigui Song
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China
| | - Jin Yang
- The College of Life, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Wei Duan
- School of Medicine, Deakin University, Waurn Ponds, VIC, 3216, Australia
| | - Yingchun Hou
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, 710119, Shaanxi, China.
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23
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Wieczorek L, Peachman K, Steers N, Schoen J, Rao M, Polonis V, Rao V. Selection and immune recognition of HIV-1 MPER mimotopes. Virology 2020; 550:99-108. [PMID: 32980676 DOI: 10.1016/j.virol.2020.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/20/2020] [Accepted: 06/26/2020] [Indexed: 11/20/2022]
Abstract
The membrane proximal external region (MPER) of HIV-1 gp41 is targeted by several neutralizing antibodies (NAbs) and is of interest for vaccine design. In this study, we identified novel MPER peptide mimotopes and evaluated their reactivity with HIV + plasma antibodies to characterize the diversity of the immune responses to MPER during natural infection. We utilized phage display technology to generate novel mimotopes that fit antigen-binding sites of MPER NAbs 4E10, 2F5 and Z13. Plasma antibodies from 10 HIV + patients were mapped by phage immunoprecipitation, to identify unique patient MPER binding profiles that were distinct from, and overlapping with, those of MPER NAbs. 4E10 mimotope binding profiles correlated with plasma neutralization of HIV-2/HIV-1 MPER chimeric virus, and with overall plasma neutralization breadth and potency. When administered as vaccines, 4E10 mimotopes elicited low titer NAb responses in mice. HIV mimotopes may be useful for detailed analysis of plasma antibody specificity.
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24
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Stellwagen SD, Sarkes DA, Adams BL, Hunt MA, Renberg RL, Hurley MM, Stratis-Cullum DN. The next generation of biopanning: next gen sequencing improves analysis of bacterial display libraries. BMC Biotechnol 2019; 19:100. [PMID: 31864334 PMCID: PMC6925417 DOI: 10.1186/s12896-019-0577-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/12/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Bacterial surface display libraries are a popular tool for novel ligand discovery due to their ease of manipulation and rapid growth rates. These libraries typically express a scaffold protein embedded within the outer membrane with a short, surface-exposed peptide that is either terminal or is incorporated into an outer loop, and can therefore interact with and bind to substrates of interest. RESULTS In this study, we employed a novel bacterial peptide display library which incorporates short 15-mer peptides on the surface of E. coli, co-expressed with the inducible red fluorescent protein DsRed in the cytosol, to investigate population diversity over two rounds of biopanning. The naive library was used in panning trials to select for binding affinity against 3D printing plastic coupons made from polylactic acid (PLA). Resulting libraries were then deep-sequenced using next generation sequencing (NGS) to investigate selection and diversity. CONCLUSIONS We demonstrated enrichment for PLA binding versus a sapphire control surface, analyzed population composition, and compared sorting rounds using a binding assay and fluorescence microscopy. The capability to produce and describe display libraries through NGS across rounds of selection allows a deeper understanding of population dynamics that can be better directed towards peptide discovery.
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Affiliation(s)
- Sarah D. Stellwagen
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, 21250 MD USA
| | - Deborah A. Sarkes
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
| | - Bryn L. Adams
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
| | - Mia A. Hunt
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
- General Technical Services, Suite 301, 1451 Route 34 South, Wall Township, 07727 NJ USA
| | - Rebecca L. Renberg
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
- General Technical Services, Suite 301, 1451 Route 34 South, Wall Township, 07727 NJ USA
| | - Margaret M. Hurley
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
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25
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Nakazawa H, Umetsu M, Hirose T, Hattori T, Kumagai I. Identification of Indium Tin Oxide Nanoparticle-Binding Peptides via Phage Display and Biopanning Under Various Buffer Conditions. Protein Pept Lett 2019; 27:557-566. [PMID: 31729292 DOI: 10.2174/0929866526666191113151934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/04/2019] [Accepted: 10/08/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND By recent advances in phage-display approaches, many oligopeptides exhibiting binding affinities for metal oxides have been identified. Indium tin oxide is one of the most widely used conductive oxides, because it has a large band gap of 3.7-4.0 eV. In recent years, there have been reports about several ITO-based biosensors. Development of an ITO binding interface for the clustering of sensor proteins without complex bioconjugates is required. OBJECTIVE In this article, we aimed to identify peptides that bind to indium tin oxide nanoparticles via different binding mechanisms. METHODS Indium tin oxide nanoparticles binding peptide ware selected using phage display and biopanning against indium tin oxide, under five different buffer conditions and these peptides characterized about binding affinity and specificity. RESULTS Three types of indium tin oxide nanoparticles-binding peptides were selected from 10 types of peptide candidates identified in phage display and biopanning. These included ITOBP8, which had an acidic isoelectric point, and was identified when a buffer containing guanidine was used, and ITOBP6 and ITOBP7, which contained a His-His-Lys sequence at their N-termini, and were identified when a highly concentrated phosphate elution buffer with a low ionic strength was used. Among these peptides, ITOBP6 exhibited the strongest indium tin oxide nanoparticlesbinding affinity (dissociation constant, 585 nmol/L; amount of protein bound at saturation, 17.5 nmol/m 2 - particles). CONCLUSION These results indicate that peptides with specific binding properties can be obtained through careful selection of the buffer conditions in which the biopanning procedure is performed.
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Affiliation(s)
- Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Tatsuya Hirose
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Takamitsu Hattori
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
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26
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Read J, Suphioglu C. Identification of a BACE1 Binding Peptide Candidate for the Prevention of Amyloid Beta in Alzheimer's Disease. Cell Physiol Biochem 2019; 53:413-428. [PMID: 31415717 DOI: 10.33594/000000147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/13/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND/AIMS Amyloid plaques, generated during the progression of Alzheimer's disease, cause major neurological deficits due to substantial cell toxicity and death. The underlying cause of plaque generation stems from cleavage of the amyloid precursor protein (APP) by β-secretase (BACE1). A resulting amyloid-β (Aβ) fragment forms aggregates to produce the main constituent of a plaque. METHODS Phage display and biopanning techniques were used to identify a 12-mer peptide that had a natural affinity for the BACE1 enzyme. The peptide was translated from phage DNA and synthetically produced. The peptide, at concentrations of 1nM, 10nM and 100nM, was used to confirm binding by direct assay. Non-specific binding to BACE2, renin and cathepsin D was tested by direct binding assay. A BACE1 activity assay was used to determine the peptide effect on cleavage of an APP substrate. Treatment of SY5Y cells with the peptide was used to determine toxicity and prevention of Aβ40 and Aβ42 production. RESULTS After identification and synthetic production, the peptide exhibited a strong affinity for BACE1 at nanomolar concentrations in the direct assay. In case of non-specific binding to homologous BACE2, renin and cathepsin D, the peptide showed minor binding but was nullified when in solution with BACE1. The peptide addition to a BACE1 activity assay was able to significantly reduce the amount of substrate cleavage. SY5Y cells, when treated with the peptide, did not show any detrimental morphological changes while being able to reduce the production of natural Aβ40 and Aβ42. Even under stressed conditions (H2O2 treatment) where the Aβ production was higher, the peptide was still able to significantly reduce the effect of BACE1 while not effecting cell viability. CONCLUSION The identified peptide exhibited strong binding to BACE1 in vitro and was able to reduce production of Aβ, suggesting a favourable BACE1 inhibitor for future refining and characterisation.
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Affiliation(s)
- Justin Read
- NeuroAllergy Research Laboratory (NARL), School of Life and Environmental Science, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds, VIC, Australia.,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Health Science Centre, Calgary, AB, Canada
| | - Cenk Suphioglu
- NeuroAllergy Research Laboratory (NARL), School of Life and Environmental Science, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds, VIC, Australia,
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Jalilzadeh-Razin S, Mantegi M, Tohidkia MR, Pazhang Y, Pourseif MM, Barar J, Omidi Y. Phage antibody library screening for the selection of novel high-affinity human single-chain variable fragment against gastrin receptor: an in silico and in vitro study. ACTA ACUST UNITED AC 2019; 27:21-34. [PMID: 30607886 DOI: 10.1007/s40199-018-0233-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND As a membrane G protein coupled receptors (GPCRs) family, gastrin/cholecystokinin-2 receptor (CCK2R) plays a key role in the initiation and development of gastric cancer. OBJECTIVES Targeting CCK2R by immunotherapeutics such as single-chain variable fragments (scFvs) may provide an effective treatment modality against gastric cancer. Thus, the main objective of this study was to isolate scFvs specific to CCK2R. METHODS To isolate scFvs specific to the CCK2R, we capitalized on a semi-synthetic diverse phage antibody library (PAL) and a solution-phase biopanning process. The library was panned against a biotinylated peptide of the second extracellular loop (ECL2) of CCK2R. After four rounds of biopanning, the selected soluble scFv clones were screened by enzyme-linked immunosorbent assay (ELISA) and examined for specific binding to the peptide. The selected scFvs were purified using immobilized metal affinity chromatography (IMAC). The binding affinity and specificity of the scFvs were examined by the surface plasmon resonance (SPR), immunoblotting and flow cytometry assays and molecular docking using ZDOCK v3.0.2. RESULTS Ten different scFvs were isolated, which displayed binding affinity ranging from 0.68 to 8.0 (nM). Immunoblotting and molecular docking analysis revealed that eight scFvs were able to detect the denatured form of CCK2R protein. Of the isolated scFvs, two scFvs showed high-binding affinity to the human gastric adenocarcinoma AGS cells. CONCLUSIONS Based on our findings, a couple of the selected scFvs showed markedly high-binding affinity to immobilized CCK2R peptide and CCK2R-overexpressing AGS cells. Therefore, these scFvs are proposed to serve as targeting and/or treatment agents in the diagnosis and immunotherapy of CCK2R-positive tumors. Graphical abstract ᅟ.
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Affiliation(s)
- Sepideh Jalilzadeh-Razin
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Malihe Mantegi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Islamic Azad University of Urmia, Urmia, Iran
| | - Mohammad R Tohidkia
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Yaghub Pazhang
- Department of Biochemistry, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Mohammad M Pourseif
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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Settele F, Zwarg M, Fiedler S, Koscheinz D, Bosse-Doenecke E. Construction and Selection of Affilin ® Phage Display Libraries. Methods Mol Biol 2018; 1701:205-238. [PMID: 29116507 DOI: 10.1007/978-1-4939-7447-4_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Affilin® molecules represent a new class of so-called scaffold proteins. The concept of scaffold proteins is to use stable and versatile protein structures which can be endowed with de novo binding properties and specificities by introducing mutations in surface exposed amino acid residues. Complex variations and combinations are generated by genetic methods of randomization resulting in large cDNA libraries. The selection for candidates binding to a desired target can be executed by display methods, especially the very robust and flexible phage display. Here, we describe the construction of ubiquitin based Affilin® phage display libraries and their use in biopanning experiments for the identification of novel protein ligands.
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Affiliation(s)
- Florian Settele
- Navigo Proteins GmbH, Heinrich-Damerow-Straße 1, 06120, Halle (Saale), Germany
| | - Madlen Zwarg
- Navigo Proteins GmbH, Heinrich-Damerow-Straße 1, 06120, Halle (Saale), Germany
| | - Sebastian Fiedler
- Navigo Proteins GmbH, Heinrich-Damerow-Straße 1, 06120, Halle (Saale), Germany
| | - Daniel Koscheinz
- Navigo Proteins GmbH, Heinrich-Damerow-Straße 1, 06120, Halle (Saale), Germany
| | - Eva Bosse-Doenecke
- Navigo Proteins GmbH, Heinrich-Damerow-Straße 1, 06120, Halle (Saale), Germany.
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29
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Gustafson HH, Olshefsky A, Sylvestre M, Sellers DL, Pun SH. Current state of in vivo panning technologies: Designing specificity and affinity into the future of drug targeting. Adv Drug Deliv Rev 2018; 130:39-49. [PMID: 29964079 DOI: 10.1016/j.addr.2018.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/24/2018] [Accepted: 06/22/2018] [Indexed: 11/20/2022]
Abstract
Targeting ligands are used in drug delivery to improve drug distribution to desired cells or tissues and to facilitate cellular entry. In vivo biopanning, whereby billions of potential ligand sequences are screened in biologically-relevant and complex conditions, is a powerful method for identification of novel target ligands. This tool has impacted drug delivery technologies and expanded our arsenal of therapeutics and diagnostics. Within this review we will discuss current in vivo panning technologies and ways that these technologies can be improved to advance next-generation drug delivery strategies.
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30
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Madrid R, de la Cruz S, García A, Martín R, González I, García T. Detection of Food Allergens by Phage-Displayed Produced Antibodies. Methods Mol Biol 2018; 1592:109-128. [PMID: 28315215 DOI: 10.1007/978-1-4939-6925-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Phage display is a powerful tool to produce recombinant antibodies against a given antigen without animal immunization. This technology employs libraries of recombinant bacteriophages that display billions of different functional antibody fragments on their surface. They are selected by panning in vitro against the target antigen in search for specific binders. In this chapter, we describe the selection of single chain variable fragment (scFv) antibodies to be used for detection of allergenic proteins from nuts in food products. The artificial libraries TomLinson I+J (MRC Laboratory of Molecular Biology and MRC Centre for Protein Engineering) were employed that resulted in successful phage-ELISA systems for detection of almond and walnut proteins in commercial food products.
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Affiliation(s)
- Raquel Madrid
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain
| | - Silvia de la Cruz
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain
| | - Aina García
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain
| | - Rosario Martín
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain
| | - Isabel González
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain
| | - Teresa García
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain.
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31
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Ayyar BV, Hearty S, O'Kennedy R. Decoding Selection Bias Imparted by Unpaired Cysteines: a Tug of War Between Expression and Affinity. Appl Biochem Biotechnol 2018; 185:778-85. [PMID: 29330770 DOI: 10.1007/s12010-017-2691-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/29/2017] [Indexed: 11/27/2022]
Abstract
In a recombinant antibody scFv format, the presence of an unpaired cysteine (Cys) is implicated in reduced soluble expression and inefficient presentation in phage display. Compared to other species, antibodies derived from rabbits are more likely to contain this unpaired Cys residue at position 80 (Cys80), when generated in a scFv format. In a screening campaign to isolate rabbit scFv against cardiac troponin I (cTnI), it was found that, a large proportion of isolated cTnI-specific clones contained unpaired Cys80. To analyze the factors that led to the selection of anti-cTnI Cys80 scFv, after five rounds of biopanning, the biopanning experiments were repeated with a Cys80 scFv (MG4Cys), its alanine variant (MG4Ala), and an irrelevant high expressing scFv control. It was found that the selection and subsequent enrichment of MG4Cys scFv was ousted by the superior expressing variant MG4Ala, indicating that the Cys80 scFv was selected primarily due to its affinity. It is evident that phage-based selection is influenced by specific sequence characteristics affecting the expression as well as the binding specificity and this needs to be taken into account for selection of optimal antibody derivatives.
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32
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Abstract
Size and variability often represent an obstacle in generating an effective antibody gene library for the detection of an abundant repertoire of antigens. Therefore, optimizing the construction of a large library is essential for the selection of high-affinity reactive fragments. Here, we report a highly efficient method for the construction of a human naïve antibody gene library for the selection of antibodies as single-chain variable fragments. This protocol is based on many different sets of oligonucleotide primers and multistep electroporation and ligation reactions.This advanced method can be adopted by any molecular biology laboratory to generate a naïve library for use in isolating single-chain fragment variables against specific targets.
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Affiliation(s)
- Michela Pasello
- CRS Development of Biomolecular Therapies, Experimental Oncology Lab, Rizzoli Orthopedic Institute, Bologna, Italy.
| | - Alessandra Mallano
- National Center For Global Health, The National Institute of Health, Rome, Italy
| | - Michela Flego
- National Center For Global Health, The National Institute of Health, Rome, Italy
| | - Silvia Zamboni
- Department of Neuroscience, The National Institute of Health, Rome, Italy
| | - Anna Maria Giudice
- CRS Development of Biomolecular Therapies, Experimental Oncology Lab, Rizzoli Orthopedic Institute, Bologna, Italy
| | - Katia Scotlandi
- CRS Development of Biomolecular Therapies, Experimental Oncology Lab, Rizzoli Orthopedic Institute, Bologna, Italy
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Takakusagi Y, Takakusagi K, Sugawara F, Sakaguchi K. Using the QCM Biosensor-Based T7 Phage Display Combined with Bioinformatics Analysis for Target Identification of Bioactive Small Molecule. Methods Mol Biol 2018; 1795:159-72. [PMID: 29846927 DOI: 10.1007/978-1-4939-7874-8_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Identification of target proteins that directly bind to bioactive small molecule is of great interest in terms of clarifying the mode of action of the small molecule as well as elucidating the biological phenomena at the molecular level. Of the experimental technologies available, T7 phage display allows comprehensive screening of small molecule-recognizing amino acid sequence from the peptide libraries displayed on the T7 phage capsid. Here, we describe the T7 phage display strategy that is combined with quartz-crystal microbalance (QCM) biosensor for affinity selection platform and bioinformatics analysis for small molecule-recognizing short peptides. This method dramatically enhances efficacy and throughput of the screening for small molecule-recognizing amino acid sequences without repeated rounds of selection. Subsequent execution of bioinformatics programs allows combinatorial and comprehensive target protein discovery of small molecules with its binding site, regardless of protein sample insolubility, instability, or inaccessibility of the fixed small molecules to internally located binding site on larger target proteins when conventional proteomics approaches are used.
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34
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Chin CF, Choong YS, Lim TS. Mass Spectrometry Immuno Assay (MSIA™) Streptavidin Disposable Automation Research Tips (D.A.R.T's ®) Antibody Phage Display Biopanning. Methods Mol Biol 2018; 1701:285-99. [PMID: 29116511 DOI: 10.1007/978-1-4939-7447-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Antibody phage display has been widely established as the method of choice to generate monoclonal antibodies with various efficacies post hybridoma technology. This technique is a popular method which takes precedence over ease of methodology, time- and cost-savings with comparable outcomes to conventional methods. Phage display technology manipulates the genome of M13 bacteriophage to display large diverse collection of antibodies that is capable of binding to various targets (nucleic acids, peptides, proteins, and carbohydrates). This subsequently leads to the discovery of target-related antibody binders. There have been several different approaches adapted for antibody phage display over the years. This chapter focuses on the semi-automated phage display antibody biopanning method utilizing the MSIA™ streptavidin D.A.R.T's® system. The system employs the use of electronic multichannel pipettes with predefined programs to carry out the panning process. The method should also be adaptable to larger liquid handling instrumentations for higher throughput.
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Grohmann C, Blank M. Upgrading Affinity Screening Experiments by Analysis of Next-Generation Sequencing Data. Methods Mol Biol 2018; 1701:411-24. [PMID: 29116519 DOI: 10.1007/978-1-4939-7447-4_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Computational analysis of next-generation sequencing data (NGS; also termed deep sequencing) enables the analysis of affinity screening procedures (or biopanning experiments) in an unprecedented depth and therewith improves the identification of relevant peptide or antibody ligands with desired binding or functional properties. Virtually any selection methodology employing the direct physical linkage of geno- and phenotype to select for desired properties can be leveraged by computational analysis. This article describes a concept how relevant ligands can be identified by harnessing NGS data. Thereby, the focus lays on improved ligand identification and describes how NGS data can be structured for single-round analysis as well as for comparative analysis of multiple selection rounds. Especially, the comparative analysis opens new avenues in the field of ligand identification. The concept of computational analysis is described at the example of the software tool "AptaAnalyzer TM ." This intuitive tool was developed for scientists without special computer skills and makes the computational approach accessible to a broad user range.
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Tan Y, Liu W, Zhu Z, Lang L, Wang J, Huang M, Zhang M, Yang C. Selection and identification of transferrin receptor-specific peptides as recognition probes for cancer cells. Anal Bioanal Chem 2017; 410:1071-1077. [PMID: 29046922 DOI: 10.1007/s00216-017-0664-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/16/2017] [Accepted: 09/20/2017] [Indexed: 01/09/2023]
Abstract
Since the transferrin receptor (CD71 or TFRC) is known to be highly expressed in numerous cancers, CD71 has become an attractive target in cancer research. Acquiring specific molecular probes for CD71, such as small molecular ligands, aptamers, peptides, or antibodies, is of great importance for cancer cell recognition and capture. In this work, we chose CD71 as the target for phage display, and after four rounds of positive selection and one round of negative selection, the specific phage library was enriched. After verification and sequence analysis, six peptides were identified to be able to bind to CD71 with high specificity. The specific recognition of the CD71-positive cells was confirmed by flow cytometry and confocal microscopy. Competition experiments demonstrated that peptide Y1 and transferrin (TF) were bound to distinct sites on CD71, indicating that peptide Y1 could replace TF as a potential probe for cell imaging and drug delivery, thus avoiding competition by endogenous TF and side effects. Graphical abstract Six peptides were successfully isolated using in vitro biopanning against CD71 with high specificity and affinity. Peptides Y1 and Y2 would be powerful tools in biosensors and biomedicine due to their unique properties.
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Affiliation(s)
- Yuyu Tan
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Wenli Liu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Zhi Zhu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China.
| | - Lijun Lang
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Junxia Wang
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Mengjiao Huang
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Mingxia Zhang
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Chaoyong Yang
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China.
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Park S, Shin HJ, Shah M, Cho HY, Anwar MA, Achek A, Kwon HK, Lee B, Yoo TH, Choi S. TLR4/MD2 specific peptides stalled in vivo LPS-induced immune exacerbation. Biomaterials 2017; 126:49-60. [PMID: 28254693 DOI: 10.1016/j.biomaterials.2017.02.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 12/22/2022]
Abstract
Negative regulation of Toll-like receptor-4 (TLR4) is anticipated to control the pathogen-induced exaggerated immune response. However, effective TLR4 antagonists with scarce off-target effects are yet to be developed. To fill this void, we sought to design small peptide-inhibitors of the TLR4/MD2-LPS interaction. Here we report novel TLR4-antagonistic peptides (TAP), identified through phage display, endowed with the LPS-induced proinflammation inhibition, and confirmed in mice. TAPs-attributed TLR4-antagonism were initially evaluated through NF-κB inhibition in HEK-blue hTLR4 and RAW264.7 cells, and further reinforced by the downregulation of MAPKs (mitogen-activated protein kinases), NF-κB, interleukin 6, and suppression of the oxidative-stress products and iNOS in macrophages and human peripheral blood mononuclear cells (hPBMCs). Among these, TAP2 specifically halted the TLR4, but not other TLRs signaling, which was further confirmed by the biophysical kinetic assay. Finally, TAP2 diminished LPS-elicited systemic cytokine response in vivo, suggesting that TAPs, specifically TAP2, have the potential to treat TLR4-mediated immune ailments.
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Abstract
Development of peptide vaccines through the phage display technology is a powerful strategy that relies on short peptides expressed in the phage capsid surface to induce highly targeted immune responses. Phage display-derived immunogenic peptides can be used directly as a phage-fused peptide reagent or as a synthetic peptide with specific modifications, according to target molecule and disease pathogen/parasite. Peptides' selection (mimotopes) can be performed against monoclonal or polyclonal antibodies to disclose determinant regions (epitopes) that can induce a neutralizing response. Validations of mimotopes are performed in vitro and in vivo, based on cell culture and animal models, to demonstrate its immunogenic potential for final vaccine formulations with an appropriate adjuvant. Here we present specific methods for the discovery of novel immunogenic peptides based on phage display.
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Affiliation(s)
- Luiz R Goulart
- Laboratory of Nanobiotechnology, Institute of Genetics and Biochemistry, Federal University of Uberlandia, Campus Umuarama, Bl 2E, Sl. 248, Uberlândia, MG, Brazil.
| | - Paula de S Santos
- Laboratory of Nanobiotechnology, Institute of Genetics and Biochemistry, Federal University of Uberlandia, Campus Umuarama, Bl 2E, Sl. 248, Uberlândia, MG, Brazil
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Veugelen S, Dewilde M, De Strooper B, Chávez-Gutiérrez L. Screening and Characterization Strategies for Nanobodies Targeting Membrane Proteins. Methods Enzymol 2016; 584:59-97. [PMID: 28065273 DOI: 10.1016/bs.mie.2016.10.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The study of membrane protein function and structure requires their successful detection, expression, solubilization, and/or reconstitution, which poses a challenging task and relies on the availability of suitable tools. Several research groups have successfully applied Nanobodies in the purification, as well as the functional and structural characterization of membrane proteins. Nanobodies are small, single-chain antibody fragments originating from camelids presenting on average a longer CDR3 which enables them to bind in cavities and clefts (such as active and allosteric sites). Notably, Nanobodies generally bind conformational epitopes making them very interesting tools to stabilize, dissect, and characterize specific protein conformations. In the clinic, several Nanobodies are under evaluation either as potential drug candidates or as diagnostic tools. In recent years, we have successfully generated high-affinity, conformation-sensitive anti-γ-secretase Nanobodies. γ-Secretase is a multimeric membrane protease involved in processing of the amyloid precursor protein with high clinical relevance as mutations in its catalytic subunit (Presenilin) cause early-onset Alzheimer's disease. Advancing our knowledge on the mechanisms governing γ-secretase intramembrane proteolysis through various strategies may lead to novel therapeutic avenues for Alzheimer's disease. In this chapter, we present the strategies we have developed and applied for the screening and characterization of anti-γ-secretase Nanobodies. These protocols could be of help in the generation of Nanobodies targeting other membrane proteins.
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Affiliation(s)
- S Veugelen
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium
| | - M Dewilde
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium
| | - B De Strooper
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium; UCL Institute of Neurology, London, United Kingdom
| | - L Chávez-Gutiérrez
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium.
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Aghebati-Maleki L, Bakhshinejad B, Baradaran B, Motallebnezhad M, Aghebati-Maleki A, Nickho H, Yousefi M, Majidi J. Phage display as a promising approach for vaccine development. J Biomed Sci 2016; 23:66. [PMID: 27680328 PMCID: PMC5041315 DOI: 10.1186/s12929-016-0285-9] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022] Open
Abstract
Bacteriophages are specific antagonists to bacterial hosts. These viral entities have attracted growing interest as optimal vaccine delivery vehicles. Phages are well-matched for vaccine design due to being highly stable under harsh environmental conditions, simple and inexpensive large scale production, and potent adjuvant capacities. Phage vaccines have efficient immunostimulatory effects and present a high safety profile because these viruses have made a constant relationship with the mammalian body during a long-standing evolutionary period. The birth of phage display technology has been a turning point in the development of phage-based vaccines. Phage display vaccines are made by expressing multiple copies of an antigen on the surface of immunogenic phage particles, thereby eliciting a powerful and effective immune response. Also, the ability to produce combinatorial peptide libraries with a highly diverse pool of randomized ligands has transformed phage display into a straightforward, versatile and high throughput screening methodology for the identification of potential vaccine candidates against different diseases in particular microbial infections. These libraries can be conveniently screened through an affinity selection-based strategy called biopanning against a wide variety of targets for the selection of mimotopes with high antigenicity and immunogenicity. Also, they can be panned against the antiserum of convalescent individuals to recognize novel peptidomimetics of pathogen-related epitopes. Phage display has represented enormous promise for finding new strategies of vaccine discovery and production and current breakthroughs promise a brilliant future for the development of different phage-based vaccine platforms.
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Affiliation(s)
- Leili Aghebati-Maleki
- Immunology Research Center, Tabriz University of Medical sciences, Tabriz, Iran.,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Babak Bakhshinejad
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Ali Aghebati-Maleki
- Immunology Research Center, Tabriz University of Medical sciences, Tabriz, Iran
| | - Hamid Nickho
- Immunology Research Center, Tabriz University of Medical sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Jafar Majidi
- Immunology Research Center, Tabriz University of Medical sciences, Tabriz, Iran. .,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Pasello M, Zamboni S, Mallano A, Flego M, Picci P, Cianfriglia M, Scotlandi K. Design and construction of a new human naïve single-chain fragment variable antibody library, IORISS1. J Biotechnol 2016; 224:1-11. [PMID: 26945728 DOI: 10.1016/j.jbiotec.2016.02.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/20/2016] [Accepted: 02/24/2016] [Indexed: 12/11/2022]
Abstract
Human monoclonal antibodies are a powerful tool with increasingly successful exploitations and the single chain fragment variable format can be considered the building block for the implementation of more complex and effective antibody-based constructs. Phage display is one of the best and most efficient methods to isolate human antibodies selected from an efficient and variable phage display library. We report a method for the construction of a human naïve single-chain variable fragment library, termed IORISS1. Many different sets of oligonucleotide primers as well as optimized electroporation and ligation reactions were used to generate this library of 1.2×10(9) individual clones. The key difference is the diversity of variable gene templates, which was derived from only 15 non-immunized human donors. The method described here, was used to make a new human naïve single-chain fragment variable phage display library that represents a valuable source of diverse antibodies that can be used as research reagents or as a starting point for the development of therapeutics. Using biopanning, we determined the ability of IORISS1 to yield antibodies. The results we obtained suggest that, by using an optimized protocol, an efficient phage antibody library can be generated.
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Affiliation(s)
- Michela Pasello
- CRS Development of Biomolecular Therapies, Experimental Oncology Laboratory, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy; PROMETEO Laboratory, STB, RIT Department, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy.
| | - Silvia Zamboni
- PROMETEO Laboratory, STB, RIT Department, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy; Section of Pharmacogenetics, Drug Resistance and Experimental Therapeutics, Department of Drug Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Alessandra Mallano
- Section of Pharmacogenetics, Drug Resistance and Experimental Therapeutics, Department of Drug Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Michela Flego
- Section of Pharmacogenetics, Drug Resistance and Experimental Therapeutics, Department of Drug Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Piero Picci
- CRS Development of Biomolecular Therapies, Experimental Oncology Laboratory, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy; PROMETEO Laboratory, STB, RIT Department, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy
| | - Maurizio Cianfriglia
- Section of Pharmacogenetics, Drug Resistance and Experimental Therapeutics, Department of Drug Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Katia Scotlandi
- CRS Development of Biomolecular Therapies, Experimental Oncology Laboratory, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy; PROMETEO Laboratory, STB, RIT Department, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy.
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Singh PK, Agrawal R, Kamboj DV, Singh L. Construction of Recombinant Single Chain Variable Fragment (ScFv) Antibody Against Superantigen for Immunodetection Using Antibody Phage Display Technology. Methods Mol Biol 2016; 1396:207-225. [PMID: 26676049 DOI: 10.1007/978-1-4939-3344-0_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Superantigens are a class of antigens that bind to the major histocompatibility complex class (MHC) II and T-cell receptor (TCR) and cause the nonspecific activation of T cells, resulting in a massive release of pro-inflammatory mediators. They are produced by the gram-positive organisms Staphylococcus aureus and Streptococcus pyogenes, and by a variety of other microbes such as viruses and mycoplasma, and cause toxic shock syndrome (TSS) and even death in some cases. The immunodetection of superantigens is difficult due to the polyclonal activation of T-cells leading to nonspecific antibody production. The production of recombinant monoclonal antibodies against superantigens can solve this problem and are far better than polyclonal antibodies in terms of detection. Here, we describe the construction of recombinant single chain variable fragments (ScFv) antibodies against superantigens with specific reference to SEB (staphylococcal enterotoxin B) using antibody phage display technology.
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Affiliation(s)
- Pawan Kumar Singh
- Department of Ophthalmology, Anatomy and Cell Biology, Wayne State University School of Medicine, 4717 St. Antoine, Detroit, MI, 48201, USA.
| | - Ranu Agrawal
- Biotechnology Division, Defense R&D Establishment, Jhansi Road, Gwalior, 474002, India
- Department of Chemistry, Chaudhary Charan Singh University, Meerut, 250004, India
| | - D V Kamboj
- Biotechnology Division, Defense R&D Establishment, Jhansi Road, Gwalior, 474002, India.
| | - Lokendra Singh
- Biotechnology Division, Defense R&D Establishment, Jhansi Road, Gwalior, 474002, India
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Lewis LA, Radulović ŽM, Kim TK, Porter LM, Mulenga A. Identification of 24h Ixodes scapularis immunogenic tick saliva proteins. Ticks Tick Borne Dis 2015; 6:424-34. [PMID: 25825233 DOI: 10.1016/j.ttbdis.2015.03.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 02/19/2015] [Accepted: 03/09/2015] [Indexed: 12/13/2022]
Abstract
Ixodes scapularis is arguably the most medically important tick species in the United States. This tick transmits 5 of the 14 human tick-borne disease (TBD) agents in the USA: Borrelia burgdorferi, Anaplasma phagocytophilum, B. miyamotoi, Babesia microti, and Powassan virus disease. Except for the Powassan virus disease, I. scapularis-vectored TBD agents require more than 24h post attachment to be transmitted. This study describes identification of 24h immunogenic I. scapularis tick saliva proteins, which could provide opportunities to develop strategies to stop tick feeding before transmission of the majority of pathogens. A 24h fed female I. scapularis phage display cDNA expression library was biopanned using rabbit antibodies to 24h fed I. scapularis female tick saliva proteins, subjected to next generation sequencing, de novo assembly, and bioinformatic analyses. A total of 182 contigs were assembled, of which ∼19% (35/182) are novel and did not show identity to any known proteins in GenBank. The remaining ∼81% (147/182) of contigs were provisionally identified based on matches in GenBank including ∼18% (27/147) that matched protein sequences previously annotated as hypothetical and putative tick saliva proteins. Others include proteases and protease inhibitors (∼3%, 5/147), transporters and/or ligand binding proteins (∼6%, 9/147), immunogenic tick saliva housekeeping enzyme-like (17%, 25/147), ribosomal protein-like (∼31%, 46/147), and those classified as miscellaneous (∼24%, 35/147). Notable among the miscellaneous class include antimicrobial peptides (microplusin and ricinusin), myosin-like proteins that have been previously found in tick saliva, and heat shock tick saliva protein. Data in this study provides the foundation for in-depth analysis of I. scapularis feeding during the first 24h, before the majority of TBD agents can be transmitted.
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Affiliation(s)
- Lauren A Lewis
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, United States
| | - Željko M Radulović
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, United States
| | - Tae K Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, United States
| | - Lindsay M Porter
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, United States
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, United States.
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Bakhshinejad B, Sadeghizadeh M. Bacteriophages and their applications in the diagnosis and treatment of hepatitis B virus infection. World J Gastroenterol 2014; 20:11671-11683. [PMID: 25206272 PMCID: PMC4155358 DOI: 10.3748/wjg.v20.i33.11671] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/11/2014] [Accepted: 04/16/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) infection is a major global health challenge leading to serious disorders such as cirrhosis and hepatocellular carcinoma. Currently, there exist various diagnostic and therapeutic approaches for HBV infection. However, prevalence and hazardous effects of chronic viral infection heighten the need to develop novel methodologies for the detection and treatment of this infection. Bacteriophages, viruses that specifically infect bacterial cells, with a long-established tradition in molecular biology and biotechnology have recently been introduced as novel tools for the prevention, diagnosis and treatment of HBV infection. Bacteriophages, due to tremendous genetic flexibility, represent potential to undergo a huge variety of surface modifications. This property has been the rationale behind introduction of phage display concept. This powerful approach, together with combinatorial chemistry, has shaped the concept of phage display libraries with diverse applications for the detection and therapy of HBV infection. This review aims to offer an insightful overview of the potential of bacteriophages in the development of helpful prophylactic (vaccine design), diagnostic and therapeutic strategies for HBV infection thereby providing new perspectives to the growing field of bacteriophage researches directing towards HBV infection.
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Endo H, Kobayashi Y, Hoshino Y, Tanaka S, Kikuta S, Tabunoki H, Sato R. Affinity maturation of Cry1Aa toxin to the Bombyx mori cadherin-like receptor by directed evolution based on phage display and biopanning selections of domain II loop 2 mutant toxins. Microbiologyopen 2014; 3:568-77. [PMID: 25044375 PMCID: PMC4287183 DOI: 10.1002/mbo3.188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/12/2014] [Accepted: 05/26/2014] [Indexed: 01/14/2023] Open
Abstract
Directed evolution of a Cry1Aa toxin using phage display and biopanning was performed to generate an increased binding affinity to the Bombyx mori cadherin-like receptor (BtR175). Three mutant toxins (371WGLA374, 371WPHH374, 371WRPQ37425) with 16-, 16-, and 50-fold higher binding affinities, respectively, for BtR175 were selected from a phage library containing toxins with mutations in domain II loop 2. However, the observed toxicities of the three mutants against B. mori larvae and cultured cells expressing the BtR175 toxin-binding region did not increase, suggesting that increased binding affinity to cadherins does not contribute to the insecticidal activity. Affinity maturation of a Cry toxin to a receptor via directed evolution was relatively simple to achieve, and seems to have potential for generating a toxin with increased insecticidal activity.
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Affiliation(s)
- Haruka Endo
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
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Wang R, Fang S, Xiang S, Ling S, Yuan J, Wang S. Generation and Characterization of a scFv Antibody Against T3SS Needle of Vibrio parahaemolyticus. Indian J Microbiol 2014; 54:143-50. [PMID: 25320414 DOI: 10.1007/s12088-013-0428-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 09/25/2013] [Indexed: 12/31/2022] Open
Abstract
Vibrio parahaemolyticus, a halophilic gram-negative bacterium, is a food-borne pathogen that largely inhabits marine and estuarine environments, and poses a serious threat to human and animal health all over the world. The hollow "needle" channel, a specific assemble of T3SS which exists in most of gram-negative bacteria, plays a key role in the transition of virulence effectors to host cells. In this study, needle protein VP1694 was successfully expressed and purified, and the fusion protein Trx-VP1694 was used to immunize Balb/c mice. Subsequently, a phage single-chain fragment variable antibody (scFv) library was constructed, and a specific scFv against VP1694 named scFv-FA7 was screened by phage display panning. To further identify the characters of scFv, the soluble expression vector pACYC-scFv-skp was constructed and the soluble scFv was purified by Ni(2+) affinity chromatography. ELISA analysis showed that the scFv-FA7 was specific to VP1694 antigen, and its affinity constant was 1.07 × 10(8 )L/mol. These results offer a molecular basis to prevent and cure diseases by scFv, and also provide a new strategy for further research on virulence mechanism of T3SS in V. parahaemolyticus by scFv.
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Yu B, Ni M, Li WH, Lei P, Xing W, Xiao DW, Huang Y, Tang ZJ, Zhu HF, Shen GX. Human scFv antibody fragments specific for hepatocellular carcinoma selected from a phage display library. World J Gastroenterol 2005; 11:3985-9. [PMID: 15996020 PMCID: PMC4502091 DOI: 10.3748/wjg.v11.i26.3985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To identify the scFv antibody fragments specific for hepatocellular carcinoma by biopanning from a large human naive scFv phage display library.
METHODS: A large human naive scFv phage library was used to search for the specific targets by biopanning with the hepatocellular carcinoma cell line HepG2 for the positive-selecting and the normal liver cell line L02 for the counter-selecting. After three rounds of biopanning, individual scFv phages binding selectively to HepG2 cells were picked out. PCR was carried out for identification of the clones containing scFv gene sequence. The specific scFv phages were selected by ELISA and flow cytometry. DNA sequences of positive clones were analyzed by using Applied Biosystem Automated DNA sequencers 3730. The expression proteins of the specific scFv antibody fragments in E.coli HB2151 were purified by the affinity chromatography and detected by SDS-PAGE, Western blot and ELISA. The biological effect of the soluble antibody fragments on the HepG2 cells was investigated by observing the cell proliferation.
RESULTS: Two different positive clones were obtained and the functional variable sequences were identified. Their DNA sequences of the scFv antibody fragments were submitted to GenBank (accession nos: AY686498 and AY686499). The soluble scFv antibody fragments were successfully expressed in E.coli HB2151. The relative molecular mass of the expression products was about 36 ku, according to its predicted Mr value. The two soluble scFv antibody fragments also had specific binding activity and obvious growth inhibition properties to HepG2 cells.
CONCLUSION: The phage library biopanning permits identification of specific antibody fragments for hepatocellular carcinoma and affords experiment evidence for its immunotherapy study.
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Affiliation(s)
- Bing Yu
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
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