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Taguchi K, Sakai Y, Furuhashi T, Hara S, Wada A. Development of Uniform Ribosome Display Technology Enabling Easy and Efficient Identification of Full-Length Proteins that Interact with Bioactive Small and Large Molecules. Chembiochem 2025; 26:e202400352. [PMID: 39073256 DOI: 10.1002/cbic.202400352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 07/30/2024]
Abstract
Identifying target proteins that interact with bioactive molecules is indispensable for understanding their mechanisms of action. In this study, we developed a uniform ribosome display technology using equal-length DNAs and mRNAs to improve molecular display principle for target identification. The equal-length DNAs were designed to contain various coding sequences for full-length proteins with molecular weights of up to 130 kDa and were used to synthesize equal-length mRNAs, which allowed the formation of full-length protein-ribosome-equal-length mRNA complexes. Uniform ribosome display selections of dihydrofolate reductase and haloalkane dehalogenase mutant were performed against methotrexate and chlorohexane, respectively. Quantitative changes of proteins after each selection indicated that the target protein-displaying ribosomal complexes were specifically selected through non-covalent or covalent interactions with the corresponding bioactive molecules. Furthermore, selection of full-length proteins interacting with methotrexate or anti-DDX46 antibody from protein pools showed that only the target proteins could be precisely identified even though the molar amounts of equal-length mRNAs encoding them were adjusted to 1/20,000 of the total equal-length mRNAs. Thus, the uniform ribosome display technology enabled efficient identification of target proteins that interact with bioactive small and large molecules through simplified operations without deep sequencing.
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Affiliation(s)
- Kenshiro Taguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuichi Sakai
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takuto Furuhashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Shuta Hara
- Department of Material and Life Chemistry, Kanagawa University, 3-6-1, Kanagawa-ku, Yokohama, Kanagawa, 221-8686, Japan
| | - Akira Wada
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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2
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Istomina PV, Gorchakov AA, Paoin C, Yamabhai M. Phage display for discovery of anticancer antibodies. N Biotechnol 2024; 83:205-218. [PMID: 39186973 DOI: 10.1016/j.nbt.2024.08.506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
Antibodies and antibody-based immunotherapeutics are the mainstays of cancer immunotherapy. Expanding the repertoire of cancer-specific and cancer-associated epitopes targetable with antibodies represents an important area of research. Phage display is a powerful approach allowing the use of diverse antibody libraries to be screened for binding to a wide range of targets. In this review, we summarize the basics of phage display technology and highlight the advances in anticancer antibody identification and modification via phage display platform. Finally, we describe phage display-derived anticancer monoclonal antibodies that have been approved to date or are in clinical development.
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Affiliation(s)
- Polina V Istomina
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Suranaree, Muang, 111 University Avenue, Nakhon Ratchasima 30000, Thailand
| | - Andrey A Gorchakov
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Lavrentieva 8/2, Novosibirsk 630090, Russia
| | - Chatchanok Paoin
- Medical Oncology Division, Institute of Medicine, Suranaree University of Technology, Suranaree, Muang, 111 University Avenue, Nakhon Ratchasima 30000, Thailand
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Suranaree, Muang, 111 University Avenue, Nakhon Ratchasima 30000, Thailand.
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3
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Mao M, Ahrens L, Luka J, Contreras F, Kurkina T, Bienstein M, Sárria Pereira de Passos M, Schirinzi G, Mehn D, Valsesia A, Desmet C, Serra MÁ, Gilliland D, Schwaneberg U. Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification. Chem Soc Rev 2024; 53:6445-6510. [PMID: 38747901 DOI: 10.1039/d2cs00991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.
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Affiliation(s)
- Maochao Mao
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Leon Ahrens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Julian Luka
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Francisca Contreras
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Tetiana Kurkina
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Marian Bienstein
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | | | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrea Valsesia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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4
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Li Y, Li XM, Yang KD, Tong WH. Advancements in ovarian cancer immunodiagnostics and therapeutics via phage display technology. Front Immunol 2024; 15:1402862. [PMID: 38863706 PMCID: PMC11165035 DOI: 10.3389/fimmu.2024.1402862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
Ovarian cancer, ranking as the seventh most prevalent malignancy among women globally, faces significant challenges in diagnosis and therapeutic intervention. The difficulties in early detection are amplified by the limitations and inefficacies inherent in current screening methodologies, highlighting a pressing need for more efficacious diagnostic and treatment strategies. Phage display technology emerges as a pivotal innovation in this context, utilizing extensive phage-peptide libraries to identify ligands with specificity for cancer cell markers, thus enabling precision-targeted therapeutic strategies. This technology promises a paradigm shift in ovarian cancer management, concentrating on targeted drug delivery systems to improve treatment accuracy and efficacy while minimizing adverse effects. Through a meticulous review, this paper evaluates the revolutionary potential of phage display in enhancing ovarian cancer therapy, representing a significant advancement in combating this challenging disease. Phage display technology is heralded as an essential instrument for developing effective immunodiagnostic and therapeutic approaches in ovarian cancer, facilitating early detection, precision-targeted medication, and the implementation of customized treatment plans.
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Affiliation(s)
- Yang Li
- Obstetrics and Gynecology Center, First Hospital of Jilin University, Changchun, Jilin, China
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Xiao-meng Li
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Kai-di Yang
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Wei-hua Tong
- Obstetrics and Gynecology Center, First Hospital of Jilin University, Changchun, Jilin, China
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Ribeiro AJ, Silva KA, Lopes LDS, Resende CAA, Couto CAP, Gandra IB, Pereira IAG, Barcelos ICDS, Pereira SP, Xavier SR, Tavares GDSV, Machado JM, Da Paz MC, Chávez-Fumagalli MA, Coelho EAF, Giunchetti RC, Chaves AT, Dutra WO, Gonçalves AAM, Galdino AS. The use of peptides for immunodiagnosis of human Chagas disease. Amino Acids 2024; 56:35. [PMID: 38698213 PMCID: PMC11065921 DOI: 10.1007/s00726-024-03394-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 04/10/2024] [Indexed: 05/05/2024]
Abstract
Chagas disease, caused by the protozoa Trypanosoma cruzi, continues to be a serious public health problem in Latin America, worsened by the limitations in its detection. Given the importance of developing new diagnostic methods for this disease, the present review aimed to verify the number of publications dedicated to research on peptides that demonstrate their usefulness in serodiagnosis. To this end, a bibliographic survey was conducted on the PubMed platform using the keyword "peptide" or "epitope" combined with "Chagas disease" or "Trypanosoma cruzi"; "diagno*" or "serodiagnosis" or "immunodiagnosis", without period restriction. An increasing number of publications on studies employing peptides in ELISA and rapid tests assays was verified, which confirms the expansion of research in this field. It is possible to observe that many of the peptides tested so far originate from proteins widely used in the diagnosis of Chagas, and many of them are part of commercial tests developed. In this sense, as expected, promising results were obtained for several peptides when tested in ELISA, as many of them exhibited sensitivity and specificity values above 90%. Furthermore, some peptides have been tested in several studies, confirming their diagnostic potential. Despite the promising results observed, it is possible to emphasize the need for extensive testing of peptides, using different serological panels, in order to confirm their potential. The importance of producing an effective assay capable of detecting the clinical stages of the disease, as well as new immunogenic antigens that enable new serological diagnostic tools for Chagas disease, is evident.
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Affiliation(s)
- Anna Julia Ribeiro
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Kamila Alves Silva
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Lucas da Silva Lopes
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Carlos Ananias Aparecido Resende
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Carolina Alves Petit Couto
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Isadora Braga Gandra
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Isabela Amorim Gonçalves Pereira
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 30130-100, Brazil
| | - Isabelle Caroline Dos Santos Barcelos
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Sabrina Paula Pereira
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Sandra Rodrigues Xavier
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Grasiele de Sousa Viera Tavares
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 30130-100, Brazil
| | - Juliana Martins Machado
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Mariana Campos Da Paz
- Laboratório de Bioativos e Nanobiotecnologia, Universidade Federal de São João Del-Rei, Divinópolis, MG, 35501-296, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, 04000, Peru
| | - Eduardo Antonio Ferraz Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 30130-100, Brazil
| | - Rodolfo Cordeiro Giunchetti
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, e Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Belo Horizonte, MG, 31270-901, Brazil
| | - Ana Thereza Chaves
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 30130-100, Brazil
| | - Walderez Ornelas Dutra
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, e Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Belo Horizonte, MG, 31270-901, Brazil
| | - Ana Alice Maia Gonçalves
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil
| | - Alexsandro Sobreira Galdino
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal de São João Del-Rei, Divinópolis, e Instituto Nacional de Ciência e Tecnologia em Biotecnologia Industrial (INCT-BI), Divinópolis, MG, 35501-296, Brazil.
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Szymczak M, Pankowski JA, Kwiatek A, Grygorcewicz B, Karczewska-Golec J, Sadowska K, Golec P. An effective antibiofilm strategy based on bacteriophages armed with silver nanoparticles. Sci Rep 2024; 14:9088. [PMID: 38643290 PMCID: PMC11032367 DOI: 10.1038/s41598-024-59866-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/15/2024] [Indexed: 04/22/2024] Open
Abstract
The emerging antibiotic resistance in pathogenic bacteria is a key problem in modern medicine that has led to a search for novel therapeutic strategies. A potential approach for managing such bacteria involves the use of their natural killers, namely lytic bacteriophages. Another effective method involves the use of metal nanoparticles with antimicrobial properties. However, the use of lytic phages armed with nanoparticles as an effective antimicrobial strategy, particularly with respect to biofilms, remains unexplored. Here, we show that T7 phages armed with silver nanoparticles exhibit greater efficacy in terms of controlling bacterial biofilm, compared with phages or nanoparticles alone. We initially identified a novel silver nanoparticle-binding peptide, then constructed T7 phages that successfully displayed the peptide on the outer surface of the viral head. These recombinant, AgNP-binding phages could effectively eradicate bacterial biofilm, even when used at low concentrations. Additionally, when used at concentrations that could eradicate bacterial biofilm, T7 phages armed with silver nanoparticles were not toxic to eukaryotic cells. Our results show that the novel combination of lytic phages with phage-bound silver nanoparticles is an effective, synergistic and safe strategy for the treatment of bacterial biofilms.
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Affiliation(s)
- Mateusz Szymczak
- Department of Molecular Virology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jarosław A Pankowski
- Department of Molecular Virology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
- Dioscuri Centre for Physics and Chemistry of Bacteria, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Agnieszka Kwiatek
- Department of Molecular Virology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Bartłomiej Grygorcewicz
- Department of Molecular Virology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Joanna Karczewska-Golec
- Department of Molecular Virology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Kamila Sadowska
- Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Piotr Golec
- Department of Molecular Virology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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Hu D, Irving AT. Massively-multiplexed epitope mapping techniques for viral antigen discovery. Front Immunol 2023; 14:1192385. [PMID: 37818363 PMCID: PMC10561112 DOI: 10.3389/fimmu.2023.1192385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Following viral infection, viral antigens bind specifically to receptors on the surface of lymphocytes thereby activating adaptive immunity in the host. An epitope, the smallest structural and functional unit of an antigen, binds specifically to an antibody or antigen receptor, to serve as key sites for the activation of adaptive immunity. The complexity and diverse range of epitopes are essential to study and map for the diagnosis of disease, the design of vaccines and for immunotherapy. Mapping the location of these specific epitopes has become a hot topic in immunology and immune therapy. Recently, epitope mapping techniques have evolved to become multiplexed, with the advent of high-throughput sequencing and techniques such as bacteriophage-display libraries and deep mutational scanning. Here, we briefly introduce the principles, advantages, and disadvantages of the latest epitope mapping techniques with examples for viral antigen discovery.
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Affiliation(s)
- Diya Hu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Aaron T. Irving
- Department of Clinical Laboratory Studies, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Infection, Immunity & Cancer, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
- Biomedical and Health Translational Research Centre of Zhejiang Province (BIMET), Haining, China
- College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
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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 IMMUNOLOGY 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] [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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9
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Li Y, Yang KD, Duan HY, Du YN, Ye JF. Phage-based peptides for pancreatic cancer diagnosis and treatment: alternative approach. Front Microbiol 2023; 14:1231503. [PMID: 37601380 PMCID: PMC10433397 DOI: 10.3389/fmicb.2023.1231503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/06/2023] [Indexed: 08/22/2023] Open
Abstract
Pancreatic cancer is a devastating disease with a high mortality rate and a lack of effective therapies. The challenges associated with early detection and the highly aggressive nature of pancreatic cancer have limited treatment options, underscoring the urgent need for better disease-modifying therapies. Peptide-based biotherapeutics have become an attractive area of research due to their favorable properties such as high selectivity and affinity, chemical modifiability, good tissue permeability, and easy metabolism and excretion. Phage display, a powerful technique for identifying peptides with high affinity and specificity for their target molecules, has emerged as a key tool in the discovery of peptide-based drugs. Phage display technology involves the use of bacteriophages to express peptide libraries, which are then screened against a target of interest to identify peptides with desired properties. This approach has shown great promise in cancer diagnosis and treatment, with potential applications in targeting cancer cells and developing new therapies. In this comprehensive review, we provide an overview of the basic biology of phage vectors, the principles of phage library construction, and various methods for binding affinity assessment. We then describe the applications of phage display in pancreatic cancer therapy, targeted drug delivery, and early detection. Despite its promising potential, there are still challenges to be addressed, such as optimizing the selection process and improving the pharmacokinetic properties of phage-based drugs. Nevertheless, phage display represents a promising approach for the development of novel targeted therapies in pancreatic cancer and other tumors.
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Affiliation(s)
- Yang Li
- General Surgery Center, First Hospital of Jilin University, Changchun, China
- School of Nursing, Jilin University, Changchun, China
| | - Kai-di Yang
- General Surgery Center, First Hospital of Jilin University, Changchun, China
- School of Nursing, Jilin University, Changchun, China
| | - Hao-yu Duan
- General Surgery Center, First Hospital of Jilin University, Changchun, China
- School of Nursing, Jilin University, Changchun, China
| | - Ya-nan Du
- General Surgery Center, First Hospital of Jilin University, Changchun, China
- School of Nursing, Jilin University, Changchun, China
| | - Jun-feng Ye
- General Surgery Center, First Hospital of Jilin University, Changchun, China
- School of Nursing, Jilin University, Changchun, China
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Akhtar A, Lata M, Sunsunwal S, Yadav A, Lnu K, Subramanian S, Ramya TNC. New carbohydrate binding domains identified by phage display based functional metagenomic screens of human gut microbiota. Commun Biol 2023; 6:371. [PMID: 37019943 PMCID: PMC10076258 DOI: 10.1038/s42003-023-04718-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/16/2023] [Indexed: 04/07/2023] Open
Abstract
Uncultured microbes represent a huge untapped biological resource of novel genes and gene products. Although recent genomic and metagenomic sequencing efforts have led to the identification of numerous genes that are homologous to existing annotated genes, there remains, yet, an enormous pool of unannotated genes that do not find significant sequence homology to existing annotated genes. Functional metagenomics offers a way to identify and annotate novel gene products. Here, we use functional metagenomics to mine novel carbohydrate binding domains that might aid human gut commensals in adherence, gut colonization, and metabolism of complex carbohydrates. We report the construction and functional screening of a metagenomic phage display library from healthy human fecal samples against dietary, microbial and host polysaccharides/glycoconjugates. We identify several protein sequences that do not find a hit to any known protein domain but are predicted to contain carbohydrate binding module-like folds. We heterologously express, purify and biochemically characterize some of these protein domains and demonstrate their carbohydrate-binding function. Our study reveals several previously unannotated carbohydrate-binding domains, including a levan binding domain and four complex N-glycan binding domains that might be useful for the labeling, visualization, and isolation of these glycans.
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Affiliation(s)
- Akil Akhtar
- CSIR- Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Madhu Lata
- CSIR- Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sonali Sunsunwal
- CSIR- Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
| | - Amit Yadav
- CSIR- Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Kajal Lnu
- CSIR- Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Srikrishna Subramanian
- CSIR- Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - T N C Ramya
- CSIR- Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India.
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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11
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Li Y, Sun R, Li S, Tan Z, Li Z, Liu Y, Guo Y, Huang J. ASFV proteins presented at the surface of T7 phages induce strong antibody responses in mice. J Virol Methods 2023; 316:114725. [PMID: 36965632 DOI: 10.1016/j.jviromet.2023.114725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/27/2023]
Abstract
African swine fever virus (ASFV) infection causes substantial economic losses to the swine industry worldwide, and there are still no safe and effective vaccines or therapeutics available. The granulated virus antigen improves the antigen present process and elicits high antibody reaction than the subunit antigen. In this study, the SpyTag peptide-p10 fusion protein was altered and displayed on the surface of the T7 phage to construct an engineered phage (T7-ST). At the same time, ASFV antigen-Spycatcher C-terminal-fused protein (antigen-SC) was expressed and purified by an E. coli prokaryotic expression system. Five virus-like particles (VLPs) displaying the main ASFV antigenic proteins P30, P54, P72, CD2v, and K145R were reconstructed by the isopeptide bond between SpyTag and antigen-SC proteins. The stability of five ASFV VLPs in high temperature and extreme pH conditions was evaluated by transmission electron microscopy (TEM) and plaque analysis. All ASFV VLPs induced a high titer antigen-specific antibody response in mice. Our results showed that the granulated antigen displaying ASFV protein on the surface of the T7 phage provides a robust potential vaccine and diagnostic tool to address the challenge of the ASFV pandemic.
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Affiliation(s)
- Yuanfang Li
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
| | - Ruiqi Sun
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
| | - Shujun Li
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
| | - Zheng Tan
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
| | - Zexing Li
- School of Life Sciences, Tianjin University, Tianjin, China, 300072
| | - Yebin Liu
- China Institute of Veterinary Drug Control, Beijing, China, 100081
| | - Yanyu Guo
- School of Life Sciences, Tianjin University, Tianjin, China, 300072.
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Tianjin, China, 300072.
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12
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Yue H, Li Y, Yang M, Mao C. T7 Phage as an Emerging Nanobiomaterial with Genetically Tunable Target Specificity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103645. [PMID: 34914854 PMCID: PMC8811829 DOI: 10.1002/advs.202103645] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/27/2021] [Indexed: 05/05/2023]
Abstract
Bacteriophages, also known as phages, are specific antagonists against bacteria. T7 phage has drawn massive attention in precision medicine owing to its distinctive advantages, such as short replication cycle, ease in displaying peptides and proteins, high stability and cloning efficiency, facile manipulation, and convenient storage. By introducing foreign gene into phage DNA, T7 phage can present foreign peptides or proteins site-specifically on its capsid, enabling it to become a nanoparticle that can be genetically engineered to screen and display a peptide or protein capable of recognizing a specific target with high affinity. This review critically introduces the biomedical use of T7 phage, ranging from the detection of serological biomarkers and bacterial pathogens, recognition of cells or tissues with high affinity, design of gene vectors or vaccines, to targeted therapy of different challenging diseases (e.g., bacterial infection, cancer, neurodegenerative disease, inflammatory disease, and foot-mouth disease). It also discusses perspectives and challenges in exploring T7 phage, including the understanding of its interactions with human body, assembly into scaffolds for tissue regeneration, integration with genome editing, and theranostic use in clinics. As a genetically modifiable biological nanoparticle, T7 phage holds promise as biomedical imaging probes, therapeutic agents, drug and gene carriers, and detection tools.
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Affiliation(s)
- Hui Yue
- School of Materials Science and EngineeringZhejiang UniversityHangzhouZhejiang310027P. R. China
| | - Yan Li
- Institute of Applied Bioresource ResearchCollege of Animal ScienceZhejiang UniversityYuhangtang Road 866HangzhouZhejiang310058P. R. China
| | - Mingying Yang
- Institute of Applied Bioresource ResearchCollege of Animal ScienceZhejiang UniversityYuhangtang Road 866HangzhouZhejiang310058P. R. China
| | - Chuanbin Mao
- School of Materials Science and EngineeringZhejiang UniversityHangzhouZhejiang310027P. R. China
- Department of Chemistry and BiochemistryStephenson Life Science Research CenterInstitute for Biomedical Engineering, Science and TechnologyUniversity of Oklahoma101 Stephenson ParkwayNormanOklahoma73019‐5251USA
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Mycoplasma genitalium Protein of Adhesion Promotes the Early Proliferation of Human Urothelial Cells by Interacting with RPL35. Pathogens 2021; 10:pathogens10111449. [PMID: 34832605 PMCID: PMC8621731 DOI: 10.3390/pathogens10111449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022] Open
Abstract
Mycoplasma genitalium is a newly recognized pathogen associated with sexually transmitted diseases (STDs). MgPa, the adhesion protein of Mycoplasma genitalium, is the main adhesin and the key factor for M. genitalium interacting with host cells. Currently, the long-term survival mechanism of M. genitalium in the host is not clear. In this study, a T7 phage-displayed human urothelial cell (SV-HUC-1) cDNA library was constructed, and the interaction of MgPa was screened from this library using the recombinant MgPa (rMgPa) as a target molecule. We verified that 60S ribosomal protein L35 (RPL35) can interact with MgPa using far-Western blot and co-localization analysis. According to the results of tandem mass tag (TMT) labeling and proteome quantitative analysis, there were altogether 407 differentially expressed proteins between the pcDNA3.1(+)/MgPa-transfected cells and non-transfected cells, of which there were 6 downregulated proteins and 401 upregulated proteins. The results of qRT-PCR demonstrated that interaction between rMgPa and RPL35 could promote the expressions of EIF2, SRP68, SERBP1, RPL35A, EGF, and TGF-β. 3-(4,5)-Dimethylthiahiazo(-z-y1)-3,5-di-phenytetrazoliumromide bromide (MTT) assays corroborated that the interaction between rMgPa and RPL35 could promote SV-HUC-1 cell proliferation. Therefore, our findings indicated that the interaction between rMgPa and RPL35 can enhance the expressions of transcription-initiation and translation-related proteins and thus promote cell proliferation. This study elucidates a new biological function of MgPa and can explain this new mechanism of M. genitalium in the host.
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14
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Jaroszewicz W, Morcinek-Orłowska J, Pierzynowska K, Gaffke L, Węgrzyn G. Phage display and other peptide display technologies. FEMS Microbiol Rev 2021; 46:6407522. [PMID: 34673942 DOI: 10.1093/femsre/fuab052] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Phage display technology, which is based on the presentation of peptide sequences on the surface of bacteriophage virions, was developed over 30 years ago. Improvements in phage display systems have allowed us to employ this method in numerous fields of biotechnology, as diverse as immunological and biomedical applications, the formation of novel materials and many others. The importance of phage display platforms was recognized by awarding the Nobel Prize in 2018 "for the phage display of peptides and antibodies". In contrast to many review articles concerning specific applications of phage display systems published in recent years, we present an overview of this technology, including a comparison of various display systems, their advantages and disadvantages, and examples of applications in various fields of science, medicine, and the broad sense of biotechnology. Other peptide display technologies, which employ bacterial, yeast and mammalian cells, as well as eukaryotic viruses and cell-free systems, are also discussed. These powerful methods are still being developed and improved; thus, novel sophisticated tools based on phage display and other peptide display systems are constantly emerging, and new opportunities to solve various scientific, medical and technological problems can be expected to become available in the near future.
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Affiliation(s)
- Weronika Jaroszewicz
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | | | - Karolina Pierzynowska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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15
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Gilchrist CLM, Lacey HJ, Vuong D, Pitt JI, Lange L, Lacey E, Pilgaard B, Chooi YH, Piggott AM. Comprehensive chemotaxonomic and genomic profiling of a biosynthetically talented Australian fungus, Aspergillus burnettii sp. nov. Fungal Genet Biol 2020; 143:103435. [PMID: 32702474 DOI: 10.1016/j.fgb.2020.103435] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 01/09/2023]
Abstract
Aspergillus burnettii is a new species belonging to the A. alliaceus clade in Aspergillus subgenus Circumdati section Flavi isolated from peanut-growing properties in southern Queensland, Australia. A. burnettii is a fast-growing, floccose fungus with distinctive brown conidia and is a talented producer of biomass-degrading enzymes and secondary metabolites. Chemical profiling of A. burnettii revealed the metabolites ochratoxin A, kotanins, isokotanins, asperlicin E, anominine and paspalinine, which are common to subgenus Circumdati, together with burnettiene A, burnettramic acids, burnettides, and high levels of 14α-hydroxypaspalinine and hirsutide. The genome of A. burnettii was sequenced and an annotated draft genome is presented. A. burnettii is rich in secondary metabolite biosynthetic gene clusters, containing 51 polyketide synthases, 28 non-ribosomal peptide synthetases and 19 genes related to terpene biosynthesis. Functional annotation of digestive enzymes of A. burnettii and A. alliaceus revealed overlapping carbon utilisation profiles, consistent with a close phylogenetic relationship.
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Affiliation(s)
- Cameron L M Gilchrist
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Heather J Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - John I Pitt
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Lene Lange
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; BioEconomy, Research & Advisory, Karensgade 5, 2500 Valby, Copenhagen, Denmark
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia; Department of Molecular Sciences, Macquarie University, NSW 2109, Australia
| | - Bo Pilgaard
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
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16
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Takakusagi Y, Takakusagi K, Sakaguchi K, Sugawara F. Phage display technology for target determination of small-molecule therapeutics: an update. Expert Opin Drug Discov 2020; 15:1199-1211. [DOI: 10.1080/17460441.2020.1790523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yoichi Takakusagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
- Institute of Quantum Life Science (iQLS), National Institutes of Quantum and Radiological Science and Technology (QST), Chiba, Japan
| | - Kaori Takakusagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
- Institute of Quantum Life Science (iQLS), National Institutes of Quantum and Radiological Science and Technology (QST), Chiba, Japan
| | - Kengo Sakaguchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Fumio Sugawara
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
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17
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Nishimura S, Matsumori N. Chemical diversity and mode of action of natural products targeting lipids in the eukaryotic cell membrane. Nat Prod Rep 2020; 37:677-702. [PMID: 32022056 DOI: 10.1039/c9np00059c] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Covering: up to 2019Nature furnishes bioactive compounds (natural products) with complex chemical structures, yet with simple, sophisticated molecular mechanisms. When natural products exhibit their activities in cells or bodies, they first have to bind or react with a target molecule in/on the cell. The cell membrane is a major target for bioactive compounds. Recently, our understanding of the molecular mechanism of interactions between natural products and membrane lipids progressed with the aid of newly-developed analytical methods. New technology reconnects old compounds with membrane lipids, while new membrane-targeting molecules are being discovered through the screening for antimicrobial potential of natural products. This review article focuses on natural products that bind to eukaryotic membrane lipids, and includes clinically important molecules and key research tools. The chemical diversity of membrane-targeting natural products and the molecular basis of lipid recognition are described. The history of how their mechanism was unveiled, and how these natural products are used in research are also mentioned.
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Affiliation(s)
- Shinichi Nishimura
- Department of Biotechnology, Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan.
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18
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Luo D, Wang L, Liu H, Li L, Liao Y, Yi X, Yan X, Wan K, Zeng Y. Ribokinase screened from T7 phage displayed Mycobacterium tuberculosis genomic DNA library had good potential for the serodiagnosis of tuberculosis. Appl Microbiol Biotechnol 2019; 103:5259-5267. [PMID: 31069485 DOI: 10.1007/s00253-019-09756-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (M. tuberculosis) is the leading cause of death among infectious diseases in the worldwide. Lack of more sensitive and effective diagnostic reagents has increased the awareness of rapid diagnosis for tuberculosis. In this study, T7 phage displayed genomic DNA library of M. tuberculosis was constructed to screen the antigens that specially bind with TB-positive serum from the whole genome of M. tuberculosis and to improve the sensitivity and specificity of tuberculosis serological diagnosis. After three rounds of biopanning, results of DNA sequencing and BLAST analysis showed that 19 positive phages displayed four different proteins and the occurrence frequency of the phage which displayed ribokinase was the highest. The results of indirect ELISA and dot immunoblotting indicated that representative phages could specifically bind to tuberculosis-positive serum. The prokaryotic expression vector containing the DNA sequence of ribokinase gene was then constructed and the recombinant protein was expressed and purified to evaluate the serodiagnosis value of ribokinase. The reactivity of the recombinant ribokinase with different clinical serum was detected and the sensitivities and specificities in tuberculosis serodiagnosis were 90% and 86%, respectively by screening serum from tuberculosis patients (n = 90) and uninfected individuals (n = 90) based on ELISA. Therefore, this study demonstrated that ribokinase had good potential for the serodiagnosis of tuberculosis.
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Affiliation(s)
- Dan Luo
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, People's Republic of China
| | - Li Wang
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, People's Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control/National Institute for communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Lingling Li
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, People's Republic of China
| | - Yating Liao
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, People's Republic of China
| | - Xiaomei Yi
- Reproductive Medical Center, The Affiliated First Hospital, University of South China, Hengyang, 421001, People's Republic of China
| | - Xiaoliang Yan
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, People's Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control/National Institute for communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.
| | - Yanhua Zeng
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, People's Republic of China.
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19
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Cho SM, Lee HK, Liu Q, Wang MW, Kwon HJ. A Guanidine-Based Synthetic Compound Suppresses Angiogenesis via Inhibition of Acid Ceramidase. ACS Chem Biol 2019; 14:11-19. [PMID: 30507149 DOI: 10.1021/acschembio.8b00558] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Angiogenesis generates new blood vessels from pre-existing vessels. Tumors induce the formation of new blood vessels to ensure sufficient oxygen and nutrients for their growth. Normally, angiogenesis is induced by various pro-angiogenesis factors, including vascular endothelial growth factor (VEGF). Inhibition of VEGF is a promising approach to cancer treatment. A guanidine-based synthetic compound, E2, was identified as a potent hit from 68 guanidine-based derivatives by screening for angiogenesis inhibitors showing antiproliferative activity in human umbilical vein endothelial cells (HUVECs). To explore the mode of action of E2, target proteins were investigated using phage display biopanning, and acid ceramidase 1 (ASAH1) was identified as an E2-binding protein. Drug affinity responsive target stability (DARTS) and ASAH1 activity assays revealed the direct binding of E2 to ASAH1. Moreover, siRNA knockdown of ASAH1 demonstrated its role as an angiogenesis factor. Consequently, E2 inhibited chemoinvasion and tube formation of HUVECs in a dose-dependent manner. E2 also potently suppressed neo-vascularization of chorioallantoic membranes in vivo. Collectively, these data suggest that E2 is a novel angiogenesis inhibitor and ASAH1 is proposed to be a new antiangiogenesis target.
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Affiliation(s)
- Sung Min Cho
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Hyung Keun Lee
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Qing Liu
- The National Center for Drug Screening and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ming-Wei Wang
- The National Center for Drug Screening and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Ho Jeong Kwon
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
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20
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Van Vleet TR, Liguori MJ, Lynch JJ, Rao M, Warder S. Screening Strategies and Methods for Better Off-Target Liability Prediction and Identification of Small-Molecule Pharmaceuticals. SLAS DISCOVERY 2018; 24:1-24. [PMID: 30196745 DOI: 10.1177/2472555218799713] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pharmaceutical discovery and development is a long and expensive process that, unfortunately, still results in a low success rate, with drug safety continuing to be a major impedance. Improved safety screening strategies and methods are needed to more effectively fill this critical gap. Recent advances in informatics are now making it possible to manage bigger data sets and integrate multiple sources of screening data in a manner that can potentially improve the selection of higher-quality drug candidates. Integrated screening paradigms have become the norm in Pharma, both in discovery screening and in the identification of off-target toxicity mechanisms during later-stage development. Furthermore, advances in computational methods are making in silico screens more relevant and suggest that they may represent a feasible option for augmenting the current screening paradigm. This paper outlines several fundamental methods of the current drug screening processes across Pharma and emerging techniques/technologies that promise to improve molecule selection. In addition, the authors discuss integrated screening strategies and provide examples of advanced screening paradigms.
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Affiliation(s)
- Terry R Van Vleet
- 1 Department of Investigative Toxicology and Pathology, AbbVie, N Chicago, IL, USA
| | - Michael J Liguori
- 1 Department of Investigative Toxicology and Pathology, AbbVie, N Chicago, IL, USA
| | - James J Lynch
- 2 Department of Integrated Science and Technology, AbbVie, N Chicago, IL, USA
| | - Mohan Rao
- 1 Department of Investigative Toxicology and Pathology, AbbVie, N Chicago, IL, USA
| | - Scott Warder
- 3 Department of Target Enabling Science and Technology, AbbVie, N Chicago, IL, USA
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21
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Comess KM, McLoughlin SM, Oyer JA, Richardson PL, Stöckmann H, Vasudevan A, Warder SE. Emerging Approaches for the Identification of Protein Targets of Small Molecules - A Practitioners’ Perspective. J Med Chem 2018; 61:8504-8535. [DOI: 10.1021/acs.jmedchem.7b01921] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kenneth M. Comess
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Shaun M. McLoughlin
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Jon A. Oyer
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Paul L. Richardson
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Henning Stöckmann
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Scott E. Warder
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
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22
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Kwon HJ, Karuso P. Chemical proteomics, an integrated research engine for exploring drug-target-phenotype interactions. Proteome Sci 2018; 16:1. [PMID: 29339928 PMCID: PMC5759357 DOI: 10.1186/s12953-017-0129-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 01/05/2023] Open
Affiliation(s)
- Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749 South Korea
| | - Peter Karuso
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
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23
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Using the QCM Biosensor-Based T7 Phage Display Combined with Bioinformatics Analysis for Target Identification of Bioactive Small Molecule. Methods Mol Biol 2018; 1795:159-172. [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] [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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Abstract
Novel affinity agents with high specificity are needed to make progress in disease diagnosis and therapy. Over the last several years, peptides have been considered to have fundamental benefits over other affinity agents, such as antibodies, due to their fast blood clearance, low immunogenicity, rapid tissue penetration, and reproducible chemical synthesis. These features make peptides ideal affinity agents for applications in disease diagnostics and therapeutics for a wide variety of afflictions. Virus-derived peptide techniques provide a rapid, robust, and high-throughput way to identify organism-targeting peptides with high affinity and selectivity. Here, we will review viral peptide display techniques, how these techniques have been utilized to select new organism-targeting peptides, and their numerous biomedical applications with an emphasis on targeted imaging, diagnosis, and therapeutic techniques. In the future, these virus-derived peptides may be used as common diagnosis and therapeutics tools in local clinics.
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Affiliation(s)
- Mingying Yang
- Institute of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Kegan Sunderland
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
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Daptomycin, a last-resort antibiotic, binds ribosomal protein S19 in humans. Proteome Sci 2017; 15:16. [PMID: 28680364 PMCID: PMC5494143 DOI: 10.1186/s12953-017-0124-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Daptomycin is a recently introduced, last-resort antibiotic that displays a unique mode of action against Gram-positive bacteria that is not fully understood. Several bacterial targets have been proposed but no human binding partner is known. METHODS In the present study we tested daptomycin in cell viability and proliferation assays against six human cell lines, describe the synthesis of biotinylated and fluorescently labeled analogues of daptomycin. Biotinylated daptomycin was used as bait to isolate the human binding partner by the application of reverse chemical proteomics using T7 phage display of five human tumor cDNA libraries. The interaction between the rescued protein and daptomycin was validated via siRNA knockdown, DARTS assay and immunocytochemistry. RESULTS We have found that daptomycin possesses selective growth inhibition of some cancer cell lines, especially MCF7. The unbiased interrogation of human cDNA libraries, displayed on bacteriophage T7, revealed a single human target of daptomycin; ribosomal protein S19. Using a drug affinity responsive target stability (DARTS) assay in vitro, we show that daptomycin stabilizes RPS19 toward pronase. Fluorescently labeled daptomycin stained specific structures in HeLa cells and co-localized with a RPS19 antibody. CONCLUSION This study provides, for the first time, a human protein target of daptomycin and identifies RPS19 as a possible anticancer drug target for the development of new pharmacological applications and research.
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Li P, Li J, Wang L, Di LJ. Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Peipei Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Jingjing Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li Wang
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
- Metabolomics Core; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li-Jun Di
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
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