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Bang J, Hwang YL, Kim MY, Yun JN, Hyun E, Chang MY, Shin DH, Kim S, Lee JH. Wrinkle-Improving Effect of Novel Peptide That Binds to Nicotinic Acetylcholine Receptor. Int J Mol Sci 2024; 25:7860. [PMID: 39063099 PMCID: PMC11277145 DOI: 10.3390/ijms25147860] [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: 05/20/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Wrinkles, one of the most common signs of aging, are primarily caused by the continuous contraction of muscles. Muscle contraction is induced by the binding of acetylcholine (ACh), released at the neuromuscular junction, to nicotinic acetylcholine receptor (nAChR) present on the muscle cell surface. In this study, we aimed to develop a wrinkle-improving peptide that inhibits the binding of ACh to nAChR using peptide phage display technology. Our peptide showed a remarkably high binding affinity to nAChR subunit α1, with a value below 1 µM, and was found to inhibit the action of ACh through its interaction with these receptors. Furthermore, it increased collagen synthesis in skin cells and upregulated the expression of the aquaporin-3 (AQP3) and hyaluronan synthase-2 (HAS2) genes. These results confirm that the peptide effectively inhibits muscle contraction and enhances skin elasticity and hydration, contributing to its wrinkle-reducing effects. Clinical studies on humans observed significant improvement in wrinkles after three weeks of use, with substantial reduction observed after six weeks. In conclusion, these findings demonstrate the efficacy of the peptide (named Medipep) in reducing wrinkles.
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Affiliation(s)
- Jinho Bang
- SKINMED R&D Center, Daejeon 34037, Republic of Korea; (J.B.); (Y.-L.H.); (M.Y.K.); (J.N.Y.); (E.H.)
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea;
| | - Yul-Lye Hwang
- SKINMED R&D Center, Daejeon 34037, Republic of Korea; (J.B.); (Y.-L.H.); (M.Y.K.); (J.N.Y.); (E.H.)
| | - Mi Yoon Kim
- SKINMED R&D Center, Daejeon 34037, Republic of Korea; (J.B.); (Y.-L.H.); (M.Y.K.); (J.N.Y.); (E.H.)
| | - Jae Nam Yun
- SKINMED R&D Center, Daejeon 34037, Republic of Korea; (J.B.); (Y.-L.H.); (M.Y.K.); (J.N.Y.); (E.H.)
| | - Eujin Hyun
- SKINMED R&D Center, Daejeon 34037, Republic of Korea; (J.B.); (Y.-L.H.); (M.Y.K.); (J.N.Y.); (E.H.)
| | - Min Youl Chang
- SKINMED Clinical Trials Center, Daejeon 34050, Republic of Korea;
| | - Dae Hwan Shin
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea;
| | - Sunghyun Kim
- Bio-Healthcare Materials Center, Korea Institute of Ceramic Engineering and Technology, Cheongju 28160, Republic of Korea
| | - Jeung-Hoon Lee
- SKINMED R&D Center, Daejeon 34037, Republic of Korea; (J.B.); (Y.-L.H.); (M.Y.K.); (J.N.Y.); (E.H.)
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Han SW, Won HS. Advancements in the Application of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs). Biomolecules 2024; 14:479. [PMID: 38672495 PMCID: PMC11048544 DOI: 10.3390/biom14040479] [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: 03/19/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a significant potential for novel therapeutic applications because of their bioactive properties, stability, and specificity. RiPPs are synthesized on ribosomes, followed by intricate post-translational modifications (PTMs), crucial for their diverse structures and functions. PTMs, such as cyclization, methylation, and proteolysis, play crucial roles in enhancing RiPP stability and bioactivity. Advances in synthetic biology and bioinformatics have significantly advanced the field, introducing new methods for RiPP production and engineering. These methods encompass strategies for heterologous expression, genetic refactoring, and exploiting the substrate tolerance of tailoring enzymes to create novel RiPP analogs with improved or entirely new functions. Furthermore, the introduction and implementation of cutting-edge screening methods, including mRNA display, surface display, and two-hybrid systems, have expedited the identification of RiPPs with significant pharmaceutical potential. This comprehensive review not only discusses the current advancements in RiPP research but also the promising opportunities that leveraging these bioactive peptides for therapeutic applications presents, illustrating the synergy between traditional biochemistry and contemporary synthetic biology and genetic engineering approaches.
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Affiliation(s)
- Sang-Woo Han
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical & Health Science, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea;
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical & Health Science, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea;
- BK21 Project Team, Department of Applied Life Science, Graduate School, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea
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Asar M, Newton-Northup J, Soendergaard M. Improving Pharmacokinetics of Peptides Using Phage Display. Viruses 2024; 16:570. [PMID: 38675913 PMCID: PMC11055145 DOI: 10.3390/v16040570] [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: 02/19/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Phage display is a versatile method often used in the discovery of peptides that targets disease-related biomarkers. A major advantage of this technology is the ease and cost efficiency of affinity selection, also known as biopanning, to identify novel peptides. While it is relatively straightforward to identify peptides with optimal binding affinity, the pharmacokinetics of the selected peptides often prove to be suboptimal. Therefore, careful consideration of the experimental conditions, including the choice of using in vitro, in situ, or in vivo affinity selections, is essential in generating peptides with high affinity and specificity that also demonstrate desirable pharmacokinetics. Specifically, in vivo biopanning, or the combination of in vitro, in situ, and in vivo affinity selections, has been proven to influence the biodistribution and clearance of peptides and peptide-conjugated nanoparticles. Additionally, the marked difference in properties between peptides and nanoparticles must be considered. While peptide biodistribution depends primarily on physiochemical properties and can be modified by amino acid modifications, the size and shape of nanoparticles also affect both absorption and distribution. Thus, optimization of the desired pharmacokinetic properties should be an important consideration in biopanning strategies to enable the selection of peptides and peptide-conjugated nanoparticles that effectively target biomarkers in vivo.
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Affiliation(s)
- Mallika Asar
- College of Osteopathic Medicine, Kansas City University, Kansas City, MO 64106, USA;
| | | | - Mette Soendergaard
- Cell Origins LLC, 1601 South Providence Road Columbia, Columbia, MO 65203, USA;
- Department of Chemistry, Western Illinois University, Macomb, IL 61455, USA
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Sharifi M, Alizadeh AA, Mivehroud MH, Dastmalchi S. Construction of a bacteriophage-derived vector with potential applications in targeted drug delivery and cell imaging. Biotechnol Lett 2024; 46:147-159. [PMID: 38184487 DOI: 10.1007/s10529-023-03455-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: 10/12/2022] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 01/08/2024]
Abstract
There is a strong relationship between the dysregulation of epidermal growth factor receptor (EGFR) and the development of epithelial-derived cancers. Therefore, EGFR has usually been considered the desired target for gene therapy. Here, we propose an approach for targeting EGFR-expressing cells by phage particles capable of displaying EGF and GFP as tumor-targeting and reporting elements, respectively. For this purpose, the superfolder GFP-EGF (sfGFP-EGF) coding sequence was inserted at the N-terminus of the pIII gene in the pIT2 phagemid. The capability of the constructed phage to recognize EGFR-overexpressing cells was monitored by fluorescence microscopy, fluorescence-activated cell sorting (FACS), and cell-based ELISA experiments. FACS analysis showed a significant shift in the mean fluorescence intensity (MFI) of the cells treated with phage displaying sfGFP-EGF compared to phage displaying only sfGFP. The binding of phage displaying sfGFP-EGF to A-431 cells, monitored by fluorescence microscopy, indicated the formation of the sfGFP-EGF-EGFR complex on the surface of the treated cells. Cell-based ELISA experiments showed that phages displaying either EGF or sfGFP-EGF can specifically bind EGFR-expressing cells. The vector constructed in the current study has the potential to be engineered for gene delivery purposes as well as cell-based imaging for tumor detection.
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Affiliation(s)
- Mehdi Sharifi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Akbar Alizadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Medicinal Plants Research Center, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Maryam Hamzeh Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
- Faculty of Pharmacy, Near East University, Po. Box: 99138, Nicosia, North Cyprus, Mersin 10, Turkey.
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Li Y, Yang KD, Kong DC, Ye JF. Advances in phage display based nano immunosensors for cholera toxin. Front Immunol 2023; 14:1224397. [PMID: 37781379 PMCID: PMC10534012 DOI: 10.3389/fimmu.2023.1224397] [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: 05/17/2023] [Accepted: 08/23/2023] [Indexed: 10/03/2023] Open
Abstract
Cholera, a persistent global public health concern, continues to cause outbreaks in approximately 30 countries and territories this year. The imperative to safeguard water sources and food from Vibrio cholerae, the causative pathogen, remains urgent. The bacterium is mainly disseminated via ingestion of contaminated water or food. Despite the plate method's gold standard status for detection, its time-consuming nature, taking several days to provide results, remains a challenge. The emergence of novel virulence serotypes raises public health concerns, potentially compromising existing detection methods. Hence, exploiting Vibrio cholerae toxin testing holds promise due to its inherent stability. Immunobiosensors, leveraging antibody specificity and sensitivity, present formidable tools for detecting diverse small molecules, encompassing drugs, hormones, toxins, and environmental pollutants. This review explores cholera toxin detection, highlighting phage display-based nano immunosensors' potential. Engineered bacteriophages exhibit exceptional cholera toxin affinity, through specific antibody fragments or mimotopes, enabling precise quantification. This innovative approach promises to reshape cholera toxin detection, offering an alternative to animal-derived methods. Harnessing engineered bacteriophages aligns with ethical detection and emphasizes sensitivity and accuracy, a pivotal stride in the evolution of detection strategies. This review primarily introduces recent advancements in phage display-based nano immunosensors for cholera toxin, encompassing technical aspects, current challenges, and future prospects.
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Affiliation(s)
- Yang Li
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
- School of Nursing, Jilin University, Changchun, China
| | - Kai-di Yang
- School of Nursing, Jilin University, Changchun, China
| | - De-cai Kong
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jun-feng Ye
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
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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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Flynn CD, Chang D, Mahmud A, Yousefi H, Das J, Riordan KT, Sargent EH, Kelley SO. Biomolecular sensors for advanced physiological monitoring. NATURE REVIEWS BIOENGINEERING 2023; 1:1-16. [PMID: 37359771 PMCID: PMC10173248 DOI: 10.1038/s44222-023-00067-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 06/28/2023]
Abstract
Body-based biomolecular sensing systems, including wearable, implantable and consumable sensors allow comprehensive health-related monitoring. Glucose sensors have long dominated wearable bioanalysis applications owing to their robust continuous detection of glucose, which has not yet been achieved for other biomarkers. However, access to diverse biological fluids and the development of reagentless sensing approaches may enable the design of body-based sensing systems for various analytes. Importantly, enhancing the selectivity and sensitivity of biomolecular sensors is essential for biomarker detection in complex physiological conditions. In this Review, we discuss approaches for the signal amplification of biomolecular sensors, including techniques to overcome Debye and mass transport limitations, and selectivity improvement, such as the integration of artificial affinity recognition elements. We highlight reagentless sensing approaches that can enable sequential real-time measurements, for example, the implementation of thin-film transistors in wearable devices. In addition to sensor construction, careful consideration of physical, psychological and security concerns related to body-based sensor integration is required to ensure that the transition from the laboratory to the human body is as seamless as possible.
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Affiliation(s)
- Connor D. Flynn
- Department of Chemistry, Faculty of Arts & Science, University of Toronto, Toronto, ON Canada
- Department of Chemistry, Weinberg College of Arts & Sciences, Northwestern University, Evanston, IL USA
| | - Dingran Chang
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON Canada
| | - Alam Mahmud
- The Edward S. Rogers Sr Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON Canada
| | - Hanie Yousefi
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL USA
| | - Jagotamoy Das
- Department of Chemistry, Weinberg College of Arts & Sciences, Northwestern University, Evanston, IL USA
| | - Kimberly T. Riordan
- Department of Chemistry, Weinberg College of Arts & Sciences, Northwestern University, Evanston, IL USA
| | - Edward H. Sargent
- Department of Chemistry, Weinberg College of Arts & Sciences, Northwestern University, Evanston, IL USA
- The Edward S. Rogers Sr Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON Canada
- Department of Electrical and Computer Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL USA
| | - Shana O. Kelley
- Department of Chemistry, Faculty of Arts & Science, University of Toronto, Toronto, ON Canada
- Department of Chemistry, Weinberg College of Arts & Sciences, Northwestern University, Evanston, IL USA
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON Canada
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL USA
- International Institute for Nanotechnology, Northwestern University, Evanston, IL USA
- Chan Zuckerberg Biohub Chicago, Chicago, IL USA
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Makky S, Abdelrahman F, Easwaran M, Safwat A, El-Shibiny A. Phages as delivery vehicles and phage display. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:119-132. [PMID: 37770167 DOI: 10.1016/bs.pmbts.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Bacteriophages (Phages in short) were introduced as the natural enemy of bacteria that may act as alternatives to antibiotics to overcome the challenge of antibiotic resistance. However, in the recent history of science, phages have been employed in different molecular tools and used in numerous therapeutic and diagnostic approaches. Furthermore, thanks to the phage`s highly specific host range limited to prokaryotes, phage particles can be used as safe delivery vehicles and display systems. In this chapter, different phage display systems are introduced, in addition to various applications of phage display as a molecular and therapeutic tool in developing vaccines, antibacterial, and anti-cancer treatments.
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Affiliation(s)
- Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, Egypt
| | - Fatma Abdelrahman
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, Egypt
| | - Maheswaran Easwaran
- Department of Biomedical Engineering, Sethu Institute of Technology, Virudhunagar, Tamil Nadu, India
| | - Anan Safwat
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, Egypt; Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt.
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Sinha A, Simnani FZ, Singh D, Nandi A, Choudhury A, Patel P, Jha E, chouhan RS, Kaushik NK, Mishra YK, Panda PK, Suar M, Verma SK. The translational paradigm of nanobiomaterials: Biological chemistry to modern applications. Mater Today Bio 2022; 17:100463. [PMID: 36310541 PMCID: PMC9615318 DOI: 10.1016/j.mtbio.2022.100463] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/11/2022] Open
Abstract
Recently nanotechnology has evolved as one of the most revolutionary technologies in the world. It has now become a multi-trillion-dollar business that covers the production of physical, chemical, and biological systems at scales ranging from atomic and molecular levels to a wide range of industrial applications, such as electronics, medicine, and cosmetics. Nanobiomaterials synthesis are promising approaches produced from various biological elements be it plants, bacteria, peptides, nucleic acids, etc. Owing to the better biocompatibility and biological approach of synthesis, they have gained immense attention in the biomedical field. Moreover, due to their scaled-down sized property, nanobiomaterials exhibit remarkable features which make them the potential candidate for different domains of tissue engineering, materials science, pharmacology, biosensors, etc. Miscellaneous characterization techniques have been utilized for the characterization of nanobiomaterials. Currently, the commercial transition of nanotechnology from the research level to the industrial level in the form of nano-scaffolds, implants, and biosensors is stimulating the whole biomedical field starting from bio-mimetic nacres to 3D printing, multiple nanofibers like silk fibers functionalizing as drug delivery systems and in cancer therapy. The contribution of single quantum dot nanoparticles in biological tagging typically in the discipline of genomics and proteomics is noteworthy. This review focuses on the diverse emerging applications of Nanobiomaterials and their mechanistic advancements owing to their physiochemical properties leading to the growth of industries on different biomedical measures. Alongside the implementation of such nanobiomaterials in several drug and gene delivery approaches, optical coding, photodynamic cancer therapy, and vapor sensing have been elaborately discussed in this review. Different parameters based on current challenges and future perspectives are also discussed here.
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Affiliation(s)
- Adrija Sinha
- KIIT School of Biotechnology, KIIT University, Bhubaneswar, 751024, Odisha, India
| | | | - Dibyangshee Singh
- KIIT School of Biotechnology, KIIT University, Bhubaneswar, 751024, Odisha, India
| | - Aditya Nandi
- KIIT School of Biotechnology, KIIT University, Bhubaneswar, 751024, Odisha, India
| | - Anmol Choudhury
- KIIT School of Biotechnology, KIIT University, Bhubaneswar, 751024, Odisha, India
| | - Paritosh Patel
- KIIT School of Biotechnology, KIIT University, Bhubaneswar, 751024, Odisha, India
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897, Seoul, South Korea
| | - Ealisha Jha
- KIIT School of Biotechnology, KIIT University, Bhubaneswar, 751024, Odisha, India
| | - Raghuraj Singh chouhan
- Department of Environmental Sciences, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897, Seoul, South Korea
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark, Alsion 2, 6400, Sønderborg, Denmark
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Mrutyunjay Suar
- KIIT School of Biotechnology, KIIT University, Bhubaneswar, 751024, Odisha, India
| | - Suresh K. Verma
- KIIT School of Biotechnology, KIIT University, Bhubaneswar, 751024, Odisha, India
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Isolation and characterization of human anti-CD20 single-chain variable fragment (scFv) from a Naive human scFv library. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:177. [PMID: 35999405 PMCID: PMC9398497 DOI: 10.1007/s12032-022-01757-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/30/2022] [Indexed: 12/03/2022]
Abstract
CD20 is a receptor expressed on B cells with anonymous functions. The receptor is the target of some food and drug administration (FDA) approved monoclonal antibodies (mAb), such as Rituximab and Obinutuzumab. Blocking CD20 using the aforementioned mAbs has improved Non-Hodgkin Lymphoma (NHL) therapy. All commercial mAbs on the market were raised in non-human animal models. Antibody humanization is inevitable to mitigate immune response. In order to keep the affinity of antibody intact, humanizations are only applied to frameworks which do not eliminate immune response to foreign CDRs sequences. To address this issue, human monoclonal antibody deemed imperative. Herein, we report the isolation and characterization of a fully human single-chain variable fragment (scFv) against the large loop of CD20 from naïve human antibody library. After three rounds of phage display, a library of enriched anti-CD20 scFv was obtained. The polyclonal phage ELISA demonstrated that after each round of phage display, the population of anti-CD20 scFv became dominant. The scFv, G7, with the most robust interaction with CD20 was selected for further characterization. The specificity of G7 scFv was evaluated by ELISA, western blot, and flow cytometry. Detecting CD20 in western blot showed that G7 binds to a linear epitope on CD20 large loop. Next, G7 scFv was also bound to Raji cell (CD20+) while no interaction was recorded with K562 cell line (CD20—). This data attested that the epitope recognized by G7 scFv is accessible on the cell membrane. The affinity of G7 scFv was estimated to be 63.41 ± 3.9 nM. Next, the sensitivity was evaluated to be 2 ng/ml. Finally, G7 scFv tertiary structure was modeled using Graylab software. The 3D structure illustrated two domains of variable heavy (VH) and variable light (VL) connected through a linker. Afterward, G7 scFv and CD20 were applied to in-silico docking using ClusPro to illustrate the interaction of G7 with the large loop of CD20. As the selected scFv from the human antibody library is devoid of interspecies immunogenic amino acids sequences, no humanization or any other modifications are required prior to clinical applications.
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Manivannan AC, Dhandapani R, Velmurugan P, Thangavelu S, Paramasivam R, Ragunathan L, Saravanan M. Phage in cancer treatment - Biology of therapeutic phage and screening of tumor targeting peptide. Expert Opin Drug Deliv 2022; 19:873-882. [PMID: 35748094 DOI: 10.1080/17425247.2022.2094363] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION There is a constant drive to improve disease treatments. Much effort has been directed at identifying less immunogenic anti-cancer agents that produce fewer and less severe side effects. For more than a decade, bacteriophages have been discussed as an effective treatment for cancer with an exact mode of delivery. AREAS COVERED We review how bacteriophages are used in cancer treatment, the underlying therapeutic mechanisms, and the tumour attacking peptide screening process. The filamentous bacteriophages are an effective vehicle for delivering displayed peptides toward the tumour target. The peptide must be expressed at the appropriate coat protein, and the peptide must be effective enough to disrupt the complex cancer matrix. The present review also sheds light on the dynamic use of phage in cancer treatment, from detection and diagnostics to treatment. EXPERT OPINION Phage has a versatile role as a diagnostic and therapeutic tool. By acting as an appropriate recombinant drug, this phage has every potential to replace existing laborious, high capital investing therapies that may at many times result in failure or drastic side effects. One of the most significant challenges would be identifying tumour homing peptides. Although a few have been discovered, the most effective ones are yet to be determined. This therapeutic method plays a significant role in tumour therapy with high accuracy and efficiency, irrespective of the target location.
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Affiliation(s)
- Arun Chandra Manivannan
- Department of Microbiology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | - Ranjithkumar Dhandapani
- Department of Microbiology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India.,Chimertech Private Limited, Chennai- 600082, India
| | - Palanivel Velmurugan
- Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research (BIHER), Chennai 600073, Tamil Nadu, India
| | - Sathiamoorthi Thangavelu
- Department of Microbiology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | - Ragul Paramasivam
- Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research (BIHER), Chennai 600073, Tamil Nadu, India
| | - Latha Ragunathan
- Department of Microbiology, Aarupadi Veedu Medical College, Puducherry 607402, India
| | - Muthupandian Saravanan
- AMR and Nanotherapeutics Laboratory, Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai 600077, Tamilnadu, India
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12
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Zhang MQ, Wang ZG, Fu DD, Zhang JM, Liu HY, Liu SL, Pang DW. Quantum Dots Tracking Endocytosis and Transport of Proteins Displayed by Mammalian Cells. Anal Chem 2022; 94:7567-7575. [PMID: 35581735 DOI: 10.1021/acs.analchem.2c00411] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mammalian cell display technology uses eukaryotic protein expression system to display proteins on cell surfaces and has become an important method in biological research. Although mammalian cell display technology has many advantages and development potential, certain attributes of the displayed protein remain uncharacterized, such as whether the displayed proteins re-enter the cell and how displayed proteins move into the cell. Here, we present the endocytosis mechanism, motility behavior, and transport kinetics of displayed proteins determined using HaloTag as the displayed protein and quantum dot-based single-particle tracking. The displayed protein enters the cell through clathrin-mediated endocytosis and is transported through the cell in three stages, which is dependent on microfilaments and microtubules. The dynamic information obtained in this study provides answers to questions about endocytosis and postendocytosis transport of displayed proteins and, therefore, is expected to facilitate the development of surface display technology.
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Affiliation(s)
- Meng-Qian Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Dan-Dan Fu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Ju-Mei Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Hao-Yang Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Dai-Wen Pang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
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13
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Characterization of a novel affinity binding ligand for tyrosine nitrated peptides from a phage-displayed peptide library. Talanta 2022; 241:123225. [DOI: 10.1016/j.talanta.2022.123225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/29/2021] [Accepted: 01/09/2022] [Indexed: 01/10/2023]
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14
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Ch'ng ACW, Lam P, Alassiri M, Lim TS. Application of phage display for T-cell receptor discovery. Biotechnol Adv 2021; 54:107870. [PMID: 34801662 DOI: 10.1016/j.biotechadv.2021.107870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/23/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022]
Abstract
The immune system is tasked to keep our body unharmed and healthy. In the immune system, B- and T-lymphocytes are the two main components working together to stop and eliminate invading threats like virus particles, bacteria, fungi and parasite from attacking our healthy cells. The function of antibodies is relatively more direct in target recognition as compared to T-cell receptors (TCR) which recognizes antigenic peptides being presented on the major histocompatibility complex (MHC). Although phage display has been widely applied for antibody presentation, this is the opposite in the case of TCR. The cell surface TCR is a relatively large and complex molecule, making presentation on phage surfaces challenging. Even so, recombinant versions and modifications have been introduced to allow the growing development of TCR in phage display. In addition, the increasing application of TCR for immunotherapy has made it an important binding motif to be developed by phage display. This review will emphasize on the application of phage display for TCR discovery as well as the engineering aspect of TCR for improved characteristics.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Paula Lam
- CellVec Private Limited, 118518, Singapore; National University of Singapore, Department of Physiology, 117597, Singapore; Duke-NUS Graduate Medical School, Cancer and Stem Cells Biology Program, 169857, Singapore
| | - Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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15
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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: 85] [Impact Index Per Article: 28.3] [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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16
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Alizadeh AA, Morris MB, Church WB, Yaqoubi S, Dastmalchi S. A mechanistic perspective, clinical applications, and phage-display-assisted discovery of TNFα inhibitors. Drug Discov Today 2021; 27:503-518. [PMID: 34628042 DOI: 10.1016/j.drudis.2021.09.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/20/2021] [Accepted: 09/30/2021] [Indexed: 11/03/2022]
Abstract
TNFα participates in a variety of physiological processes, but at supra-physiological concentrations it has been implicated in the pathology of inflammatory and autoimmune diseases. Therefore, much attention has been devoted to the development of strategies that overcome the effects of aberrant TNFα concentration. Promising strategies include drugs that destabilize the active (trimeric) form of TNFα and antagonists of TNFα receptor type I. Underpinning these strategies is the successful application of phage-display technology to identify anti-TNFα peptides and antibodies. Here, we review the development of inhibitors of the TNFα-TNF receptor system, with particular focus on the phage-display-assisted identification of molecules that interfere with this system by acting as inhibitors of TNFα or by sequestering TNFα away from its receptor.
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Affiliation(s)
- Ali Akbar Alizadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Michael B Morris
- Discipline of Physiology and Bosch Institute, School of Medical Sciences, University of Sydney, NSW 2006, Australia
| | - W Bret Church
- Group in Biomolecular Structure and Informatics, Faculty of Pharmacy A15, University of Sydney, Sydney, NSW 2006, Australia
| | - Shadi Yaqoubi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Pharmaceutical Analysis Research Center, Tabriz University Medical Sciences, Tabriz, Iran
| | - Siavoush Dastmalchi
- Department of Medicinal Chemistry, School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Pharmacy, Near East University, PO Box 99138, Nicosia, North Cyprus, Mersin 10, Turkey.
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17
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Aloisio A, Nisticò N, Mimmi S, Maisano D, Vecchio E, Fiume G, Iaccino E, Quinto I. Phage-Displayed Peptides for Targeting Tyrosine Kinase Membrane Receptors in Cancer Therapy. Viruses 2021; 13:649. [PMID: 33918836 PMCID: PMC8070105 DOI: 10.3390/v13040649] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Receptor tyrosine kinases (RTKs) regulate critical physiological processes, such as cell growth, survival, motility, and metabolism. Abnormal activation of RTKs and relative downstream signaling is implicated in cancer pathogenesis. Phage display allows the rapid selection of peptide ligands of membrane receptors. These peptides can target in vitro and in vivo tumor cells and represent a novel therapeutic approach for cancer therapy. Further, they are more convenient compared to antibodies, being less expensive and non-immunogenic. In this review, we describe the state-of-the-art of phage display for development of peptide ligands of tyrosine kinase membrane receptors and discuss their potential applications for tumor-targeted therapy.
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Affiliation(s)
| | | | | | | | | | | | | | - Ileana Quinto
- Correspondence: (A.A.); (I.Q.): Tel.: +39-0961-3694057 (I.Q.)
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18
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Nchinda GW, Al-Atoom N, Coats MT, Cameron JM, Waffo AB. Uniqueness of RNA Coliphage Qβ Display System in Directed Evolutionary Biotechnology. Viruses 2021; 13:v13040568. [PMID: 33801772 PMCID: PMC8067240 DOI: 10.3390/v13040568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022] Open
Abstract
Phage display technology involves the surface genetic engineering of phages to expose desirable proteins or peptides whose gene sequences are packaged within phage genomes, thereby rendering direct linkage between genotype with phenotype feasible. This has resulted in phage display systems becoming invaluable components of directed evolutionary biotechnology. The M13 is a DNA phage display system which dominates this technology and usually involves selected proteins or peptides being displayed through surface engineering of its minor coat proteins. The displayed protein or peptide’s functionality is often highly reduced due to harsh treatment of M13 variants. Recently, we developed a novel phage display system using the coliphage Qβ as a nano-biotechnology platform. The coliphage Qβ is an RNA phage belonging to the family of Leviviridae, a long investigated virus. Qβ phages exist as a quasispecies and possess features making them comparatively more suitable and unique for directed evolutionary biotechnology. As a quasispecies, Qβ benefits from the promiscuity of its RNA dependent RNA polymerase replicase, which lacks proofreading activity, and thereby permits rapid variant generation, mutation, and adaptation. The minor coat protein of Qβ is the readthrough protein, A1. It shares the same initiation codon with the major coat protein and is produced each time the ribosome translates the UGA stop codon of the major coat protein with the of misincorporation of tryptophan. This misincorporation occurs at a low level (1/15). Per convention and definition, A1 is the target for display technology, as this minor coat protein does not play a role in initiating the life cycle of Qβ phage like the pIII of M13. The maturation protein A2 of Qβ initiates the life cycle by binding to the pilus of the F+ host bacteria. The extension of the A1 protein with a foreign peptide probe recognizes and binds to the target freely, while the A2 initiates the infection. This avoids any disturbance of the complex and the necessity for acidic elution and neutralization prior to infection. The combined use of both the A1 and A2 proteins of Qβ in this display system allows for novel bio-panning, in vitro maturation, and evolution. Additionally, methods for large library size construction have been improved with our directed evolutionary phage display system. This novel phage display technology allows 12 copies of a specific desired peptide to be displayed on the exterior surface of Qβ in uniform distribution at the corners of the phage icosahedron. Through the recently optimized subtractive bio-panning strategy, fusion probes containing up to 80 amino acids altogether with linkers, can be displayed for target selection. Thus, combined uniqueness of its genome, structure, and proteins make the Qβ phage a desirable suitable innovation applicable in affinity maturation and directed evolutionary biotechnology. The evolutionary adaptability of the Qβ phage display strategy is still in its infancy. However, it has the potential to evolve functional domains of the desirable proteins, glycoproteins, and lipoproteins, rendering them superior to their natural counterparts.
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Affiliation(s)
- Godwin W. Nchinda
- Laboratory of Vaccinology and Biobanking, International Reference Centre CIRCB), BP 3077 Yaoundé, Cameroon;
- Department of Pharmaceutical Microbiology & Biotechnology, Nnamdi Azikiwe University, 420110 Awka, Nigeria
| | - Nadia Al-Atoom
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USA;
| | - Mamie T. Coats
- Clinical and Diagnostic Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Jacqueline M. Cameron
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Alain B. Waffo
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Correspondence: ; Tel.: +1-317-274-9640
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19
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Kadkhodazadeh M, Rajabibazl M, Motedayen M, Shahidi S, Veisi Malekshahi Z, Rahimpour A, Yarahmadi M. Isolation of Polyclonal Single-Chain Fragment Variable (scFv) Antibodies Against Venomous Snakes of Iran and Evaluation of Their Capability in Neutralizing the Venom. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 19:288-296. [PMID: 33680030 PMCID: PMC7758004 DOI: 10.22037/ijpr.2019.14400.12358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several species of dangerous snakes are found in Iran and, according to the Emergency Response Center of Iran from 2002 to 2011, 53,787 Iranians have suffered from snakebite. Although the mortalities caused by snakebite are very low, snakebite-related amputations are still a major concern. Currently, anti-venom polyclonal antibodies derived from animals, such as horses are used to treat snakebites; however, in some cases they can cause anaphylactic shock and serum sickness. In line with this premise, generation of recombinant anti-venom antibodies can be considered as an alternative strategy. Single-chain fragment variable (scFv) antibodies offer several advantages compared to the whole antibodies, including ease of production, high affinity and specificity. In the present study, scFv antibodies were selected against the venom of the most poisonous snakes in Iran using phage display technology. Phage particles harboring anti-venom specific scFv were separated and scFv antibodies were produced in bacteria. In-vitro assay showed that polyclonal scFvs specifically bind to the venom. Furthermore, in-vivo experiment in mice BALB/c indicated effective toxin neutralization using 20 µg of polyclonal scFv. Our study indicates the neutralizing capacity of anti-venom polyclonal scFvs, although further neutralization assays are needed to confirm their effectiveness.
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Affiliation(s)
- Maryam Kadkhodazadeh
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Rajabibazl
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Motedayen
- Department of Serotherapy, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Solmaz Shahidi
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ziba Veisi Malekshahi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University, Tehran, Iran
| | - Azam Rahimpour
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maral Yarahmadi
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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20
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Cao J, Fan T, Li Y, Du Z, Chen L, Wang Y, Wang X, Shen J, Huang X, Xiong B, Cao D. Phage-Display Based Discovery and Characterization of Peptide Ligands against WDR5. Molecules 2021; 26:1225. [PMID: 33668971 PMCID: PMC7956166 DOI: 10.3390/molecules26051225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/17/2021] [Accepted: 02/21/2021] [Indexed: 11/16/2022] Open
Abstract
WD40 is a ubiquitous domain presented in at least 361 human proteins and acts as scaffold to form protein complexes. Among them, WDR5 protein is an important mediator in several protein complexes to exert its functions in histone modification and chromatin remodeling. Therefore, it was considered as a promising epigenetic target involving in anti-cancer drug development. In view of the protein-protein interaction nature of WDR5, we initialized a campaign to discover new peptide-mimic inhibitors of WDR5. In current study, we utilized the phage display technique and screened with a disulfide-based cyclic peptide phage library. Five rounds of biopanning were performed and isolated clones were sequenced. By analyzing the sequences, total five peptides were synthesized for binding assay. The four peptides are shown to have the moderate binding affinity. Finally, the detailed binding interactions were revealed by solving a WDR5-peptide cocrystal structure.
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Affiliation(s)
- Jiawen Cao
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Tiantian Fan
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yanlian Li
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhiyan Du
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin Chen
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Ying Wang
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xin Wang
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jingkang Shen
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xun Huang
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Division of Anti-Tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Bing Xiong
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Danyan Cao
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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21
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Lown PS, Cai JJ, Ritter SC, Otolski JJ, Wong R, Hackel BJ. Extended yeast surface display linkers enhance the enrichment of ligands in direct mammalian cell selections. Protein Eng Des Sel 2021; 34:gzab004. [PMID: 33880560 PMCID: PMC8058008 DOI: 10.1093/protein/gzab004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 12/21/2022] Open
Abstract
Selections of yeast-displayed ligands on mammalian cell monolayers benefit from high target expression and nanomolar affinity, which are not always available. Prior work extending the yeast-protein linker from 40 to 80 amino acids improved yield and enrichment but is hypothesized to be below the optimal length, prompting evaluation of an extended amino acid linker. A 641-residue linker provided enhanced enrichment with a 2-nM affinity fibronectin ligand and 105 epidermal growth factor receptors (EGFR) per cell (14 ± 2 vs. 8 ± 1, P = 0.008) and a >600-nM affinity ligand, 106 EGFR per cell system (23 ± 7 vs. 0.8 ± 0.2, P = 0.004). Enhanced enrichment was also observed with a 310-nM affinity affibody ligand and 104 CD276 per cell, suggesting a generalizable benefit to other scaffolds and targets. Spatial modeling of the linker suggests that improved extracellular accessibility of ligand enables the observed enrichment under conditions not previously possible.
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Affiliation(s)
- Patrick S Lown
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Jessy J Cai
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Seth C Ritter
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Jacob J Otolski
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Ryan Wong
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
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22
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Kim C, Park M, Yang J, Shin J, Park YC, Kim SK, Kweon DH. Inducible plasmid display system for high-throughput selection of proteins with improved solubility. J Biotechnol 2020; 329:143-150. [PMID: 33373627 DOI: 10.1016/j.jbiotec.2020.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 12/24/2022]
Abstract
Soluble expression of enzymes inside the cell is a prerequisite for the successful biotransformation of valuable products. Some key enzymes involved in biotransformation processes, however, are hardly expressed in their soluble forms. Here, we propose an inducible plasmid display, which is a molecular evolution strategy coupled with a high-throughput screening and/or selection method, as a simple and powerful tool for improving the solubility of target enzymes. Specifically, the Oct-1 DNA-binding domain and intein (i.e., auto-processing domain) were employed as anchoring and protein trans-splicing motifs to develop the system, in which the probability of protein trans-splicing is dependent on the soluble property of target proteins. The applicability of inducible plasmid display was investigated using an α-1,2-fucosyltransferase (FucT2) from Helicobacter pylori, a highly insoluble and unstable enzyme in the cytoplasmic space of Escherichia coli, as a model protein. One round of the overall inducible plasmid display process, which consists of in vivo production of FucT2 mutants and in vitro screening, enabled soluble expression of FucT2 and selection of plasmids containing the corresponding genetic information. The inducible plasmid display developed in this study will contribute to the rapid and efficient screening and/or selection of soluble proteins.
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Affiliation(s)
- Chakhee Kim
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Myungseo Park
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Jinkyeong Yang
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Jonghyeok Shin
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Yong-Cheol Park
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul, 02707, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea.
| | - Dae-Hyuk Kweon
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea; Biomedical Institute for Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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Ishina IA, Filimonova IN, Zakharova MY, Ovchinnikova LA, Mamedov AE, Lomakin YA, Belogurov AA. Exhaustive Search of the Receptor Ligands by the CyCLOPS (Cytometry Cell-Labeling Operable Phage Screening) Technique. Int J Mol Sci 2020; 21:ijms21176258. [PMID: 32872428 PMCID: PMC7504098 DOI: 10.3390/ijms21176258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 01/01/2023] Open
Abstract
Effective and versatile screening of the peptide ligands capable of selectively binding to diverse receptors is in high demand for the state-of-the-art technologies in life sciences, including probing of specificity of the cell surface receptors and drug development. Complex microenvironment and structure of the surface receptors significantly reduce the possibility to determine their specificity, especially when in vitro conditions are utilized. Previously, we designed a publicly available platform for the ultra-high-throughput screening (uHTS) of the specificity of surface-exposed receptors of the living eukaryotic cells, which was done by consolidating the phage display and flow cytometry techniques. Here, we significantly improved this methodology and designed the fADL-1e-based phage vectors that do not require a helper hyperphage for the virion assembly. The enhanced screening procedure was tested on soluble human leukocyte antigen (HLA) class II molecules and transgenic antigen-specific B cells that express recombinant lymphoid B-cell receptor (BCR). Our data suggest that the improved vector system may be successfully used for the comprehensive search of the receptor ligands in either cell-based or surface-immobilized assays.
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Affiliation(s)
- Irina A. Ishina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
| | - Ioanna N. Filimonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
| | - Maria Y. Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Leyla A. Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
| | - Azad E. Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
| | - Yakov A. Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
- Correspondence: (Y.A.L.); (A.A.B.J.)
| | - Alexey A. Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
- Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (Y.A.L.); (A.A.B.J.)
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24
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Jarrald RM, Liang Alvin AW, Rawlings AE, Tanaka M, Okochi M, Staniland SS. Systematic Screening and Deep Analysis of CoPt Binding Peptides Leads to Enhanced CoPt Nanoparticles Using Designed Peptides. Bioconjug Chem 2020; 31:1981-1994. [PMID: 32657572 DOI: 10.1021/acs.bioconjchem.0c00348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using protein and peptide additives to direct the crystallization of inorganic materials is a very attractive and environmentally friendly strategy to access complex and sometimes inaccessible mineral phases. CoPt is a very desirable high-magnetoanisotropic material in its L10 phase, but this is acquired by annealing at high temperatures which is incompatible with delicate nanomaterial assembly. Previous studies identified one peptide with high affinity to CoPt and four peptides with high affinity to FePt L10 phase nanoparticles (NPs) through phage display biopanning selection. While synthesis mediated by these peptides offered a small degree of L10 character to the NPs, they do not have the magnetoanistropy required for applications. In this study, we improve the activity of peptide directed crystallization by designing second generation peptides. We use the five literature sequences (LS) to probe the binding affinity deeper through dissection (alanine scanning), reduction (truncations), and substitution of the LS to find key amino acids and motifs. This is performed using a SPOT peptide array, importantly probing interactions at three stages of NP formation: with precursor, during synthesis, and with NPs. We found four universal features: 1) the importance of basic residues, particularly lysine flanking both ends of the sequence; 2) the importance of methionine; 3) shorter sequences show higher affinity than longer ones; and 4) acidic residues have a negative impact on binding with aspartic acid less favorable than glutamic acid. However, an acidic amino acid benefits, presumably to balance charge. The short motif KSLS had high affinity in all assays. Three sequences were selected from the screening, and three sequences were designed from the rules above. These were used to mediate a green synthesis of CoPt nanoparticles. The screened peptides mediated the formation of NPs with improved coercivity (90-110 Oe) compared to the LS (30-80 Oe), while the designed peptides facilitated formation of CoPt NPs with the highest coercivity (109 to 132 Oe), representing a massive improvement on L10 character. This result along with deeper insight this methodology brings offers vast potential for the future.
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Affiliation(s)
- Rosie M Jarrald
- Department of Chemistry, The University of Sheffield, Dainton Building, Sheffield S3 7HF, United Kingdom of Great Britain and Northern Ireland
| | - Aw W Liang Alvin
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8522, Japan
| | - Andrea E Rawlings
- Department of Chemistry, The University of Sheffield, Dainton Building, Sheffield S3 7HF, United Kingdom of Great Britain and Northern Ireland
| | - Masayoshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8522, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8522, Japan
| | - Sarah S Staniland
- Department of Chemistry, The University of Sheffield, Dainton Building, Sheffield S3 7HF, United Kingdom of Great Britain and Northern Ireland
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25
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Lown PS, Hackel BJ. Magnetic Bead-Immobilized Mammalian Cells Are Effective Targets to Enrich Ligand-Displaying Yeast. ACS COMBINATORIAL SCIENCE 2020; 22:274-284. [PMID: 32283920 DOI: 10.1021/acscombsci.0c00036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Yeast surface display empowers selection of protein binding ligands, typically using recombinant soluble antigens. However, ectodomain fragments of transmembrane targets may fail to recapitulate their true, membrane-bound form. Direct selections against adhered mammalian cells empower enrichment of genuine binders yet benefit from high target expression, robustly adherent mammalian cells, and nanomolar affinity ligands. This study evaluates a modified format with mammalian cells immobilized to magnetic beads; yeast-displayed fibronectin domain and affibody ligands of known affinities and cells with expression ranges of epidermal growth factor receptor (EGFR) and CD276 elucidate important parameters to ligand enrichment and yield in cell suspension panning with comparison to adherent panning. Cell suspension panning is hindered by significant background of nondisplaying yeast but exhibits yield advantages in model EGFR systems for a high affinity (KD = 2 nM) binder on cells with both high (106 per cell) target expression (9.6 ± 0.6% vs 3.2 ± 0.4%, p < 0.0001) and mid (105) target expression (2.3 ± 0.5% vs 0.41 ± 0.09%, p = 0.0008), as well as for a low affinity (KD > 600 nM) binder on high target expression cells (2.0 ± 0.5% vs 0.017 ± 0.005%; p = 0.001). Significant enrichment was observed for all EGFR systems except the low-affinity, high expression system. The CD276 system failed to provide significant enrichment, indicating that this technique may not be suitable for all targets. Collectively, this study highlights new approaches that yield successful enrichment of yeast-displayed ligands via panning on immobilized mammalian cells.
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Affiliation(s)
- Patrick S. Lown
- Department of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Avenue Southeast, 356 Amundson Hall, Minneapolis, Minnesota 55455, United States
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Avenue Southeast, 356 Amundson Hall, Minneapolis, Minnesota 55455, United States
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26
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Xu H, Cao B, Li Y, Mao C. Phage nanofibers in nanomedicine: Biopanning for early diagnosis, targeted therapy, and proteomics analysis. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1623. [PMID: 32147974 DOI: 10.1002/wnan.1623] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/02/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022]
Abstract
Display of a peptide or protein of interest on the filamentous phage (also known as bacteriophage), a biological nanofiber, has opened a new route for disease diagnosis and therapy as well as proteomics. Earlier phage display was widely used in protein-protein or antigen-antibody studies. In recent years, its application in nanomedicine is becoming increasingly popular and encouraging. We aim to review the current status in this research direction. For better understanding, we start with a brief introduction of basic biology and structure of the filamentous phage. We present the principle of phage display and library construction method on the basis of the filamentous phage. We summarize the use of the phage displayed peptide library for selecting peptides with high affinity against cells or tissues. We then review the recent applications of the selected cell or tissue targeting peptides in developing new targeting probes and therapeutics to advance the early diagnosis and targeted therapy of different diseases in nanomedicine. We also discuss the integration of antibody phage display and modern proteomics in discovering new biomarkers or target proteins for disease diagnosis and therapy. Finally, we propose an outlook for further advancing the potential impact of phage display on future nanomedicine. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Hong Xu
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Binrui Cao
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Yan Li
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
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27
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Stern LA, Lown PS, Hackel BJ. Ligand Engineering via Yeast Surface Display and Adherent Cell Panning. Methods Mol Biol 2020; 2070:303-320. [PMID: 31625103 PMCID: PMC6996137 DOI: 10.1007/978-1-4939-9853-1_17] [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] [Indexed: 06/10/2023]
Abstract
High-throughput ligand discovery and evolution-via genotype-phenotype linkage strategies-empower molecularly targeted therapy, diagnostics, and fundamental science. Maintaining high-quality target antigen in these selections, particularly for membrane targets, is often a technical challenge. Panning yeast-displayed ligand libraries on intact mammalian cells expressing the molecular target has emerged as an effective strategy. Herein we describe the techniques used to select target-binding ligands via this approach including the use of target-negative cells to deplete non-specific binders and avidity reduction to preferentially select high-affinity ligands.
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Affiliation(s)
- Lawrence A Stern
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Patrick S Lown
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
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28
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Bozovičar K, Bratkovič T. Evolving a Peptide: Library Platforms and Diversification Strategies. Int J Mol Sci 2019; 21:E215. [PMID: 31892275 PMCID: PMC6981544 DOI: 10.3390/ijms21010215] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/22/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022] Open
Abstract
Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.
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Affiliation(s)
| | - Tomaž Bratkovič
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, SI-1000 Ljubljana, Slovenia;
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29
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Sugimoto R, Lee JH, Lee JH, Jin HE, Yoo SY, Lee SW. Bacteriophage nanofiber fabrication using near field electrospinning. RSC Adv 2019; 9:39111-39118. [PMID: 35540674 PMCID: PMC9075989 DOI: 10.1039/c9ra07510k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/08/2019] [Indexed: 12/11/2022] Open
Abstract
M13 bacteriophage (phage) nano- and microfibers were fabricated using electrospinning. Using liquid crystalline suspension of the phage, we successfully fabricated nano- and microscale pure phage fibers. Through a near field electrospinning process, we fabricated the desired phage fiber pattern with tunable direction and spacing. In addition, we demonstrated that the resulting phage fibers could be utilized as an electrostatic-stimulus responsive actuator. The near field electrospinning would be a very useful tool to design phage-based chemical sensors, tissue regenerative materials, energy generators, metallic and semiconductor nanowires in the future.
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Affiliation(s)
- Ryota Sugimoto
- Department of Bioengineering, University of California at Berkeley Berkeley CA 94720 USA
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Ju Hun Lee
- Department of Bioengineering, University of California at Berkeley Berkeley CA 94720 USA
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Ju-Hyuck Lee
- Department of Bioengineering, University of California at Berkeley Berkeley CA 94720 USA
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Hyo-Eon Jin
- Department of Bioengineering, University of California at Berkeley Berkeley CA 94720 USA
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - So Young Yoo
- BIO-IT Foundry Technology Institute, Pusan National University Busan 609-735 Republic of Korea
- Research Institute for Convergence of Biomedical Science and Technology Yangsan 626-770 Republic of Korea
| | - Seung-Wuk Lee
- Department of Bioengineering, University of California at Berkeley Berkeley CA 94720 USA
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
- Tsinghua Berkeley Shenzhen Institute Berkeley USA
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30
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Deng H, Zhou J, Gong B, Xiao M, Zhang M, Pang Q, Zhang X, Zhao B, Zhou X. Screening and identification of a human domain antibody against Brucella abortus VirB5. Acta Trop 2019; 197:105026. [PMID: 31103700 DOI: 10.1016/j.actatropica.2019.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 04/02/2019] [Accepted: 05/15/2019] [Indexed: 01/18/2023]
Abstract
Brucellosis is caused by the genus Brucella. Brucella is widely distributed in cattle, swine, sheep, goat and other mammals including human. Animal brucellosis causes severe economic losses and affects related international transportation and trade. Human brucellosis causes both acute and chronic symptoms of multi-organ dysfunction. Brucella type IV secretion system (T4SS) VirB5 was required for macrophages infection and essential for virulence in mice. VirB5 is located on the cell surface and serves as a specific adhesin targeting host cell receptors. The aim of this study was to isolate and characterize a specific human domain antibody against Brucella abortus (B. abortus) VirB5 from human single domain antibody (sdAb or VHH) phage display library. Following five rounds of screening, an sdAb named as BaV5VH4 showed the highest affinity by enzyme-linked immunosorbent assay (ELISA). Its interaction with B. abortus VirB5 was verified by binding assay, dot blot and molecular docking. These findings in this paper could greatly help elucidate the molecular mechanisms of Brucella infection, and accelerate the development of sdAbs-based vaccines and neutralizing therapeutics of brucellosis.
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31
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Zhao M, Vandersluis M, Stout J, Haupts U, Sanders M, Jacquemart R. Affinity chromatography for vaccines manufacturing: Finally ready for prime time? Vaccine 2019; 37:5491-5503. [DOI: 10.1016/j.vaccine.2018.02.090] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 01/22/2018] [Accepted: 02/22/2018] [Indexed: 01/15/2023]
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32
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Li H, Dong W, Liu Y, Zhang H, Wang G. Enhanced Biosorption of Nickel Ions on Immobilized Surface-Engineered Yeast Using Nickel-Binding Peptides. Front Microbiol 2019; 10:1254. [PMID: 31297097 PMCID: PMC6608678 DOI: 10.3389/fmicb.2019.01254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 05/20/2019] [Indexed: 12/26/2022] Open
Abstract
Three nickel-binding peptides were screened from a phage peptide library and displayed separately or in combination with surface-engineered Saccharomyces cerevisiae EBY100. The sorption of nickel ions on the surface of yeast cells increased with the increasing number of nickel Ni(II)-binding peptides displayed. The combined expression of the three peptides by EBY100/pYD1-N123 demonstrated the highest sorption of Ni(II) (2.603 ± 0.004 g g-1, dry weight) and an enhanced sorption capacity of 60.15%, compared to S. cerevisiae EBY100. An orthogonal test for yeast immobilization was designed. A maximum sorption capability of 68.62% was observed for a treatment at 25°C with 2.0% calcium chloride and 3.0% sodium alginate.
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Affiliation(s)
- Hua Li
- Institute of Microbial Engineering, Henan University, Kaifeng, China.,School of Life Sciencel, Henan University, Kaifeng, China
| | - Wei Dong
- School of Life Sciencel, Henan University, Kaifeng, China
| | - Yong Liu
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, China
| | - Haiyan Zhang
- Institute of Microbial Engineering, Henan University, Kaifeng, China.,School of Life Sciencel, Henan University, Kaifeng, China
| | - Gang Wang
- School of Life Sciencel, Henan University, Kaifeng, China
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33
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Sokullu E, Soleymani Abyaneh H, Gauthier MA. Plant/Bacterial Virus-Based Drug Discovery, Drug Delivery, and Therapeutics. Pharmaceutics 2019; 11:E211. [PMID: 31058814 PMCID: PMC6572107 DOI: 10.3390/pharmaceutics11050211] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Viruses have recently emerged as promising nanomaterials for biotechnological applications. One of the most important applications of viruses is phage display, which has already been employed to identify a broad range of potential therapeutic peptides and antibodies, as well as other biotechnologically relevant polypeptides (including protease inhibitors, minimizing proteins, and cell/organ targeting peptides). Additionally, their high stability, easily modifiable surface, and enormous diversity in shape and size, distinguish viruses from synthetic nanocarriers used for drug delivery. Indeed, several plant and bacterial viruses (e.g., phages) have been investigated and applied as drug carriers. The ability to remove the genetic material within the capsids of some plant viruses and phages produces empty viral-like particles that are replication-deficient and can be loaded with therapeutic agents. This review summarizes the current applications of plant viruses and phages in drug discovery and as drug delivery systems and includes a discussion of the present status of virus-based materials in clinical research, alongside the observed challenges and opportunities.
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Affiliation(s)
- Esen Sokullu
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| | - Hoda Soleymani Abyaneh
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
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34
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Mompó SM, González-Fernández Á. Antigen-Specific Human Monoclonal Antibodies from Transgenic Mice. Methods Mol Biol 2018; 1904:253-291. [PMID: 30539474 DOI: 10.1007/978-1-4939-8958-4_11] [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: 12/24/2022]
Abstract
Due to the difficulties found when generating fully human monoclonal antibodies (mAbs) by the traditional method, several efforts have attempted to overcome these problems, with varying levels of success. One approach has been the development of transgenic mice carrying immunoglobulin (Ig) genes in germline configuration. The engineered mouse genome can undergo productive rearrangement in the B-cell population, with the generation of mouse B lymphocytes expressing human Ig (hIg) chains. To avoid the expression of mouse heavy or light chains, the endogenous mouse Ig (mIg) loci must be silenced by gene-targeting techniques. Subsequently, to obtain antigen-specific mAbs, conventional immunization protocols can be followed and the mAb technique used (fusion of activated B cells with mouse myeloma cells, screening, cloning, freezing, and testing) with these animThis chapter summarizes the most common chromatographic mAb andals expressing human Ig genes. This chapter describes the type of transgenic-knockout mice generated for various research groups, provides examples of human mAbs developed by research groups and companies, and includes protocols of immunization, generation, production, and purification of human mAbs from such mice. In addition, it also addresses the problems detected, and includes some of the methods that can be used to analyze functional activities with human mAbs.
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Affiliation(s)
- Susana Magadán Mompó
- Immunology, Centro de Investigaciones Biomédicas (CINBIO), Centro de Investigación Singular de Galicia, Instituto de Investigación Sanitaria Galicia Sur, Universidad de Vigo, Vigo, Spain
| | - África González-Fernández
- Immunology, Centro de Investigaciones Biomédicas (CINBIO), Centro de Investigación Singular de Galicia, Instituto de Investigación Sanitaria Galicia Sur, Universidad de Vigo, Vigo, Spain.
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35
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Settele F, Zwarg M, Fiedler S, Koscheinz D, Bosse-Doenecke E. Construction and Selection of Affilin ® Phage Display Libraries. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 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] [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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36
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Array-In-Well Epitope Mapping of Phage-Displayed Antibodies. Methods Mol Biol 2018. [PMID: 29714016 DOI: 10.1007/978-1-4939-7841-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Novel affinity reagents, such as single chain (scFv) antibody fragments, can be generated by isolating them from recombinant protein libraries using phage display selection. A successful selection process against a target protein can produce a number of binder candidates among which the desired binders are identified by screening and characterization of individual clones. Obtaining information on the binding properties, such as the binding epitope, already during the screening step helps to choose the most useful candidates for further development at early phase saving time and resources. To this end, we describe here an Array-in-Well-based screening procedure to perform activity testing and epitope mapping for filamentous phage-displayed scFvs in an integrated manner with a single assay.
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37
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Adolf-Bryfogle J, Kalyuzhniy O, Kubitz M, Weitzner BD, Hu X, Adachi Y, Schief WR, Dunbrack RL. RosettaAntibodyDesign (RAbD): A general framework for computational antibody design. PLoS Comput Biol 2018; 14:e1006112. [PMID: 29702641 PMCID: PMC5942852 DOI: 10.1371/journal.pcbi.1006112] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 05/09/2018] [Accepted: 04/02/2018] [Indexed: 01/12/2023] Open
Abstract
A structural-bioinformatics-based computational methodology and framework have been developed for the design of antibodies to targets of interest. RosettaAntibodyDesign (RAbD) samples the diverse sequence, structure, and binding space of an antibody to an antigen in highly customizable protocols for the design of antibodies in a broad range of applications. The program samples antibody sequences and structures by grafting structures from a widely accepted set of the canonical clusters of CDRs (North et al., J. Mol. Biol., 406:228-256, 2011). It then performs sequence design according to amino acid sequence profiles of each cluster, and samples CDR backbones using a flexible-backbone design protocol incorporating cluster-based CDR constraints. Starting from an existing experimental or computationally modeled antigen-antibody structure, RAbD can be used to redesign a single CDR or multiple CDRs with loops of different length, conformation, and sequence. We rigorously benchmarked RAbD on a set of 60 diverse antibody-antigen complexes, using two design strategies-optimizing total Rosetta energy and optimizing interface energy alone. We utilized two novel metrics for measuring success in computational protein design. The design risk ratio (DRR) is equal to the frequency of recovery of native CDR lengths and clusters divided by the frequency of sampling of those features during the Monte Carlo design procedure. Ratios greater than 1.0 indicate that the design process is picking out the native more frequently than expected from their sampled rate. We achieved DRRs for the non-H3 CDRs of between 2.4 and 4.0. The antigen risk ratio (ARR) is the ratio of frequencies of the native amino acid types, CDR lengths, and clusters in the output decoys for simulations performed in the presence and absence of the antigen. For CDRs, we achieved cluster ARRs as high as 2.5 for L1 and 1.5 for H2. For sequence design simulations without CDR grafting, the overall recovery for the native amino acid types for residues that contact the antigen in the native structures was 72% in simulations performed in the presence of the antigen and 48% in simulations performed without the antigen, for an ARR of 1.5. For the non-contacting residues, the ARR was 1.08. This shows that the sequence profiles are able to maintain the amino acid types of these conserved, buried sites, while recovery of the exposed, contacting residues requires the presence of the antigen-antibody interface. We tested RAbD experimentally on both a lambda and kappa antibody-antigen complex, successfully improving their affinities 10 to 50 fold by replacing individual CDRs of the native antibody with new CDR lengths and clusters.
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Affiliation(s)
- Jared Adolf-Bryfogle
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, United States of America
- Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA, United States of America
- The Scripps Research Institute, La Jolla, CA, United States of America
| | - Oleks Kalyuzhniy
- The Scripps Research Institute, La Jolla, CA, United States of America
- IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America
| | - Michael Kubitz
- The Scripps Research Institute, La Jolla, CA, United States of America
| | - Brian D. Weitzner
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
- Institute for Protein Design, University of Washington, Seattle, WA, United States of America
| | - Xiaozhen Hu
- The Scripps Research Institute, La Jolla, CA, United States of America
| | - Yumiko Adachi
- IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America
| | - William R. Schief
- The Scripps Research Institute, La Jolla, CA, United States of America
- IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America
| | - Roland L. Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, United States of America
- * E-mail:
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Li X, Yuan S, Huang M, Gao J, Wu Z, Tong P, Yang A, Chen H. Identification of IgE and IgG epitopes on native Bos d 4 allergen specific to allergic children. Food Funct 2018; 7:2996-3005. [PMID: 27273451 DOI: 10.1039/c6fo00416d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alpha-lactalbumin (ALA) is one of the major allergens in cow's milk. However, research on its conformational epitopes has been relatively limited. In our study, specific antibodies against cow's milk ALA were purified from eight children by two-step affinity chromatography. Subsequently, mimotopes against IgG and IgE were biopanned from Ph.D.-12 and Ph.D.-C7C, respectively. Based on the mimotopes, linear epitopes were defined with the UniProt alignment tool. Conformational epitopes were computed using the Pepitope Server. Six IgE and seven IgG linear epitopes were identified. Meanwhile, five IgE and three IgG conformational epitopes were revealed with PyMOL. The results showed that common residues were identified in both IgE and IgG epitopes and some residues of the conformational epitopes were composed of linear epitopes on bovine α-lactalbumin. The results indicated that the data could be used for developing hypoallergenic dairy products on the basis of epitopes and providing a diagnostic tool for the assessment of patients who are allergic to cow's milk.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and School of Food Science & Technology, Nanchang University, Nanchang 330047, P.R.China
| | - Shuilin Yuan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and School of Food Science & Technology, Nanchang University, Nanchang 330047, P.R.China
| | - Meijia Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and School of Food Science & Technology, Nanchang University, Nanchang 330047, P.R.China
| | - Jinyan Gao
- School of Food Science & Technology, Nanchang University, Nanchang 330047, P.R.China
| | - Zhihua Wu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, P.R.China.
| | - Ping Tong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and School of Food Science & Technology, Nanchang University, Nanchang 330047, P.R.China
| | - Anshu Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, P.R.China.
| | - Hongbing Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, P.R.China.
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Abstract
The last decade has seen a dramatic increase in the utilization of enzymes as green and sustainable (bio)catalysts in pharmaceutical and industrial applications. This trend has to a significant degree been fueled by advances in scientists' and engineers' ability to customize native enzymes by protein engineering. A review of the literature quickly reveals the tremendous success of this approach; protein engineering has generated enzyme variants with improved catalytic activity, broadened or altered substrate specificity, as well as raised or reversed stereoselectivity. Enzymes have been tailored to retain activity at elevated temperatures and to function in the presence of organic solvents, salts and pH values far from physiological conditions. However, readers unfamiliar with the field will soon encounter the confusingly large number of experimental techniques that have been employed to accomplish these engineering feats. Herein, we use history to guide a brief overview of the major strategies for protein engineering-past, present, and future.
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Affiliation(s)
- Stefan Lutz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA.
| | - Samantha M Iamurri
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA
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Friedrich L, Kornberger P, Mendler CT, Multhoff G, Schwaiger M, Skerra A. Selection of an Anticalin® against the membrane form of Hsp70 via bacterial surface display and its theranostic application in tumour models. Biol Chem 2017; 399:235-252. [DOI: 10.1515/hsz-2017-0207] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/23/2017] [Indexed: 01/08/2023]
Abstract
Abstract
We describe the selection of Anticalins against a common tumour surface antigen, human Hsp70, using functional display on live Escherichia coli cells as fusion with a truncated EspP autotransporter. While found intracellularly in normal cells, Hsp70 is frequently exposed in a membrane-bound state on the surface of tumour cells and, even more pronounced, in metastases or after radiochemotherapy. Employing a recombinant Hsp70 fragment comprising residues 383-548 as the target, Anticalins were selected from a naïve bacterial library. The Anticalin with the highest affinity (K
D=13 nm), as determined towards recombinant full-length Hsp70 by real-time surface plasmon resonance analysis, was improved to K
D=510 pm by doped random mutagenesis and another cycle of E. coli surface display, followed by rational combination of mutations. This Anticalin, which recognises a linear peptide epitope located in the interdomain linker of Hsp70, was demonstrated to specifically bind Hsp70 in its membrane-associated form in immunofluorescence microscopy and via flow cytometry using the FaDu cell line, which is positive for surface Hsp70. The radiolabelled and PASylated Anticalin revealed specific tumour accumulation in xenograft mice using positron emission tomography (PET) imaging. Furthermore, after enzymatic coupling to the protein toxin gelonin, the Anticalin showed potent cytotoxicity on FaDu cells in vitro.
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Affiliation(s)
- Lars Friedrich
- Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie , Technische Universität München , D-85354 Freising (Weihenstephan) , Germany
| | - Petra Kornberger
- Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie , Technische Universität München , D-85354 Freising (Weihenstephan) , Germany
| | - Claudia T. Mendler
- Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie , Technische Universität München , D-85354 Freising (Weihenstephan) , Germany
| | - Gabriele Multhoff
- Department of Radiation Oncology , Klinikum rechts der Isar, Technische Universität München , D-81675 München , Germany
| | - Markus Schwaiger
- Department of Nuclear Medicine, Klinikum rechts der Isar , Technische Universität München , D-81675 München , Germany
| | - Arne Skerra
- Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie , Technische Universität München , D-85354 Freising (Weihenstephan) , Germany
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Khan KH, Himeno A, Kosugi S, Nakashima Y, Rafique A, Imamura A, Hatanaka T, Kato DI, Ito Y. IgY-binding peptide screened from a random peptide library as a ligand for IgY purification. J Pept Sci 2017; 23:790-797. [PMID: 28758361 PMCID: PMC5637892 DOI: 10.1002/psc.3027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/22/2017] [Accepted: 07/01/2017] [Indexed: 01/29/2023]
Abstract
Chicken egg yolk immunoglobulin (IgY) is a functional substitute for mammalian IgG for antigen detection. Traditional IgY purification methods involve multi-step procedures resulting in low purity and recovery of IgY. In this study, we developed a simple IgY purification system using IgY-specific peptides identified by T7 phage display technology. From disulfide-constrained random peptide libraries constructed on a T7 phage, we identified three specific binding clones (Y4-4, Y5-14, and Y5-55) through repeated biopanning. The synthetic peptides showed high binding specificity to IgY-Fc and moderate affinity for IgY-Fc (Kd : Y4-4 = 7.3 ± 0.2 μM and Y5-55 = 4.4 ± 0.1 μM) by surface plasmon resonance analysis. To evaluate the ability to purify IgY, we performed immunoprecipitation and affinity high-performance liquid chromatography using IgY-binding peptides; the result indicated that these peptides can be used as affinity ligands for IgY purification. We then used a peptide-conjugated column to purify IgY from egg yolks pre-treated using an optimized delipidation technique. Here, we report the construction of a cost-effective, one-step IgY purification system, with high purity and recovery. © 2017 The Authors. Journal of Peptide Science published by European Peptide Society and John Wiley & Sons Ltd.
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Affiliation(s)
- Kamrul Hasan Khan
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Arisa Himeno
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Shouhei Kosugi
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Yosuke Nakashima
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Abdur Rafique
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Ayana Imamura
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Takaaki Hatanaka
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Dai-Ichiro Kato
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Yuji Ito
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
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Kuzmicheva GA, Belyavskaya VA. Peptide phage display in biotechnology and biomedicine. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2017. [DOI: 10.1134/s1990750817010061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kuzmicheva GA, Belyavskaya VA. [Peptide phage display in biotechnology and biomedicine]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 62:481-495. [PMID: 27797323 DOI: 10.18097/pbmc20166205481] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To date peptide phage display is one of the most common combinatorial methods used for identifying specific peptide ligands. Phage display peptide libraries containing billions different clones successfully used for selection of ligands with high affinity and selectivity toward wide range of targets including individual proteins, bacteria, viruses, spores, different kind of cancer cells and variety of nonorganic targets (metals, alloys, semiconductors etc.) Success of using filamentous phage in phage display technologies relays on the robustness of phage particles and a possibility to genetically modify its DNA to construct new phage variants with novel properties. In this review we are discussing characteristics of the most known non-commercial peptide phage display libraries of different formats (landscape libraries in particular) and their successful applications in several fields of biotechnology and biomedicine: discovery of peptides with diagnostic values against different pathogens, discovery and using of peptides recognizing cancer cells, trends in using of phage display technologies in human interactome studies, application of phage display technologies in construction of novel nano materials.
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Affiliation(s)
- G A Kuzmicheva
- Research Center of Virology and Biotechnology Vector, Koltsovo, Novosibirsk region, Russia; XBiotech USA, Austin, TX, USA
| | - V A Belyavskaya
- Research Center of Virology and Biotechnology Vector, Koltsovo, Novosibirsk region, Russia
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44
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Fang X, Tong Y, Tian H, Ning H, Gao X, Yao W. Rapid de novo generation of antigen specific human B cells with expression of Blimp-1 and AID by in vitro immunization. Exp Cell Res 2017; 352:53-62. [PMID: 28153782 DOI: 10.1016/j.yexcr.2017.01.020] [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] [Received: 10/28/2016] [Revised: 01/07/2017] [Accepted: 01/29/2017] [Indexed: 02/01/2023]
Abstract
In vitro immunization with antigens and cytokines triggers specific human B-cell response in short periods and is therefore superior to conventional in vivo immunization for antibody development. However, this new technology is limited by low efficiency, poor reproducibility, and requirement of pre-immunized lymphocytes. In this study, we demonstrate a novel method for de novo inducing antigen-specific human B cells in vitro. Unlike previous in vitro immunization of unfractionated PBMCs, we firstly optimized the conditions for inducing monocyte-derived dendritic cells (DCs) to efficiently capture, process, and present antigens. Instead of using the conventional method to activate Th2 cells for in vitro immunization, we succeeded to differentiate naïve CD4+ T cells into T follicular helper (Tfh) cells using antigen-sensitized DCs and cytokine cocktail. We discovered the differentiated T cells expressed ICOS, PD-1, BCL-6, and IL-21 at high levels. After 12 days of T-B co-culture, we observed induced T cells efficiently promoted naïve B cells to differentiate into plasmablasts secreting antigen-specific antibodies, with expression of Blimp-1 and AID related to affinity maturation and class switching. Thus, we established a new co-culture system with naïve lymphocyte populations for de novo acquisition of specifically in vitro immunized B cells potentially for development of therapeutic antibodies, which also provides novel insights into understanding the complex interactions among immune cells in lymph nodes.
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Affiliation(s)
- Xu Fang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Yue Tong
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Hong Tian
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Hongyu Ning
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
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45
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Kohli N, Geddie ML. Novel HPLC-Based Screening Method to Assess Developability of Antibody-Like Molecules. Methods Mol Biol 2017; 1575:189-196. [PMID: 28255881 DOI: 10.1007/978-1-4939-6857-2_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The discovery of antibodies that bind to targets with high affinity is now a routine exercise. However, it is still challenging to screen for candidates that, in addition to having excellent biological properties, also have optimal biophysical characteristics. Here, we describe a simple HPLC-based screening method to assess for developability factors earlier in the discovery process.
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Affiliation(s)
- Neeraj Kohli
- Merrimack Pharmaceuticals, Inc., Suite B7201, 1 Kendall Square, Cambridge, MA, 02139, USA.
| | - Melissa L Geddie
- Merrimack Pharmaceuticals, Inc., Suite B7201, 1 Kendall Square, Cambridge, MA, 02139, USA
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46
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Martins IM, Reis RL, Azevedo HS. Phage Display Technology in Biomaterials Engineering: Progress and Opportunities for Applications in Regenerative Medicine. ACS Chem Biol 2016; 11:2962-2980. [PMID: 27661443 DOI: 10.1021/acschembio.5b00717] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The field of regenerative medicine has been gaining momentum steadily over the past few years. The emphasis in regenerative medicine is to use various in vitro and in vivo approaches that leverage the intrinsic healing mechanisms of the body to treat patients with disabling injuries and chronic diseases such as diabetes, osteoarthritis, and degenerative disorders of the cardiovascular and central nervous system. Phage display has been successfully employed to identify peptide ligands for a wide variety of targets, ranging from relatively small molecules (enzymes, cell receptors) to inorganic, organic, and biological (tissues) materials. Over the past two decades, phage display technology has advanced tremendously and has become a powerful tool in the most varied fields of research, including biotechnology, materials science, cell biology, pharmacology, and diagnostics. The growing interest in and success of phage display libraries is largely due to its incredible versatility and practical use. This review discusses the potential of phage display technology in biomaterials engineering for applications in regenerative medicine.
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Affiliation(s)
- Ivone M. Martins
- 3B’s Research Group - Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of
the European Institute of Excellence on Tissue Engineering and Regenerative
Medicine, AvePark, 4805-717 Barco, Guimarães, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
- CEB − Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Rui L. Reis
- 3B’s Research Group - Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of
the European Institute of Excellence on Tissue Engineering and Regenerative
Medicine, AvePark, 4805-717 Barco, Guimarães, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Helena S. Azevedo
- 3B’s Research Group - Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of
the European Institute of Excellence on Tissue Engineering and Regenerative
Medicine, AvePark, 4805-717 Barco, Guimarães, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
- School of Engineering & Materials Science, Queen Mary University of London, London E1 4NS, United Kingdom
- Institute
of Bioengineering, Queen Mary University of London, London E1 4NS, United Kingdom
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Karimi M, Mirshekari H, Moosavi Basri SM, Bahrami S, Moghoofei M, Hamblin MR. Bacteriophages and phage-inspired nanocarriers for targeted delivery of therapeutic cargos. Adv Drug Deliv Rev 2016; 106:45-62. [PMID: 26994592 PMCID: PMC5026880 DOI: 10.1016/j.addr.2016.03.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 02/08/2023]
Abstract
The main goal of drug delivery systems is to target therapeutic cargoes to desired cells and to ensure their efficient uptake. Recently a number of studies have focused on designing bio-inspired nanocarriers, such as bacteriophages, and synthetic carriers based on the bacteriophage structure. Bacteriophages are viruses that specifically recognize their bacterial hosts. They can replicate only inside their host cell and can act as natural gene carriers. Each type of phage has a particular shape, a different capacity for loading cargo, a specific production time, and their own mechanisms of supramolecular assembly, that have enabled them to act as tunable carriers. New phage-based technologies have led to the construction of different peptide libraries, and recognition abilities provided by novel targeting ligands. Phage hybridization with non-organic compounds introduces new properties to phages and could be a suitable strategy for construction of bio-inorganic carriers. In this review we try to cover the major phage species that have been used in drug and gene delivery systems, and the biological application of phages as novel targeting ligands and targeted therapeutics.
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Affiliation(s)
- Mahdi Karimi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Mirshekari
- Advanced Nanobiotechnology & Nanomedicine Research Group [ANNRG], Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Masoud Moosavi Basri
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran; Civil & Environmental Engineering Department, Shahid Beheshti University, Tehran, Iran
| | - Sajad Bahrami
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Student Research Committee, Iran University of Medical Sciences, Tehran, IR, Iran
| | - Mohsen Moghoofei
- Student Research Committee, Iran University of Medical Sciences, Tehran, IR, Iran; Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.
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48
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Schwarz B, Uchida M, Douglas T. Biomedical and Catalytic Opportunities of Virus-Like Particles in Nanotechnology. Adv Virus Res 2016; 97:1-60. [PMID: 28057256 DOI: 10.1016/bs.aivir.2016.09.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Within biology, molecules are arranged in hierarchical structures that coordinate and control the many processes that allow for complex organisms to exist. Proteins and other functional macromolecules are often studied outside their natural nanostructural context because it remains difficult to create controlled arrangements of proteins at this size scale. Viruses are elegantly simple nanosystems that exist at the interface of living organisms and nonliving biological machines. Studied and viewed primarily as pathogens to be combatted, viruses have emerged as models of structural efficiency at the nanoscale and have spurred the development of biomimetic nanoparticle systems. Virus-like particles (VLPs) are noninfectious protein cages derived from viruses or other cage-forming systems. VLPs provide incredibly regular scaffolds for building at the nanoscale. Composed of self-assembling protein subunits, VLPs provide both a model for studying materials' assembly at the nanoscale and useful building blocks for materials design. The robustness and degree of understanding of many VLP structures allow for the ready use of these systems as versatile nanoparticle platforms for the conjugation of active molecules or as scaffolds for the structural organization of chemical processes. Lastly the prevalence of viruses in all domains of life has led to unique activities of VLPs in biological systems most notably the immune system. Here we discuss recent efforts to apply VLPs in a wide variety of applications with the aim of highlighting how the common structural elements of VLPs have led to their emergence as paradigms for the understanding and design of biological nanomaterials.
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Affiliation(s)
- B Schwarz
- Indiana University, Bloomington, IN, United States
| | - M Uchida
- Indiana University, Bloomington, IN, United States
| | - T Douglas
- Indiana University, Bloomington, IN, United States.
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Jafari N, Abediankenari S. Phage Particles as Vaccine Delivery Vehicles: Concepts, Applications and Prospects. Asian Pac J Cancer Prev 2016; 16:8019-29. [PMID: 26745034 DOI: 10.7314/apjcp.2015.16.18.8019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The development of new strategies for vaccine delivery for generating protective and long-lasting immune responses has become an expanding field of research. In the last years, it has been recognized that bacteriophages have several potential applications in the biotechnology and medical fields because of their intrinsic advantages, such as ease of manipulation and large-scale production. Over the past two decades, bacteriophages have gained special attention as vehicles for protein/peptide or DNA vaccine delivery. In fact, whole phage particles are used as vaccine delivery vehicles to achieve the aim of enhanced immunization. In this strategy, the carried vaccine is protected from environmental damage by phage particles. In this review, phage-based vaccine categories and their development are presented in detail, with discussion of the potential of phage-based vaccines for protection against microbial diseases and cancer treatment. Also reviewed are some recent advances in the field of phage- based vaccines.
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Affiliation(s)
- Narjes Jafari
- Cellular and Molecular Biology, Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran E-mail :
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Helft L, Thompson M, Bent AF. Directed Evolution of FLS2 towards Novel Flagellin Peptide Recognition. PLoS One 2016; 11:e0157155. [PMID: 27270917 PMCID: PMC4894583 DOI: 10.1371/journal.pone.0157155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/25/2016] [Indexed: 12/20/2022] Open
Abstract
Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wild-type Arabidopsis FLS2 confers little or no response. A targeted approach generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. These studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.
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Affiliation(s)
- Laura Helft
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Cellular and Molecular Biology Program, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mikayla Thompson
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Andrew F. Bent
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
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