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da Fonseca Alves R, Pallarès-Rusiñol A, Rossi R, Martí M, Vaz ER, de Araújo TG, Sotomayor MDPT, Pividori MI. Peptide-based biosensing approaches for targeting breast cancer-derived exosomes. Biosens Bioelectron 2024; 255:116211. [PMID: 38537428 DOI: 10.1016/j.bios.2024.116211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 04/15/2024]
Abstract
Exosomes are nanovesicles present in all the biological fluids, making them attractive as non-invasive biomarkers for diseases like cancer, among many others. However, exosomes are complex to separate and detect, requiring comprehensive molecular characterization for their routine use in diagnostics. This study explores the use of peptides as cost-effective and stable alternatives to antibodies for exosome binding. To achieve that, phage display technology was employed to select peptides with high specificity for target molecules in exosomes. Specifically, a selected peptide was evaluated for its ability to selectively bind breast cancer-derived exosomes. Proteomic analysis identified 38 protein candidates targeted by the peptide on exosome membranes. The binding of the peptide to breast cancer-derived exosomes was successfully demonstrated by flow cytometry and magneto-actuated immunoassays. Furthermore, an electrochemical biosensor was also tested for breast cancer-derived exosome detection and quantification. The peptide demonstrated effective binding to exosomes from aggressive cancer cell lines, offering promising results in terms of specificity and recovery. This research shows potential for developing rapid, accessible diagnostic tools for breast cancer, especially in low-resource healthcare settings.
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Affiliation(s)
- Rafael da Fonseca Alves
- Biosensing and Bioanalysis Group, Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Spain; Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain; Institute of Chemistry, State University of São Paulo (UNESP), Brazil
| | - Arnau Pallarès-Rusiñol
- Biosensing and Bioanalysis Group, Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Spain; Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Rosanna Rossi
- Biosensing and Bioanalysis Group, Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Spain; Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Merce Martí
- Biosensing and Bioanalysis Group, Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Spain
| | - Emilia Rezende Vaz
- Institute of Biotechnology (IBTEC), Federal University of Uberlandia (UFU), Uberlandia, MG, Brazil
| | | | | | - Maria Isabel Pividori
- Biosensing and Bioanalysis Group, Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Spain; Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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Öz H, Dudak FC. Peptide-Based Recognition Agents of Histamine: A Biopanning Approach with Enhanced Specificity. Chembiochem 2024:e202400154. [PMID: 38616168 DOI: 10.1002/cbic.202400154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Histamine is a biogenic amine that poses a potential threat to public health due to its toxicological effects. In this study, we identified histamine-binding peptides by screening a random 12-mer peptide library, employing a novel biopanning approach that excluded histidine-binding sequences in the final round. This additional step enhanced the selectivity of the peptides and prevented interference from histidine during detection. The binding affinities of synthesized peptides to histamine were assessed using isothermal titration calorimetry (ITC). Among the identified peptides, HBF10 (SGFRDGIEDFLW) and HBF26 (IPLENQHKIYST) showed significant affinity to histamine, with Kavalues of 2.56×104 (M-1) and 8.94×104 (M-1), respectively. Notably, the identified peptides did not demonstrate binding affinity towards histidine, despite its structural similarity to histamine. Subsequently, the surface plasmon resonance (SPR) sensor surface was prepared by immobilizing the peptide HBF26 to investigate the potential of the peptide as a recognition agent for histamine detection. The findings suggest that the identified peptides have an affinity to histamine specifically, showcasing their potential applications as diagnostic agents with specific targeting capabilities.
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Affiliation(s)
- Hafize Öz
- Hacettepe University, Food Engineering, 06800, Ankara, TURKEY
| | - Fahriye Ceyda Dudak
- Hacettepe Universitesi, Food Engineering, Beytepe Campus, 06800, Ankara, TURKEY
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Lin K, Xia B, Wang X, He X, Zhou M, Lin Y, Qiao Y, Li R, Chen Q, Li Y, Feng J, Chen T, Chen C, Li X, Zhang H, Lu L, Liu B, Zhang X. Development of nanobodies targeting hepatocellular carcinoma and application of nanobody-based CAR-T technology. J Transl Med 2024; 22:349. [PMID: 38610029 PMCID: PMC11015683 DOI: 10.1186/s12967-024-05159-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Chimeric antigen receptor T (CAR-T) cell therapy, as an emerging anti-tumor treatment, has garnered extensive attention in the study of targeted therapy of multiple tumor-associated antigens in hepatocellular carcinoma (HCC). However, the suppressive microenvironment and individual heterogeneity results in downregulation of these antigens in certain patients' cancer cells. Therefore, optimizing CAR-T cell therapy for HCC is imperative. METHODS In this study, we administered FGFR4-ferritin (FGFR4-HPF) nanoparticles to the alpaca and constructed a phage library of nanobodies (Nbs) derived from alpaca, following which we screened for Nbs targeting FGFR4. Then, we conducted the functional validation of Nbs. Furthermore, we developed Nb-derived CAR-T cells and evaluated their anti-tumor ability against HCC through in vitro and in vivo validation. RESULTS Our findings demonstrated that we successfully obtained high specificity and high affinity Nbs targeting FGFR4 after screening. And the specificity of Nbs targeting FGFR4 was markedly superior to their binding to other members of the FGFR family proteins. Furthermore, the Nb-derived CAR-T cells, targeting FGFR4, exhibited significantly enhanced anti-tumor efficacy in both experiments when in vitro and in vivo. CONCLUSIONS In summary, the results of this study suggest that the CAR-T cells derived from high specificity and high affinity Nbs, targeting FGFR4, exhibited significantly enhanced anti-tumor efficacy in vitro and in vivo. This is an exploration of FGFR4 in the field of Nb-derived CAR-T cell therapy for HCC, holding promise for enhancing safety and effectiveness in the clinical treatment of HCC in the future.
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Affiliation(s)
- Keming Lin
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Baijin Xia
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Xuemei Wang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Xin He
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Mo Zhou
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Yingtong Lin
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Yidan Qiao
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Rong Li
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Qier Chen
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Yuzhuang Li
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jinzhu Feng
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Tao Chen
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Cancan Chen
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Xinyu Li
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, People's Republic of China
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Lijuan Lu
- Department of Medical Oncology, The Third Affiliated Hospital of Sun Yat-sen University, No. 600 Tianhe Avenue, Guangzhou, Guangdong, 510630, People's Republic of China.
| | - Bingfeng Liu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Xu Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road 2, Yuexiu District, Guangzhou, Guangdong, 510080, People's Republic of China.
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Khalili E, Lakzaei M, Aminian M. Neutralizing anti-diphtheria toxin scFv produced by phage display. Biotechnol Lett 2024:10.1007/s10529-024-03476-1. [PMID: 38607601 DOI: 10.1007/s10529-024-03476-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 01/10/2024] [Accepted: 02/10/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Diphtheria can be prevented by vaccination, but some epidemics occur in several places, and diphtheria's threat is considerable. Administration of diphtheria antitoxin (DAT) produced from hyperimmunized animals is the most common treatment. Recombinant human antibody fragments such as single-chain variable fragments (scFv) produced by phage display library may introduce an interesting approach to overcome the limitations of the traditional antibody therapy. In the present study, B cells of immunized volunteers were used to construct a human single-chain fragment (HuscFv) library. MATERIALS AND METHODS The library was constructed with the maximum combination of heavy and light chains. As an antigen, Diphtheria toxoid (DTd) was used in four-round phage bio-panning to select phage clones that display DTd bound HuscFv from the library. After panning, individual scFv clones were selected. Clones that were able to detect DTd in an initial screening assay were transferred to Escherichia coli HB2151 to express the scFvs and purification was followed by Ni metal ion affinity chromatography. Toxin neutralization test was performed on Vero cells. The reactivity of the soluble scFv with diphtheria toxin were done and affinity calculation based on Beatty method was calculated. RESULTS The size of the constructed scFv library was calculated to be 1.3 × 106 members. Following four rounds of selection, 40 antibody clones were isolated which showed positive reactivity with DTd in an ELISA assay. Five clones were able to neutralize DTd in Vero cell assay. These neutralizing clones were used for soluble expression and purification of scFv fragments. Some of these soluble scFv fragments show neutralizing activity ranging from 0.6 to 1.2 µg against twofold cytotoxic dose of diphtheria toxin. The affinity constant of the selected scFv antibody was determined almost 107 M-1. CONCLUSION This study describes the prosperous construction and isolation of scFv from the immune library, which specifically neutralizes diphtheria toxin. The HuscFv produced in this study can be a potential candidate to substitute the animal antibody for treating diphtheria and detecting toxins.
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Affiliation(s)
- Ehsan Khalili
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Lakzaei
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Aminian
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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5
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Zheng X, Liu Q, Liang Y, Feng W, Yu H, Tong C, Song B. Advancement in the development of single chain antibodies using phage display technology. PeerJ 2024; 12:e17143. [PMID: 38618563 PMCID: PMC11015834 DOI: 10.7717/peerj.17143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/29/2024] [Indexed: 04/16/2024] Open
Abstract
Phage display technology has become an important research tool in biological research, fundamentally changing the traditional monoclonal antibody preparation process, and has been widely used in the establishment of antigen-antibody libraries, drug design, vaccine research, pathogen detection, gene therapy, antigenic epitope research, and cellular signal transduction research.The phage display is a powerful platform for technology development. Using phage display technology, single chain fragment variable (scFv) can be screened, replacing the disadvantage of the large size of traditional antibodies. Phage display single chain antibody libraries have significant biological implications. Here we describe the types of antibodies, including chimeric antibodies, bispecific antibodies, and scFvs. In addition, we describe the phage display system, phage display single chain antibody libraries, screening of specific antibodies by phage libraries and the application of phage libraries.
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Affiliation(s)
- Xiaohui Zheng
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Qi Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Yimin Liang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Wenzhi Feng
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Honghao Yu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Chunyu Tong
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Bocui Song
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
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Pagano L, Simonetti L, Pennacchietti V, Toto A, Malagrinò F, Ivarsson Y, Gianni S. Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD. Biochem Biophys Res Commun 2024; 703:149658. [PMID: 38387229 DOI: 10.1016/j.bbrc.2024.149658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Adaptor proteins play a pivotal role in cellular signaling mediating a multitude of protein-protein interaction critical for cellular homeostasis. Dysregulation of these interactions has been linked to the onset of various cancer pathologies and exploited by viral pathogens during host cell takeover. CrkL is an adaptor protein composed of an N-terminal SH2 domain followed by two SH3 domains that mediate interactions with diverse partners through the recognition of specific binding motifs. In this study, we employed proteomic peptide-phage display (ProP-PD) to comprehensively explore the short linear motif (SLiM)-based interactions of CrkL. Furthermore, we scrutinized how the binding affinity for selected peptides was influenced in the context of the full-length CrkL versus the isolated N-SH3 domain. Importantly, our results provided insights into SLiM-binding sites within previously reported interactors, as well as revealing novel human and viral ligands, expanding our understanding of the interactions mediated by CrkL and highlighting the significance of SLiM-based interactions in mediating adaptor protein function, with implications for cancer and viral pathologies.
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Affiliation(s)
- L Pagano
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - L Simonetti
- Department of Chemistry - BMC, Husargatan 3, 751 23, Uppsala, Sweden
| | - V Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - A Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - F Malagrinò
- Dipartimento di Medicina clinica, sanità pubblica, scienze della vita e dell'ambiente, Università dell'Aquila, Piazzale Salvatore Tommasi 1, L'Aquila, Coppito, 67010, Italy
| | - Y Ivarsson
- Department of Chemistry - BMC, Husargatan 3, 751 23, Uppsala, Sweden.
| | - S Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy.
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Martviset P, Thanongsaksrikul J, Geadkaew-Krenc A, Chaimon S, Glab-Ampai K, Chaibangyang W, Sornchuer P, Srimanote P, Ruangtong J, Prathaphan P, Taechadamrongtham T, Torungkitmangmi N, Sanannam B, Gordon CN, Thongsepee N, Pankao V, Chantree P. Production and immunological characterization of the novel single-chain variable fragment (scFv) antibodies against the epitopes on Opisthorchis viverrini cathepsin F (OvCatF). Acta Trop 2024; 254:107199. [PMID: 38552996 DOI: 10.1016/j.actatropica.2024.107199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/10/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND Opisthorchis viverrini infection is a significant health problem in several countries, especially Southeast Asia. The infection causes acute gastro-hepatic symptoms and also long-term infection leading to carcinogenesis of an aggressive bile duct cancer (cholangiocarcinoma; CCA). Hence, the early diagnosis of O. viverrini infection could be the way out of this situation. Still, stool examination by microscopic-based methods, the current diagnostic procedure is restricted by low parasite egg numbers in the specimen and unprofessional laboratorians. The immunological procedure provides a better chance for diagnosis of the infection. Hence, this study aims to produce single-chain variable fragment (scFv) antibodies for use as a diagnostic tool for O. viverrini infection. METHODS This study uses phage display technologies to develop the scFv antibodies against O. viverrini cathepsin F (OvCatF). The OvCatF-deduced amino acid sequence was analyzed and predicted for B-cell epitopes used for short peptide synthesis. The synthetic peptides were used to screen the phage library simultaneously with OvCatF recombinant protein (rOvCatF). The potentiated phages were collected, rescued, and reassembled in XL1-blue Escherichia coli (E. coli) as a propagative host. The positive clones of phagemids were isolated, and the single-chain variable (scFv) fragments were sequenced, computationally predicted, and molecular docked. The complete scFv fragments were digested from the phagemid, subcloned into the pOPE101 expression vector, and expressed in XL1-blue E. coli. Indirect ELISA and Western analysis were used to verify the detection efficiency. RESULTS The scFv phages specific to OvCatF were successfully isolated, subcloned, and produced as a recombinant protein. The recombinant scFv antibodies were purified and refolded to make functional scFv. The evaluation of specific recognition of the particular epitopes and detection limit results by both computational and laboratory performances demonstrated that all three recombinant scFv antibodies against OvCatF could bind specifically to rOvCatF, and the lowest detection concentration in this study was only one hundred nanograms. CONCLUSION Our produced scFv antibodies will be the potential candidates for developing a practical diagnostic procedure for O. viverrini infection in humans in the future.
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Affiliation(s)
- Pongsakorn Martviset
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Thammasat University Research Unit in Nutraceuticals and Food Safety, Thammasat University, Pathumthani, Thailand; Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Jeeraphong Thanongsaksrikul
- Graduate Studies in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Amornrat Geadkaew-Krenc
- Graduate Studies in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Salisa Chaimon
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Kantaphon Glab-Ampai
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanlapa Chaibangyang
- Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Phornphan Sornchuer
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Thammasat University Research Unit in Nutraceuticals and Food Safety, Thammasat University, Pathumthani, Thailand
| | - Potjanee Srimanote
- Graduate Studies in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Jittiporn Ruangtong
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Thammasat University, Pathumthani, Thailand
| | - Parisa Prathaphan
- Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | | | - Nattaya Torungkitmangmi
- Graduate Program in Biochemistry and Molecular Biology, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Bumpenporn Sanannam
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | | | - Nattaya Thongsepee
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Thammasat University Research Unit in Nutraceuticals and Food Safety, Thammasat University, Pathumthani, Thailand; Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Viriya Pankao
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Pathanin Chantree
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Thammasat University Research Unit in Nutraceuticals and Food Safety, Thammasat University, Pathumthani, Thailand; Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand.
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8
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Raeisi H, Safarnejad MR, Alavi SM, de Oliveira Andrade M, Farrokhi N, Elahinia SA. Transient expression of anti-HrpE scFv antibody reduces the hypersensitive response in non-host plant against bacterial phytopathogen Xanthomonas citri subsp. citri. Sci Rep 2024; 14:7121. [PMID: 38531981 DOI: 10.1038/s41598-024-57355-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Citrus canker is a bacterial disease caused by Xanthomonas citri subsp. citri (Xcc) that affects the citrus industry worldwide. Hrp pili subunits (HrpE), an essential component of Type III secretion system (T3SS) bacteria, play a crucial role in the pathogenesis of Xcc by transporting effector proteins into the host cell and causing canker symptoms. Therefore, development of antibodies that block HrpE can suppress disease progression. In this study, a specific scFv detecting HrpE was developed using phage display technique and characterized using sequencing, ELISA, Western blotting, and molecular docking. In addition, a plant expression vector of pCAMBIA-scFvH6 was constructed and agroinfiltrated into Nicotiana tabacum cv. Samson leaves. The hypersensitive response (HR) in the leaves of transformed and non-transformed plants was evaluated by inoculating leaves with Xcc. After three rounds of biopanning of the phage library, a specific human scFv antibody, named scFvH6, was identified that showed high binding activity against HrpE in ELISA and Western blotting. Molecular docking results showed that five intermolecular hydrogen bonds are involved in HrpE-scFvH6 interaction, confirming the specificity and high binding activity of scFvH6. Successful transient expression of pCAMBIA-scFvH6 in tobacco leaves was verified using immunoassay tests. The binding activity of plant-produced scFvH6 to detect HrpE in Western blotting and ELISA was similar to that of bacterial-produced scFvH6 antibody. Interestingly, tobacco plants expressing scFvH6 showed a remarkable reduction in HR induced by Xcc compared with control plants, so that incidence of necrotic lesions was significantly higher in non-transformed controls (≥ 1.5 lesions/cm2) than in the plants producing scFvH6 (≤ 0.5 lesions/cm2) after infiltration with Xcc inoculum. Our results revealed that the expression of scFvH6 in tobacco leaves can confer resistance to Xcc, indicating that this approach could be considered to provide resistance to citrus bacterial canker disease.
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Affiliation(s)
- Hamideh Raeisi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Shahid Arabi Ave., Yemen St., Velenjak, Tehran, Iran.
| | - Mohammad Reza Safarnejad
- Department of Plant Viruses, Agricultural Research Education and Extension Organization of Iran, Iranian Research Institute of Plant Protection, Tehran, Iran
| | - Seyed Mehdi Alavi
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Maxuel de Oliveira Andrade
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Naser Farrokhi
- Departement of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University G.C, Evin, Tehran, Iran
| | - Seyed Ali Elahinia
- Department of Plant Protection, College of Agricultural Sciences, Guilan University, Rasht, Iran
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9
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Zheleznyak A, Tang R, Duncan K, Manion B, Liang K, Xu B, Vanover A, Ghai A, Prior J, Lees S, Achilefu S, Kelly K, Shokeen M. Development of New CD38 Targeted Peptides for Cancer Imaging. Mol Imaging Biol 2024:10.1007/s11307-024-01901-5. [PMID: 38480650 DOI: 10.1007/s11307-024-01901-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 04/18/2024]
Abstract
PURPOSE Multiple myeloma (MM) affects over 35,000 patients each year in the US. There remains a need for versatile Positron Emission Tomography (PET) tracers for the detection, accurate staging, and monitoring of treatment response of MM that have optimal specificity and translational attributes. CD38 is uniformly overexpressed in MM and thus represents an ideal target to develop CD38-targeted small molecule PET radiopharmaceuticals to address these challenges. PROCEDURES Using phage display peptide libraries and pioneering algorithms, we identified novel CD38 specific peptides. Imaging bioconjugates were synthesized using solid phase peptide chemistry, and systematically analyzed in vitro and in vivo in relevant MM systems. RESULTS The CD38-targeted bioconjugates were radiolabeled with copper-64 (64Cu) with100% radiochemical purity and an average specific activity of 3.3 - 6.6 MBq/nmol. The analog NODAGA-PEG4-SL022-GGS (SL022: Thr-His-Tyr-Pro-Ile-Val-Ile) had a Kd of 7.55 ± 0.291 nM and was chosen as the lead candidate. 64Cu-NODAGA-PEG4-SL022-GGS demonstrated high binding affinity to CD38 expressing human myeloma MM.1S-CBR-GFP-WT cells, which was blocked by the non-radiolabeled version of the peptide analog and anti-CD38 clinical antibodies, daratumumab and isatuximab, by 58%, 73%, and 78%, respectively. The CD38 positive MM.1S-CBR-GFP-WT cells had > 68% enhanced cellular binding when compared to MM.1S-CBR-GFP-KO cells devoid of CD38. Furthermore, our new CD38-targeted radiopharmaceutical allowed visualization of tumors located in marrow rich bones, remaining there for up to 4 h. Clearance from non-target organs occurred within 60 min. Quantitative PET data from a murine disseminated tumor model showed significantly higher accumulation in the bones of tumor-bearing animals compared to tumor-naïve animals (SUVmax 2.06 ± 0.4 versus 1.24 ± 0.4, P = 0.02). Independently, tumor uptake of the target compound was significantly higher (P = 0.003) compared to the scrambled peptide, 64Cu-NODAGA-PEG4-SL041-GGS (SL041: Thr-Tyr-His-Ile-Pro-Ile-Val). The subcutaneous MM model demonstrated significantly higher accumulation in tumors compared to muscle at 1 and 4 h after tracer administration (SUVmax 0.8 ± 0.2 and 0.14 ± 0.04, P = 0.04 at 1 h; SUVmax 0.89 ± 0.01 and 0.09 ± 0.01, P = 0.0002 at 4 h). CONCLUSIONS The novel CD38-targeted, radiolabeled bioconjugates were specific and allowed visualization of MM, providing a starting point for the clinical translation of such tracers for the detection of MM.
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Affiliation(s)
- Alexander Zheleznyak
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rui Tang
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kathleen Duncan
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Brad Manion
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kexian Liang
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Baogang Xu
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Alexander Vanover
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anchal Ghai
- Department of Biomedical Engineering, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Julie Prior
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Stephen Lees
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Samuel Achilefu
- Department of Biomedical Engineering, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kimberly Kelly
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Monica Shokeen
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Alvin J. Siteman Cancer Center, Washington University School of Medicine and Barnes-Jewish Hospital, St. Louis, MO, 63110, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63110, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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10
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Lee CH, Wu CJ, Yang YY, Wang WC, Leu SJ, Wu CT, Kao PS, Liu KJ, Tsai BY, Chiang YW, Mao YC, Benedict Dlamini N, Chang J. Characterization of chicken-derived antibody against Alpha-Enolase of Streptococcus pneumoniae. Int Immunopharmacol 2024; 128:111476. [PMID: 38185035 DOI: 10.1016/j.intimp.2023.111476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/24/2023] [Accepted: 12/29/2023] [Indexed: 01/09/2024]
Abstract
Streptococcus pneumoniae is a clinically relevant pathogen notorious for causing pneumonia, meningitis, and otitis media in immunocompromised patients. Currently, antibiotic therapy is the most efficient treatment for fighting pneumococcal infections. However, an arise in antimicrobial resistance in S. pneumoniae has become a serious health issue globally. To resolve the problem, alternative and cost-effective strategies, such as monoclonal antibody-based targeted therapy, are needed for combating bacterial infection. S. pneumoniae alpha-enolase (spEno1), which is thought to be a great target, is a surface protein that binds and converts human plasminogen to plasmin, leading to accelerated bacterial infections. We first purified recombinant spEno1 protein for chicken immunization to generate specific IgY antibodies. We next constructed two single-chain variable fragments (scFv) antibody libraries by phage display technology, containing 7.2 × 107 and 4.8 × 107 transformants. After bio-panning, ten scFv antibodies were obtained, and their binding activities to spEno1 were evaluated on ELISA, Western blot and IFA. The epitopes of spEno1 were identified by these scFv antibodies, which binding affinities were determined by competitive ELISA. Moreover, inhibition assay displayed that the scFv antibodies effectively inhibit the binding between spEno1 and human plasminogen. Overall, the results suggested that these scFv antibodies have the potential to serve as an immunotherapeutic drug against S. pneumoniae infections.
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Affiliation(s)
- Chi-Hsin Lee
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan; Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Chao-Jung Wu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan; Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Yi-Yuan Yang
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan; Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan; Core Laboratory of Antibody Generation and Research, Taipei Medical University, Taipei 110301, Taiwan
| | - Wei-Chu Wang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Sy-Jye Leu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan; Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Cheng-Tsang Wu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Pei-Shih Kao
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Ko-Jiunn Liu
- National Institute of Cancer Research, National Health Research Institutes, Tainan 70456, Taiwan
| | - Bor-Yu Tsai
- Navi Bio-Therapeutics Inc., Taipei 10351, Taiwan
| | - Yu-Wei Chiang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Yan-Chiao Mao
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Nhlanhla Benedict Dlamini
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Jungshan Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan; International Master/Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
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11
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Chen F, Liu Z, Kang W, Jiang F, Yang X, Yin F, Zhou Z, Li Z. Single-domain antibodies against SARS-CoV-2 RBD from a two-stage phage screening of universal and focused synthetic libraries. BMC Infect Dis 2024; 24:199. [PMID: 38350843 PMCID: PMC10865538 DOI: 10.1186/s12879-024-09022-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is an evolving global pandemic, and nanobodies, as well as other single-domain antibodies (sdAbs), have been recognized as a potential diagnostic and therapeutic tool for infectious diseases. High-throughput screening techniques such as phage display have been developed as an alternative to in vivo immunization for the discovery of antibody-like target-specific binders. METHODS We designed and constructed a highly diverse synthetic phage library sdAb-U (single-domain Antibody - Universal library ) based on a human framework. The SARS-CoV-2 receptor-binding domain (RBD) was expressed and purified. The universal library sdAb-U was panned against the RBD protein target for two rounds, followed by monoclonal phage ELISA (enzyme-linked immunosorbent assay) to identify RBD-specific binders (the first stage). High-affinity binders were sequenced and the obtained CDR1 and CDR2 sequences were combined with fully randomized CDR3 to construct a targeted (focused) phage library sdAb-RBD, for subsequent second-stage phage panning (also two rounds) and screening. Then, sequences with high single-to-background ratios in phage ELISA were selected for expression. The binding affinities of sdAbs to RBD were measured by an ELISA-based method. In addition, we conducted competition ELISA (using ACE2 ectodomain S19-D615) and SARS-CoV-2 pseudovirus neutralization assays for the high-affinity RBD-binding sdAb39. RESULTS Significant enrichments were observed in both the first-stage (universal library) and the second-stage (focused library) phage panning. Five RBD-specific binders were identified in the first stage with high ELISA signal-to-background ratios. In the second stage, we observed a much higher possibility of finding RBD-specific clones in phage ELISA. Among 45 selected RBD-positive sequences, we found eight sdAbs can be well expressed, and five of them show high-affinity to RBD (EC50 < 100nM). We finally found that sdAb39 (EC50 ~ 4nM) can compete with ACE2 for binding to RBD. CONCLUSION Overall, this two-stage strategy of synthetic phage display libraries enables rapid selection of SARS-CoV-2 RBD sdAb with potential therapeutic activity, and this two-stage strategy can potentially be used for rapid discovery of sdAbs against other targets.
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Affiliation(s)
- Fangfang Chen
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Zhihong Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei Kang
- NanoAI Biotech Co., Ltd, Pingshan District, Shenzhen, China
| | - Fan Jiang
- NanoAI Biotech Co., Ltd, Pingshan District, Shenzhen, China.
| | - Xixiao Yang
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Ziyuan Zhou
- National Cancer Center, National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China.
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
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12
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Mustafa MI, Mohammed A. Developing recombinant antibodies by phage display technology to neutralize viral infectious diseases. SLAS Discov 2024:S2472-5552(24)00001-7. [PMID: 38182043 DOI: 10.1016/j.slasd.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
The use of recombinant antibodies developed through phage display technology offers a promising approach for combating viral infectious diseases. By specifically targeting antigens on viral surfaces, these antibodies have the potential to reduce the severity of infections or even prevent them altogether. With the emergence of new and more virulent strains of viruses, it is crucial to develop innovative methods to counteract them. Phage display technology has proven successful in generating recombinant antibodies capable of targeting specific viral antigens, thereby providing a powerful tool to fight viral infections. In this mini-review article, we examine the development of these antibodies using phage display technology, and discuss the associated challenges and opportunities in developing novel treatments for viral infectious diseases. Furthermore, we provide an overview of phage display technology. As these methods continue to evolve and improve, novel and sophisticated tools based on phage display and peptide display systems are constantly emerging, offering exciting prospects for solving scientific, medical, and technological problems related to viral infectious diseases in the near future.
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Affiliation(s)
- Mujahed I Mustafa
- Department of Biotechnology, College of Applied and Industrial Sciences, University of Bahri, Khartoum, South Sudan.
| | - Ahmed Mohammed
- Department of Biotechnology, School of Life Sciences and Technology, Omdurman Islamic university, Omdurman, South Sudan
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13
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Peabody J, Core SB, Ronsard L, Lingwood D, Peabody DS, Chackerian B. An Approach for Antigen-Agnostic Identification of Virus-Like Particle-Displayed Epitopes that Engage Specific Antibody V Gene Regions. Methods Mol Biol 2024; 2720:55-74. [PMID: 37775657 DOI: 10.1007/978-1-0716-3469-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Antibody complementarity determining regions (CDRs) participate in antigen recognition, but not all participate equally in antigen binding. Here we describe a technique for discovering strong, specific binding partners to defined motifs within the CDRs of chimeric, engineered antibodies using affinity selection and counter-selection of epitopes displayed on bacteriophage MS2-based virus-like particles (VLPs). As an example, we show how this technique can be used to identify families of VLPs that interact with antibodies displaying the CDRs encoded by the germline precursor of a broadly neutralizing monoclonal antibody against HIV-1.
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Affiliation(s)
- Julianne Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Susan B Core
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - David S Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Bryce Chackerian
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA.
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14
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Chau B, Liivak K, Gao J. Construction of Nonnatural Cysteine-Cross-Linked Phage Libraries. Methods Mol Biol 2024; 2738:317-332. [PMID: 37966607 DOI: 10.1007/978-1-0716-3549-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Phage display is a powerful technique for rapid construction and screening of peptide libraries with over 109 sequence diversity. The M13 bacteriophage genome can be edited to incorporate randomized amino acids, which will be displayed on its minor coat protein (pIII). To enable screening of nonnatural cyclic peptides on phage, the minor coat protein can be modified with a chemical cross-linker. By taking advantage of the nucleophilicity and low abundance of free cysteines on phage, a variety of cysteine cross-linkers can be installed on the pIII protein. Here, we describe the construction of a chemically modified cyclic phage library through a cysteine cross-linking reagent, 1,3-dichloroacetone (DCA).
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Affiliation(s)
- Brittney Chau
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Kristi Liivak
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA.
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15
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Peng H, Chen IA. Preparation of Bioconjugates of Chimeric M13 Phage and Gold Nanorods. Methods Mol Biol 2024; 2793:131-141. [PMID: 38526728 DOI: 10.1007/978-1-0716-3798-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Phage-nanomaterial conjugates are functional bio-nanofibers with various applications. While phage display can select for phages with desired genetically encoded functions and properties, nanomaterials can endow the phages with additional features at nanoscale dimensions. Therefore, combining phages with nanotechnology can construct bioconjugates with unique characteristics. One strategy for filamentous phages is to adsorb nanoparticles onto the side wall, composed of pVIII subunits, through electrostatic interactions. However, a noncovalent approach may cause offloading if the environment changes, potentially causing side effects especially for in vivo applications. Therefore, building stable phage-bioconjugates is an important need. We previously reported the construction of chimeric M13 phage conjugated with gold nanorods, named "phanorods," without weakening the binding affinity to the bacterial host cells. Herein, we give a detailed protocol for preparing the chimeric M13 phage and covalently conjugating gold nanorods to the phage.
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Affiliation(s)
- Huan Peng
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
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16
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Macias ALD, Alecrim LC, Almeida FCL, Giordano RJ. Understanding the Structural Requirements of Peptide-Protein Interaction and Applications for Peptidomimetic Development. Methods Mol Biol 2024; 2793:65-82. [PMID: 38526724 DOI: 10.1007/978-1-0716-3798-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Protein-protein interaction is at the heart of most biological processes, and small peptides that bind to protein binding sites are resourceful tools to explore and understand the structural requirements for these interactions. In that sense, phage display is a well-suited technology to study protein-protein interactions, as it allows for unbiased screening of billions of peptides in search for those that interact with a protein binding domain. Here, we will illustrate how two distinct but complementary approaches, phage display and nuclear magnetic resonance (NMR), can be utilized to unveil structural details of peptide-protein interaction. Finally, knowledge derived from phage mutagenesis and NMR studies can be streamlined for quick peptidomimetic design and synthesis using the retroinversion approach to validate using in vitro and in vivo assays the therapeutic potential of peptides identified by phage display.
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Affiliation(s)
| | - Lilian Costa Alecrim
- Biochemistry Department, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo Jose Giordano
- Biochemistry Department, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil.
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17
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Song BPC, Ch'ng ACW, Lim TS. Review of phage display: A jack-of-all-trades and master of most biomolecule display. Int J Biol Macromol 2024; 256:128455. [PMID: 38013083 DOI: 10.1016/j.ijbiomac.2023.128455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Phage display was first described by George P. Smith when it was shown that virus particles were capable of presenting foreign proteins on their surface. The technology has paved the way for the evolution of various biomolecules presentation and diverse selection strategies. This unique feature has been applied as a versatile platform for numerous applications in drug discovery, protein engineering, diagnostics, and vaccine development. Over the decades, the limits of biomolecules displayed on phage particles have expanded from peptides to proteomes and even alternative scaffolds. This has allowed phage display to be viewed as a versatile display platform to accommodate various biomolecules ranging from small peptides to larger proteomes which has significantly impacted advancements in the biomedical industry. This review will explore the vast array of biomolecules that have been successfully employed in phage display technology in biomedical research.
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Affiliation(s)
- Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - 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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18
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Song BPC, Lai JY, Lim TS. Generation of a Naïve Human scFv Phage Display Library and Panning Selection. Methods Mol Biol 2024; 2793:21-40. [PMID: 38526721 DOI: 10.1007/978-1-0716-3798-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Phage display antibody libraries have been successfully used as the essential tool to produce monoclonal antibodies against a plethora of targets ranging from diseases to native biologically important proteins as well as small molecules. It is well documented that diverse antibody genes are the major genetic source for the construction of a high-quality antibody library and selection of high-affinity antibodies. Naïve antibody libraries are derived using the IgM repertoire of healthy donors obtained from B-cells isolated from human peripheral blood mononuclear cell (PBMC). Single-chain fragment variable (scFv) is a routinely used format due to its smaller size and preference for phage display. The process involves the use of a two-step cloning method for library construction. The protocol also covers the biopanning process for target positive clone selection.
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Affiliation(s)
- Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang, Malaysia.
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19
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Van Deuren V, Plessers S, Lavigne R, Robben J. Application of Deep Sequencing in Phage Display. Methods Mol Biol 2024; 2738:333-345. [PMID: 37966608 DOI: 10.1007/978-1-0716-3549-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
This chapter describes the workflow to implement deep sequencing into standard phage display experiments on protein libraries. By harvesting the power of high throughput of these techniques, it allows for comprehensive analysis of the naïve library and library evolution in response to selection by ligand binding. The mutagenized target region of the protein variants encoded by the phage pool is analyzed by Illumina paired-end sequencing. Sequence data are processed to extract selection-enriched amino acid motifs. In addition, a complementary long-read sequencing approach is proposed enabling the monitoring of display vector stability.
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Affiliation(s)
- Vincent Van Deuren
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium
| | - Sander Plessers
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Animal and Human Health Engineering (A2H), Leuven (Arenberg), KU Leuven, Leuven, Belgium
| | - Johan Robben
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium.
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20
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Zhuang X, Chen S, Pan L. Structure-Guided and Phage-Assisted Evolution of Therapeutic Antibodies to Reverse On-Target Point Mutation-Mediated Resistance. Methods Mol Biol 2024; 2793:41-54. [PMID: 38526722 DOI: 10.1007/978-1-0716-3798-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Resistance to therapeutic antibodies caused by on-target point mutations is a major obstacle in anticancer therapy, creating an "unmet clinical need." To tackle this problem, researchers are developing new generations of antibody drugs that can overcome the resistance mechanisms of existing agents. We have previously reported a structure-guided and phage-assisted evolution (SGAPAE) approach to evolve cetuximab, a therapeutic antibody, to effectively reverse the resistance driven by EGFRS492R or EGFRG465R mutations, without changing the binding epitope or compromising the antibody efficacy. In this protocol, we provide detailed instructions on how to use the SGAPAE approach to evolve cetuximab, which can also be applied to other therapeutic antibodies for reversing on-target point mutation-mediated resistance. The protocol consists of four steps: structure preparation, computational prediction, phage display library construction, and antibody candidate selection.
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Affiliation(s)
- Xinlei Zhuang
- School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shuqing Chen
- School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Liqiang Pan
- School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
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Afsharnoori F, Forouzandeh Moghadam M. Isolation and characterization of a novel single-chain variable fragment (scFv) against Lymphocyte function-associated antigen-1 (LFA-1) using phage display method. Med Oncol 2023; 41:15. [PMID: 38078968 DOI: 10.1007/s12032-023-02242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023]
Abstract
Lymphocyte function-associated antigene-1 (LFA-1) is a well-described integrin found on lymphocytes and other leukocytes, which is known to be overexpressed in leukemias and lymphomas. This receptor plays a significant role in immune responses such as T-cell activation, leukocyte cell-cell interactions, and trafficking of leukocyte populations. Subsequently, binders of LFA-1 emerge as potential candidates for cancer and autoimmune therapy. This study used the phage display technique to construct and characterize a high-affinity single-chain fragment variable (scFv) antibody against LFA-1. After expression, purification, dialysis, and concentration of the recombinant LFA-1 protein, four female BALB/c mice were immunized, splenocyte's mRNA was extracted, and cDNA was synthesized. A scFv library was constructed by linking the amplified VH/Vκ fragments through a 72-bp linker using SOEing PCR. Next, the scFv gene fragments were cloned into the pComb-3XSS phagemid vector; thus, the phage library was developed. The selection process involved three rounds of phage-bio-panning, polyclonal, and monoclonal phage ELISA. AF17 was chosen and characterized among the positive clones through SDS-PAGE, Western blotting, indirect ELISA, and in-silico analyses. The results of the study showed the successful construction of a high-affinity scFv library against LFA-1. The accuracy of the AF17 production and its ability to bind to the LFA-1 were confirmed through SDS-PAGE, Western blot, and ELISA. This study highlights the potential application of the high-affinity AF17 against LFA-1 for targeting T lymphocytes for therapeutic purposes.
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Affiliation(s)
- Fatemeh Afsharnoori
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran
| | - Mehdi Forouzandeh Moghadam
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran.
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Ganji M, Safarzadeh Kozani P, Rahbarizadeh F. Characterization of novel CD19-specific VHHs isolated from a camelid immune library by phage display. J Transl Med 2023; 21:891. [PMID: 38066569 PMCID: PMC10709854 DOI: 10.1186/s12967-023-04524-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/13/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Monoclonal antibody (mAb)-based immunotherapies have achieved promising outcomes in the treatment of immunological and oncological indications. CD19 is considered one of the most qualified antigens in the treatment of B-cell neoplasms. VHHs (nanobodies) are known for their physicochemical advantages over conventional mAbs rendering them suitable therapeutics and diagnostic tools. Herein, we aimed to isolate CD19-specific VHHs from a novel immune library using phage display. METHODS An immune VHH gene library was constructed. Using phage display and after five biopanning rounds, two monoclonal CD19-specific VHHs were isolated. The selected VHHs were expressed, purified, and characterized in terms of their affinity, specificity, sensitivity, and ability to target CD19-positive cell lines. Moreover, in silico analyses were employed for further characterization. RESULTS A VHH library was developed, and because the outputs of the 4th biopanning round exhibited the most favorable characteristics, a panel of random VHHs was selected from them. Ultimately, two of the most favorable VHHs were selected and DNA sequenced (designated as GR37 and GR41). Precise experiments indicated that GR37 and GR41 exhibited considerable specificity, sensitivity, and affinity (1.15 × 107 M-1 and 2.08 × 107 M-1, respectively) to CD19. Flow cytometric analyses revealed that GR37 and GR41 could bind CD19 on the surface of cell lines expressing the antigen. Moreover, in silico experiments predicted that both VHHs target epitopes that are distinct from that targeted by the CD19-specific single-chain variable fragment (scFv) FMC63. CONCLUSION The selected VHHs can be used as potential targeting tools for the development of CD19-based immunotherapeutics.
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Affiliation(s)
- Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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Fadaie M, Dianat-Moghadam H, Ghafouri E, Naderi S, Darvishali MH, Ghovvati M, Khanahmad H, Boshtam M, Makvandi P. Unraveling the potential of M13 phages in biomedicine: Advancing drug nanodelivery and gene therapy. Environ Res 2023; 238:117132. [PMID: 37714365 DOI: 10.1016/j.envres.2023.117132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
M13 phages possessing filamentous phage genomes offer the benefits of selective display of molecular moieties and delivery of therapeutic agent payloads with a tolerable safety profile. M13 phage-displayed technology for resembling antigen portions led to the discovery of mimetic epitopes that applied to antibody-based therapy and could be useful in the design of anticancer vaccines. To date, the excremental experiences have engaged the M13 phage in the development of innovative biosensors for detecting biospecies, biomolecules, and human cells with an acceptable limit of detection. Addressing the emergence of antibiotic-resistant bacteria, M13 phages are potent for packaging the programmed gene editing tools, such as CRISPR/Cas, to target multiple antimicrobial genes. Moreover, their display potential in combination with nanoparticles inspires new approaches for engineering targeted theragnostic platforms targeting multiple cellular biomarkers in vivo. In this review, we present the available data on optimizing the use of bacteriophages with a focus on the to date experiences with M13 phages, either as monoagent or as part of combination regimens in the practices of biosensors, vaccines, bactericidal, modeling of specific antigen epitopes, and phage-guided nanoparticles for drug delivery systems. Despite increasing research interest, a deep understanding of the underlying biological and genetic behaviors of M13 phages is needed to enable the full potential of these bioagents in biomedicine, as discussed here. We also discuss some of the challenges that have thus far limited the development and practical marketing of M13 phages.
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Affiliation(s)
- Mahmood Fadaie
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hassan Dianat-Moghadam
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Ghafouri
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shamsi Naderi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hossein Darvishali
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahsa Ghovvati
- Department of Radiological Sciences, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Pooyan Makvandi
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China.
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Qin Y, Jin J, Zhang J, Wang H, Liu L, Zhang Y, Ling S, Hu J, Li N, Wang J, Lv C, Yang X. A fully human monoclonal antibody targeting Semaphorin 5A alleviates the progression of rheumatoid arthritis. Biomed Pharmacother 2023; 168:115666. [PMID: 37832409 DOI: 10.1016/j.biopha.2023.115666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Rheumatoid arthritis (RA) is the most common chronic autoimmune disease worldwide. Although progress has been made in RA treatment in recent decades, remission cannot be effectively achieved for a considerable proportion of RA patients. Thus, novel potential targets for therapeutic strategies are needed. Semaphorin 5A (SEMA5A) plays a pivotal role in RA progression by facilitating pannus formation, and it is a promising therapeutic target. In this study, we sought to develop an antibody treatment strategy targeting SEMA5A and evaluate its therapeutic effect using a collagen-induced arthritis (CIA) model. We generated SYD12-12, a fully human SEMA5A blocking antibody, through phage display technology. SYD12-12 intervention effectively inhibited angiogenesis and aggressive phenotypes of RA synoviocytes in vitro and dose-dependently inhibited synovial hyperplasia, pannus formation, bone destruction in CIA mice. Notably, SYD12-12 also improved the Treg/Th17 imbalance in CIA mice. We confirmed through immunofluorescence and molecular docking that SYD12-12 integrated with the unique TSP-1 domain of SEMA5A. In conclusion, we developed and characterized a fully human SEMA5A-blocking antibody for the first time. SYD12-12 effectively alleviated disease progression in CIA mice by inhibiting pannus formation and improving the Treg/Th17 imbalance, demonstrating its potential for the RA treatment.
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Affiliation(s)
- Yang Qin
- Institute of Autoimmune Diseases, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Department of Anesthesia and Critical Care, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jiayi Jin
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jiani Zhang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hui Wang
- Institute of Autoimmune Diseases, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Li Liu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yanwen Zhang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Sunwang Ling
- Institute of Autoimmune Diseases, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jinzhu Hu
- Institute of Autoimmune Diseases, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Nuan Li
- Department of Anesthesia and Critical Care, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianguang Wang
- Institute of Autoimmune Diseases, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Department of Anesthesia and Critical Care, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.
| | - Chen Lv
- Department of Orthopedics, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
| | - Xinyu Yang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China; Department of Anesthesia and Critical Care, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.
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25
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Mazzocato Y, Perin S, Morales-Sanfrutos J, Romanyuk Z, Pluda S, Acquasaliente L, Borsato G, De Filippis V, Scarso A, Angelini A. A novel genetically-encoded bicyclic peptide inhibitor of human urokinase-type plasminogen activator with better cross-reactivity toward the murine orthologue. Bioorg Med Chem 2023; 95:117499. [PMID: 37879145 DOI: 10.1016/j.bmc.2023.117499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/30/2023] [Accepted: 10/10/2023] [Indexed: 10/27/2023]
Abstract
The inhibition of human urokinase-type plasminogen activator (huPA), a serine protease that plays an important role in pericellular proteolysis, is a promising strategy to decrease the invasive and metastatic activity of tumour cells. However, the generation of selective small molecule huPA inhibitors has proven to be challenging due to the high structural similarity of huPA to other paralogue serine proteases. Efforts to generate more specific therapies have led to the development of cyclic peptide-based inhibitors with much higher selectivity against huPA. While this latter property is desired, the sparing of the orthologue murine poses difficulties for the testing of the inhibitor in preclinical mouse model. In this work, we have applied a Darwinian evolution-based approach to identify phage-encoded bicyclic peptide inhibitors of huPA with better cross-reactivity towards murine uPA (muPA). The best selected bicyclic peptide (UK132) inhibited huPA and muPA with Ki values of 0.33 and 12.58 µM, respectively. The inhibition appears to be specific for uPA, as UK132 only weakly inhibits a panel of structurally similar serine proteases. Removal or substitution of the second loop with one not evolved in vitro led to monocyclic and bicyclic peptide analogues with lower potency than UK132. Moreover, swapping of 1,3,5-tris-(bromomethyl)-benzene with different small molecules not used in the phage selection, resulted in an 80-fold reduction of potency, revealing the important structural role of the branched cyclization linker. Further substitution of an arginine in UK132 to a lysine resulted in a bicyclic peptide UK140 with enhanced inhibitory potency against both huPA (Ki = 0.20 µM) and murine orthologue (Ki = 2.79 µM). By combining good specificity, nanomolar affinity and a low molecular mass, the bicyclic peptide inhibitor developed in this work may provide a novel human and murine cross-reactive lead for the development of a potent and selective anti-metastatic therapy.
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Affiliation(s)
- Ylenia Mazzocato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Stefano Perin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Julia Morales-Sanfrutos
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), C. de Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Zhanna Romanyuk
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Stefano Pluda
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; Fidia Farmaceutici S.p.A., Via Ponte della Fabbrica 3/A, Abano Terme 35031, Italy
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Giuseppe Borsato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Vincenzo De Filippis
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Alessandro Scarso
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy.
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26
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Najafi A, Valadan R, Asgarian-Omran H, Rafiei A, Tehrani M. Single domain antibodies specific for HER2 dimerization domain effectively disrupts HER2 dimerization. Int Immunopharmacol 2023; 124:110999. [PMID: 37804659 DOI: 10.1016/j.intimp.2023.110999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/23/2023] [Accepted: 09/24/2023] [Indexed: 10/09/2023]
Abstract
Dimer-dependent phosphorylation of HER2 receptor is a key event for the signal transduction of HER family of receptors which correlates with tumor invasion and metastasis. New generation of therapies based on dimerization domain inhibition using monoclonal or fragment antibodies was introduced. A potent method for manufacturing antibodies and antibody fragments is the phage display antibody library method. A recombinant phage was generated using the phage display method from synthetic dAb library. Subtractive biopanning was performed on sepharose 4b resin. Evaluation of success of subtractive biopanning was confirmed by the PCR fingerprinting after the fourth round of biopanning. The fourth round of biopanning results in the isolation of several dimerization domain reactive clones based on the polyclonal phage ELISA results. Monoclonal phage cell ELISA was used to select the positive clones with the highest affinity, and they were subsequently employed for functional tests. Cell-ELISA, MTT assay and dimerization inhibition test revealed that the reactivity and specificity of the selected monoclonal phage to dimerization domain of HER2. Further, Annexin V/PI staining and gene expression analysis showed that increased apoptosis rates. Also, in silico binding of the selected clones to conformational structure of HER2 was applied, using protein-protein docking tool of the ICM-Pro software, and showed sdAbs were specifically interacted with dimerization domain of the receptor. In conclusion, we have identified a single domain targeting HER2 dimerization, which represents a promising therapeutic and diagnostic candidate for HER2-positive cancers. Purified sdAb needs to more research to evaluate it both in vivo and in vitro via functional tests to determine if it can be applied for treatment and diagnostics.
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Affiliation(s)
- Ahmad Najafi
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Reza Valadan
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell-Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Hossein Asgarian-Omran
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell-Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Alireza Rafiei
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell-Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Mohsen Tehrani
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell-Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
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Manzato VDM, Di Santo C, Torquato RJS, Coelho C, Gallo G, Hardy L, Würtele M, Tanaka AS. Boophilin D1, a Kunitz type protease inhibitor, as a source of inhibitors for the ZIKA virus NS2B-NS3 protease. Biochimie 2023; 214:96-101. [PMID: 37364769 DOI: 10.1016/j.biochi.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Arboviruses are a global concern for a multitude of reasons, including their increased incidence and human mortality. Vectors associated with arboviruses include the mosquito Aedes sp., which is responsible for transmitting the Zika virus. Flaviviruses, like the Zika virus, present only one chymotrypsin-like serine protease (NS3) in their genome. Together with host enzymes, the NS2B co-factor NS3 protease complex are essential for the viral replication cycle by virus polyprotein processing. To search for Zika virus NS2B-NS3 protease (ZIKVPro) inhibitors, a phage display library was constructed using the Boophilin domain 1 (BoophD1), a thrombin inhibitor from the Kunitz family. A BoophilinD1 library mutated at positions P1-P4' was constructed, presenting a titer of 2.9x106 (cfu), and screened utilizing purified ZIKVPro. The results demonstrated at the P1-P4' positions the occurrence of 47% RALHA sequence (mut 12) and 11.8% RASWA sequence (mut14), SMRPT, or KALIP (wt) sequence. BoophD1-wt and mutants 12 and 14 were expressed and purified. The purified BoophD1 wt, mut 12 and 14, presented Ki values for ZIKVPro of 0.103, 0.116, and 0.101 μM, respectively. The BoophD1 mutant inhibitors inhibit the Dengue virus 2 protease (DENV2) with Ki values of 0.298, 0.271, and 0.379 μM, respectively. In conclusion, BoophD1 mut 12 and 14 selected for ZIKVPro demonstrated inhibitory activity like BoophD1-wt, suggesting that these are the strongest Zika inhibitors present in the BoophD1 mutated phage display library. Furthermore, BoophD1 mutants selected for ZIKVPro inhibit both Zika and Dengue 2 proteases making them potential pan-flavivirus inhibitors.
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Affiliation(s)
- Veronica de Moraes Manzato
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Camila Di Santo
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Ricardo Jose Soares Torquato
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Camila Coelho
- Department of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Gloria Gallo
- Department of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Leon Hardy
- Department of Physics, University of South Florida, Tampa, USA
| | - Martin Würtele
- Department of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Aparecida Sadae Tanaka
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), RJ, Brazil.
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28
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Chang FL, Tsai KC, Lin TY, Chiang CW, Pan SL, Lee YC. Effectiveness of anti-erythropoietin producing Hepatocellular receptor Type-A2 antibody in pancreatic cancer treatment. Heliyon 2023; 9:e21774. [PMID: 38034633 PMCID: PMC10682614 DOI: 10.1016/j.heliyon.2023.e21774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Erythropoietin-producing hepatocyte receptor type A2 (EphA2) is a tyrosine kinase that binds to ephrins (e.g., ephrin-A1) to initiate bidirectional signaling between cells. The binding of EphA2 and ephrin-A1 leads to the inhibition of Ras-MAPK activity and tumor growth. During tumorigenesis, the normal interaction between EphA2 and ephrin-A1 is hindered, which leads to the overexpression of EphA2 and induces cancer. The overexpression of EphA2 has been identified as a notable tumor marker in diagnosing and treating pancreatic cancer. In this study, we used phage display to isolate specific antibodies against the active site of EphA2 by using a discontinuous recombinant epitope for immunization. The therapeutic efficacy and inhibition mechanism of the generated antibody against pancreatic cancer was validated and clarified. The generated antibodies were bound to the conformational epitope of endogenous EphA2 on cancer cells, thus inducing cellular endocytosis and causing EphA2 degradation. Molecule signals pAKT, pERK, pFAK, and pSTAT3 were weakened, inhibiting the proliferation and migration of pancreatic cancer cells. The humanized antibody hSD5 could effectively inhibit the growth of the xenograft pancreatic cancer tumor cells BxPc-3 and Mia PaCa-2 in mice, respectively. When antibody hSD5 was administered with gemcitabine, significantly improved effects on tumor growth inhibition were observed. Based on the efficacy of the IgG hSD5 antibodies, clinical administration of the hSD5 antibodies is likely to suppress tumors in patients with pancreatic cancer and abnormal activation or overexpression of EphA2 signaling.
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Affiliation(s)
- Fu-Ling Chang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
| | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Tsai-Yu Lin
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Chen-Wei Chiang
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Shiow-Lin Pan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, Taiwan
| | - Yu-Ching Lee
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
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29
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Peng S, Husnain Raza Shah S, Mei S, Gene Vong E, Sun Y, Zhan J. RBD-specific single-chain antibody protects against acute lung injury in mice. Int Immunopharmacol 2023; 124:111020. [PMID: 37812969 DOI: 10.1016/j.intimp.2023.111020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/24/2023] [Accepted: 10/01/2023] [Indexed: 10/11/2023]
Abstract
As SARS-CoV-2 variants continue spreading globally, the discovery of broad spectrum therapeutically active antibodies with retaining good protective activity is a global priority. It was reported that infection with SARS-CoV-2 could cause acute lung injury (ALI) in clinical investigations. Therefore, we discovered that anti-RBD scFv is effective against SARS-CoV-2-induced ALI. To begin, we utilized the receptor binding domain (RBD) of spike glycoprotein as a target to produce single-chain antibodies (scFvs) through an intensive phage display technology. The binding affinity and inhibitory effect of the scFvs were evaluated via ELISA and flow cytometry. Moreover, anti-RBD scFv No.35 significantly prevented ALI caused by LPS and SARS-CoV-2 spike RBD protein in mouse model. Thus, the anti-RBD scFv will aid the development of potential antibody treatments and reduce the inflammatory response of SARS-CoV-2.
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Affiliation(s)
- Shanshan Peng
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou 310056, China
| | - Syed Husnain Raza Shah
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou 310056, China
| | - Shengsheng Mei
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou 310056, China
| | - Eu Gene Vong
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou 310056, China
| | - Yisheng Sun
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Jinbiao Zhan
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou 310056, China.
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Lima MIS, Corrêa MBC, Moraes ECDS, Oliveira JDDD, de Souza Santos P, de Souza AG, Goulart IMB, Goulart LR. HSP60 mimetic peptides from Mycobacterium leprae as new antigens for immunodiagnosis of Leprosy. AMB Express 2023; 13:120. [PMID: 37891336 PMCID: PMC10611693 DOI: 10.1186/s13568-023-01625-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The early diagnosis of leprosy serves as an important tool to reduce the incidence of this disease in the world. Phage display (PD) technology can be used for mapping new antigens to the development of immunodiagnostic platforms. Our objective was to identify peptides that mimic Mycobacterium leprae proteins as serological markers using phage display technology. The phages were obtained in the biopanning using negative and positive serum from household contacts and leprosy patients, respectively. Then, the peptides were synthesized and validated in silico and in vitro for detection of IgG from patients and contacts. To characterize the native protein of M. leprae, scFv antibodies were selected against the synthetic peptides by PD. The scFv binding protein was obtained by immunocapture and confirmed using mass spectrometry. We selected two phase-fused peptides, MPML12 and MPML14, which mimic the HSP60 protein from M. leprae. The peptides MPML12 and MPML14 obtained 100% and 92.85% positivity in lepromatous patients. MPML12 and MPM14 detect IgG, especially in the multibacillary forms. The MPML12 and MPML14 peptides had positivity of 11.1% and 16.6% in household contacts, respectively. There was no cross-reaction in patient's samples with visceral leishmaniasis, tuberculosis and other mycobacteriosis for both peptides. Given these results and the easy obtainment of mimetic antigens, our peptides are promising markers for application in the diagnosis of leprosy, especially in endemic and hyperendemic regions.
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Affiliation(s)
- Mayara Ingrid Sousa Lima
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, MA, Brazil.
- Postgraduate Program on Health and Environment and Postgraduate Program on Health Sciences, Federal University of Maranhão, São Luís, MA, Brazil.
| | | | | | | | - Paula de Souza Santos
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Aline Gomes de Souza
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Isabela Maria Bernardes Goulart
- National Reference Center in Sanitary Dermatology and Leprosy, School of Medicine, Clinics' Hospital, Federal University of Uberlandia, Uberlandia, MG, Brazil.
| | - Luiz Ricardo Goulart
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, MG, Brazil
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
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Hou J, Qian X, Xu Y, Guo Z, Thierry B, Yang CT, Zhou X, Mao C. Rapid and reliable ultrasensitive detection of pathogenic H9N2 viruses through virus-binding phage nanofibers decorated with gold nanoparticles. Biosens Bioelectron 2023; 237:115423. [PMID: 37311406 DOI: 10.1016/j.bios.2023.115423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/19/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023]
Abstract
The rapid and sensitive detection of pathogenic viruses is important for controlling pandemics. Herein, a rapid, ultrasensitive, optical biosensing scheme was developed to detect avian influenza virus H9N2 using a genetically engineered filamentous M13 phage probe. The M13 phage was genetically engineered to bear an H9N2-binding peptide (H9N2BP) at the tip and a gold nanoparticle (AuNP)-binding peptide (AuBP) on the sidewall to form an engineered phage nanofiber, M13@H9N2BP@AuBP. Simulated modelling showed that M13@H9N2BP@AuBP enabled a 40-fold enhancement of the electric field enhancement in surface plasmon resonance (SPR) compared to conventional AuNPs. Experimentally, this signal enhancement scheme was employed for detecting H9N2 particles with a sensitivity down to 6.3 copies/mL (1.04 × 10-5 fM). The phage-based SPR scheme can detect H9N2 viruses in real allantoic samples within 10 min, even at very low concentrations beyond the detection limit of quantitative polymerase chain reaction (qPCR). Moreover, after capturing the H9N2 viruses on the sensor chip, the H9N2-binding phage nanofibers can be quantitatively converted into plaques that are visible to the naked eye for further quantification, thereby allowing us to enumerate the H9N2 virus particles through a second mode to cross-validate the SPR results. This novel phage-based biosensing strategy can be employed to detect other pathogens because the H9N2-binding peptides can be easily switched with other pathogen-binding peptides using phage display technology.
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Affiliation(s)
- Jinxiu Hou
- College of Veterinary Medicine, Institute of Comparative Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Xuejia Qian
- College of Veterinary Medicine, Institute of Comparative Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yi Xu
- School of Optoelectronic Engineering, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Zhirui Guo
- The Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210011, China
| | - Benjamin Thierry
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, SA 5095, Australia
| | - Chih-Tsung Yang
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, SA 5095, Australia.
| | - Xin Zhou
- College of Veterinary Medicine, Institute of Comparative Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Chuanbin Mao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China; School of Materials Science & Engineering, Zhejiang University, Hangzhou, 310027, China.
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Kumada Y, Tanibata R, Yamamoto K, Noguchi H, Angelini A, Horiuchi JI. Development and characterization of a latex turbidimetric immunoassay using rabbit anti-CRP single-chain Fv antibodies. J Immunol Methods 2023; 520:113522. [PMID: 37423589 DOI: 10.1016/j.jim.2023.113522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/19/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
In this study, we developed and demonstrated a latex turbidimetric immunoassay (LTIA) using latex beads immobilized with rabbit monoclonal single-chain variable fragments (scFvs) selected from an scFv-displayed phage library. Sixty-five different anti-c-reactive protein (anti-CRP) scFv clones were identified after biopanning selection using antigen-coupled multi-lamellar vesicles. By ranking antigen-binding clones using the apparent dissociation rate constant (appkoff) as a sorting index, scFv clones with a dissociation constant (KD free) ranging from 4.07 × 10-9 M to 1.21 × 10-11 M were isolated. Among them, three candidates (R2-6, R2-45, and R3-2) were produced in the culture supernatant at concentrations of 50 mg/L or higher in flask culture and maintained at considerably high antigen-binding activity in immobilized state on the CM5 sensor chip surface. All the scFv-immobilized latexes (scFv-Ltxs) prepared were well-dispersed in 50 mM MOPS at pH 7.0, without additives for dispersion, and their antigen-dependent aggregation was sufficiently detectable. The reactivity of scFv-Ltx to antigen differed among the scFv clones, in particular, R2-45 scFv-Ltx detected the CRP with the highest signal. Furthermore, the reactivity of scFv-Ltx varied significantly with salt concentration, scFv immobilization density, and the type of blocking protein. Particularly, antigen-dependent latex aggregation improved significantly in all rabbit scFv clones when scFv-Ltx was blocked with horse muscle myoglobin compared with conventional bovine serum albumin; while their baseline signals in the absence of antigen were fully stable. Under optimal conditions, R2-45 scFv-Ltx exhibited greater aggregation signals with antigen concentrations higher than those produced by conventional polyclonal antibody-immobilized latex for CRP detection in LTIA. The methodology for rabbit scFv isolation, immobilization, and antigen-dependent latex aggregation demonstrated in the present study can be applicable to scFv-based LTIA for various target antigens.
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Affiliation(s)
- Yoichi Kumada
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo Kyoto 606-8585, Japan.
| | - Reina Tanibata
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo Kyoto 606-8585, Japan
| | | | | | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Jun-Ichi Horiuchi
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo Kyoto 606-8585, Japan
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Németh BZ, Nagy ZA, Kiss B, Gellén G, Schlosser G, Demcsák A, Geisz A, Hegyi E, Sahin-Tóth M, Pál G. Substrate specificity of human chymotrypsin-like protease (CTRL) characterized by phage display-selected small-protein inhibitors. Pancreatology 2023; 23:742-749. [PMID: 37604733 PMCID: PMC10528761 DOI: 10.1016/j.pan.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
Chymotrypsin-like protease (CTRL) is one of the four chymotrypsin isoforms expressed in the human exocrine pancreas. Human genetic and experimental evidence indicate that chymotrypsins B1, B2, and C (CTRB1, CTRB2 and CTRC) are important not only for protein digestion but also for protecting the pancreas against pancreatitis by degrading potentially harmful trypsinogen. CTRL has not been reported to play a similar role, possibly due to its low abundance and/or different substrate specificity. To address this problem, we investigated the specificity of the substrate-binding groove of CTRL by evolving the substrate-like canonical loop of the Schistocerca gregaria proteinase inhibitor 2 (SGPI-2), a small-protein reversible chymotrypsin inhibitor to bind CTRL. We found that phage-associated SGPI-2 variants with strong affinity to CTRL were similar to those evolved previously against CTRB1, CTRB2 or bovine chymotrypsin A (bCTRA), indicating comparable substrate specificity. When tested as recombinant proteins, SGPI-2 variants inhibited CTRL with similar or slightly weaker affinity than bCTRA, confirming that CTRL is a typical chymotrypsin. Interestingly, an SGPI-2 variant selected with a Thr29His mutation in its reactive loop was found to inhibit CTRL strongly, but it was digested rapidly by bCTRA. Finally, CTRL was shown to degrade human anionic trypsinogen, however, at a much slower rate than CTRB2, suggesting that CTRL may not have a significant role in the pancreatic defense mechanisms against inappropriate trypsinogen activation and pancreatitis.
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Affiliation(s)
- Bálint Zoltán Németh
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, H-1117, Budapest, Hungary
| | - Zoltán Attila Nagy
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, H-1117, Budapest, Hungary
| | - Bence Kiss
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, H-1117, Budapest, Hungary
| | - Gabriella Gellén
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, Budapest, H-1117, Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, Budapest, H-1117, Budapest, Hungary
| | - Alexandra Demcsák
- Department of Surgery, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Andrea Geisz
- Department of Surgery, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Eszter Hegyi
- Institute for Translational Medicine, University of Pécs, Medical School, H-7624, Pécs, Hungary
| | - Miklós Sahin-Tóth
- Department of Surgery, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Gábor Pál
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, H-1117, Budapest, Hungary.
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Chen YL, Xie XX, Zheng P, Zhu C, Ma H, Khalid Z, Xie YJ, Dang YZ, Ye Y, Sheng N, Zhong N, Lei WH, Zhang C, Zhang LJ, Jin T, Cao MJ. Selection, identification and crystal structure of shark-derived single-domain antibodies against a green fluorescent protein. Int J Biol Macromol 2023; 247:125852. [PMID: 37460076 DOI: 10.1016/j.ijbiomac.2023.125852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023]
Abstract
Shark variable domain of new antigen receptors (VNARs) are the smallest naturally occurring binding domains with properties of low complexity, small size, cytoplasmic expression, and ease of engineering. Green fluorescent protein (GFP) molecules have been analyzed in conventional microscopy, but their spectral characteristics preclude their use in techniques offering substantially higher resolution. Besides, the GFP molecules can be quenched in acidic environment, which makes it necessary to develop anti-GFP antibody to solve these problems. In view of the diverse applications of GFP and unique physicochemical features of VNAR, the present study aims to generate VNARs against GFP. Here, we identified 36 VNARs targeting eCGP123, an extremely stable GFP, by phage display from three immunized sharks. These VNARs bound to eCGP123 with affinity constant KD values ranging from 6.76 to 605 nM. Among them, two lead VNARs named aGFP-14 and aGFP-15 with nanomolar eCGP123-binding affinity were selected for in-depth characterization. aGFP-14 and aGFP-15 recognized similar epitopes on eCGP123. X-ray crystallography studies clarified the mechanism by which aGFP14 interacts with eCGP123. aGFP-14 also showed cross-reaction with EGFP, with KD values of 47.2 nM. Finally, immunostaining analyses demonstrated that aGFP-14 was able to bind effectively to the EGFP expressed in both cultured cells and mouse brain tissues, and can be used as a fluorescence amplifier for EGFP. Our research demonstrates a feasible idea for the screening and production of shark-derived VNARs. The two high-affinity VNARs developed in the study contribute to the diversity of GFP sdAbs and may enhance the applications of GFP.
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Affiliation(s)
- Yu-Lei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xin-Xin Xie
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Peiyi Zheng
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Chenchen Zhu
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Huan Ma
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Zunera Khalid
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Yang-Jie Xie
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Yi-Zhao Dang
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Yaxin Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Nengyin Sheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ning Zhong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Wen-Hui Lei
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | | | - Ling-Jing Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Tengchuan Jin
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China.
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China.
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Garcia-Calvo E, García-García A, Rodríguez Gómez S, Farrais S, Martín R, García T. Development of a new recombinant antibody, selected by phage-display technology from a celiac patient library, for detection of gluten in foods. Curr Res Food Sci 2023; 7:100578. [PMID: 37680694 PMCID: PMC10480589 DOI: 10.1016/j.crfs.2023.100578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/28/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
Gluten, a group of ethanol-soluble proteins present in the endosperm of cereals, is extensively used in the food industry due to its ability to improve dough properties. However, gluten is also associated with a range of gluten-related diseases (GRDs), such as wheat allergies, celiac disease, and gluten intolerance. The recommended treatment for GRDs patients is a gluten-free diet. To monitor adherence to this diet, it is necessary to develop gluten-detection systems in food products. Among the available methods, immunodetection systems are the most popular due to their simplicity, reproducibility, and accuracy. The aim of this study was to generate novel high-affinity antibodies against gluten to be used as the primary reactant in an enzyme-linked immunosorbent assay (ELISA) test. These antibodies were developed by constructing an immune library from mRNA obtained from two celiac patients with a high humoral response to gluten-related proteins. The resulting library (composed by 1.1x107) was subjected to selection against gliadin using phage display technology. Following several rounds of selection, the Fab-C was selected, and demonstrated good functionality in ELISA tests, presenting a limit of detection of 15 mg/kg for detection of gluten in spiked mixtures and food products. The methodology can discriminate gluten-free products according to the current legislation.
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Affiliation(s)
- Eduardo Garcia-Calvo
- Departamento de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Aina García-García
- Departamento de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Santiago Rodríguez Gómez
- Departamento de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Sergio Farrais
- Servicio de Medicina Digestiva, Hospital Universitario Fundación Jiménez Díaz, 28040, Madrid, Spain
| | - Rosario Martín
- Departamento de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Teresa García
- Departamento de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040, Madrid, Spain
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Torres Costa KC, Santana Vieira Santos V, Rezende Vaz E, Natalie Cirilo Gimenes S, Ian Veloso Correia L, Brito de Souza J, de Almeida Araújo Santos F, de Melo Rodrigues V, Ricardo Goulart L, Alonso Goulart V. A novel peptide able to reduce PLA 2 activity and modulate inflammatory cytokine production. Toxicon 2023; 231:107207. [PMID: 37364619 DOI: 10.1016/j.toxicon.2023.107207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/19/2023] [Accepted: 06/22/2023] [Indexed: 06/28/2023]
Abstract
Phospholipases A2 (PLA2s) are associated with inflammatory response, performing a complex process involving, specially, cytokines. The excess of pro-inflammatory cytokines induces a chronic inflammatory response and can cause several disorders in the body. Therefore, the inhibition or regulation of cytokines' signaling pathways is a target for new treatment development strategies. Thus, this study aimed to select PLA2 inhibitor mimetic peptides through phage display technology with anti-inflammatory activity. Specific mimetic peptides were selected using BpPLA2-TXI, a PLA2 isolated from Bothrops pauloensis, as a target, and γCdcPL, a PLA2 inhibitor isolated from Crotalus durissus collilineatus, which was used as a competitor during the elution step. We selected the peptide C2PD, which seems to play a pivotal role in the modulation of IL-6, IL-1β, and IL-10 cytokines in inflammatory cells. The C2PD showed a significant reduction in PLA2 activity. Furthermore, the synthetic peptide was tested in PBMC and showed a significant down-modulation of IL-6 and IL-1β release, whereas IL-10 responses were up-regulated. Our findings suggest that this novel peptide may be a potential therapeutic candidate for the treatment of inflammatory diseases, mainly due to its anti-inflammatory properties and absence of cytotoxicity.
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Affiliation(s)
- Kellen Cristina Torres Costa
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlândia, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Minas Gerais, Brazil.
| | - Vanessa Santana Vieira Santos
- Laboratory of Environmental Health, Department of Environmental Health, Institute of Biotechnology, Federal University of Uberlandia, Santa Monica Campus, Avenida João Naves de Ávila, 2121, 38.408-100, Uberlandia, Minas Gerais, Brazil
| | - Emília Rezende Vaz
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlândia, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Minas Gerais, Brazil
| | | | - Lucas Ian Veloso Correia
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlândia, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Minas Gerais, Brazil
| | - Jessica Brito de Souza
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlândia, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Minas Gerais, Brazil
| | - Fabiana de Almeida Araújo Santos
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlândia, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Minas Gerais, Brazil
| | - Veridiana de Melo Rodrigues
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlândia, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Minas Gerais, Brazil; Laboratory of Biochemistry and Animal Toxins, Institute of Biotechnology, Federal University of Uberlândia, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Minas Gerais, Brazil
| | - Luiz Ricardo Goulart
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlândia, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Minas Gerais, Brazil
| | - Vivian Alonso Goulart
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlândia, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Minas Gerais, Brazil
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Knejski PP, Erramilli SK, Kossiakoff AA. Chaperone-assisted cryo-EM structure of P. aeruginosa PhuR reveals molecular basis for heme uptake. bioRxiv 2023:2023.08.01.551527. [PMID: 37577460 PMCID: PMC10418163 DOI: 10.1101/2023.08.01.551527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Pathogenic bacteria, such as Pseudomonas aeruginosa, depend on scavenging heme for the acquisition of iron, an essential nutrient. The TonB-dependent transporter (TBDT) PhuR is the major heme uptake protein in P. aeruginosa clinical isolates. However, a comprehensive understanding of heme recognition and TBDT transport mechanisms, especially PhuR, remains limited. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) and a phage display-generated synthetic antibody (sAB) as a fiducial marker to enable the determination of a high-resolution (2.5 Å) structure of PhuR with a bound heme. Notably, the structure reveals iron coordination by Y529 on a conserved extracellular loop, shedding light on the role of tyrosine in heme binding. Biochemical assays and negative-stain EM demonstrated that the sAB specifically targets the heme-bound state of PhuR. These findings provide insights into PhuR's heme binding and offer a template for developing conformation-specific sABs against outer membrane proteins (OMPs) for structure-function investigations.
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Affiliation(s)
- Paweł P. Knejski
- Deparment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
- Present address: Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Satchal K. Erramilli
- Deparment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Anthony A. Kossiakoff
- Deparment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
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Ma P, Liu J, Pang S, Zhou W, Yu H, Wang M, Dong T, Wang Y, Wang Q, Liu A. Biopanning of specific peptide for SARS-CoV-2 nucleocapsid protein and enzyme-linked immunosorbent assay-based antigen assay. Anal Chim Acta 2023; 1264:341300. [PMID: 37230729 DOI: 10.1016/j.aca.2023.341300] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023]
Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide which triggered serious public health issues. The search for rapid and accurate diagnosis, effective prevention, and treatment is urgent. The nucleocapsid protein (NP) of SARS-CoV-2 is one of the main structural proteins expressed and most abundant in the virus, and is considered a diagnostic marker for the accurate and sensitive detection of SARS-CoV-2. Herein, we report the screening of specific peptides from the pIII phage library that bind to SARS-CoV-2 NP. The phage monoclone expressing cyclic peptide N1 (peptide sequence, ACGTKPTKFC, with C&C bridged by disulfide bonding) specifically recognizes SARS-CoV-2 NP. Molecular docking studies reveal that the identified peptide is bound to the "pocket" region on the SARS-CoV-2 NP N-terminal domain mainly by forming a hydrogen bonding network and through hydrophobic interaction. Peptide N1 with the C-terminal linker was synthesized as the capture probe for SARS-CoV-2 NP in ELISA. The peptide-based ELISA was capable of assaying SARS-CoV-2 NP at concentrations as low as 61 pg/mL (∼1.2 pM). Furthermore, the as-proposed method could detect the SARS-CoV-2 virus at limits as low as 50 TCID50 (median tissue culture infective dose)/mL. This study demonstrates that selected peptides are powerful biomolecular tools for SARS-CoV-2 detection, providing a new and inexpensive method of rapidly screening infections as well as rapidly diagnosing coronavirus disease 2019 patients.
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Affiliation(s)
- Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Wenhao Zhou
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haipeng Yu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Yanbo Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Qiqin Wang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, 510632, China.
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China.
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Lai JY, Corona A, Ng CL, Tramontano E, Choong YS, Lim TS. Naïve antibody library derived monoclonal antibody against VP35 of Ebola virus. Int J Biol Macromol 2023:125571. [PMID: 37379953 DOI: 10.1016/j.ijbiomac.2023.125571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/13/2023] [Accepted: 06/24/2023] [Indexed: 06/30/2023]
Abstract
Ebola virus is notorious for causing severe and even deadly haemorrhagic fever in infected humans and non-human primates. The high fatality rate of Ebola virus disease (EVD) has highlighted the need for effective diagnosis and treatment. Two monoclonal antibodies (mAbs) have been approved by USFDA for treatment of EVD. Virus surface glycoprotein is the common target for diagnostic and therapy including vaccines. Even so, VP35, a viral RNA polymerase cofactor and interferon inhibitor could be a potential target to curb EVD. The present work describes the isolation of three mAb clones from a phage-displayed human naïve scFv library against recombinant VP35. The clones showed binding against rVP35 in vitro and inhibition of VP35 in luciferase reporter gene assay. Structural modelling analysis was also carried out to identify the binding interactions involved in the antibody-antigen interaction model. This allows some insight into the "fitness" of the binding pocket between the paratope and target epitope which would be useful for the design of new mAbs through in silico means in the future. In conclusion, the information obtained from the 3 isolated mAbs could be potentially useful in the quest to improve VP35 targeting for therapeutic development in the future.
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Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Chong Lee Ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - 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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Kim T, Cho BK, Kim YH, Min J. Novel peptide identified from viable-cell based phage display technique regulates growth cycle of Daphnia magna. Environ Pollut 2023; 327:121556. [PMID: 37044252 DOI: 10.1016/j.envpol.2023.121556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/27/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Phage display is a widely used technique for selecting specific binding peptides, but presenting antigens in their natural form can be challenging, as protein coating may induce structural changes. In this study, we employed a whole cell-based phage display technique without a coating step to select peptides that bind specifically to Daphnia magna eggs. Boiled eggs were used as a control to ensure that antigens were presented in their natural forms. We identified a peptide, DEP1 (LYALPLSHLKSHGGG), with the highest binding affinity to D. magna eggs. DEP1 did not affect zebrafish eggs, but it inhibited normal hatching and reproductive ability in D. magna eggs, and hindered growth in neonates before their first ecdysis. Morphological analysis revealed that DEP1 caused intestinal damage and tissue abnormalities. Our findings demonstrate that the whole cell-based phage display technique is successful in presenting antigens in their natural form, and that the DEP1 peptide can be applied to regulate the growth cycle of D. magna. These results have implications for the use of phage display in environmental research and the potential use of DEP1 for hazardous organisms in aquatic systems.
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Affiliation(s)
- Taehwan Kim
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University, Chungdae-ro 1, Seowon-Gu, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Jiho Min
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea.
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Pierzynowska K, Morcinek-Orłowska J, Gaffke L, Jaroszewicz W, Skowron PM, Węgrzyn G. Applications of the phage display technology in molecular biology, biotechnology and medicine. Crit Rev Microbiol 2023:1-41. [PMID: 37270791 DOI: 10.1080/1040841x.2023.2219741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 10/17/2022] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
The phage display technology is based on the presentation of peptide sequences on the surface of virions of bacteriophages. Its development led to creation of sophisticated systems based on the possibility of the presentation of a huge variability of peptides, attached to one of proteins of bacteriophage capsids. The use of such systems allowed for achieving enormous advantages in the processes of selection of bioactive molecules. In fact, the phage display technology has been employed in numerous fields of biotechnology, as diverse as immunological and biomedical applications (in both diagnostics and therapy), the formation of novel materials, and many others. In this paper, contrary to many other review articles which were focussed on either specific display systems or the use of phage display in selected fields, we present a comprehensive overview of various possibilities of applications of this technology. We discuss an usefulness of the phage display technology in various fields of science, medicine and the broad sense of biotechnology. This overview indicates the spread and importance of applications of microbial systems (exemplified by the phage display technology), pointing to the possibility of developing such sophisticated tools when advanced molecular methods are used in microbiological studies, accompanied with understanding of details of structures and functions of microbial entities (bacteriophages in this case).
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Affiliation(s)
- Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Weronika Jaroszewicz
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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Shi YF. Determination of the affinity constants for phage display albumin-binding peptides. PeerJ 2023; 11:e15078. [PMID: 37250708 PMCID: PMC10215749 DOI: 10.7717/peerj.15078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/24/2023] [Indexed: 05/31/2023] Open
Abstract
Background Phage display technology has been established as a powerful screening approach to select ligands or peptides for binding to proteins. Despite rapid growth in the field, there has been a relative dearth of quantitative criteria to measure the effectiveness of the process of phage display screening. Since human serum albumin (HSA) has been extensively studied as a drug carrier to extend the plasma half-life of protein therapeutics, the use of phage display technology is required for identifying albumin-binding peptides as the very promising strategy of albumin-binding against albumin fusion. The construction of albumin-binding drug requires the assessment of a large quantity of HSA-binding peptide (HSA binder) candidates for conjugation with therapeutic proteins. The use of the linear epitope mapping method has allowed researchers to discover many HSA-binding peptides. However, it may be inefficient to select these peptides based on sequence identity via randomly sequencing individual phage clones from enrichment pools. Method Here, a simple assessment method to facilitate phage display selection of HSA-binding peptides was recommended. With experimentally determined phage titer, one can calculate the specificity ratios, the recovery yields and the relative dissociation constants, which are defined as quantitative criteria for panning and characterization of the binding phage fused peptides. Results Consequently, this approach may not only enable more rapid and low-cost phage display screening, but also efficiently reduce pseudo-positive phages selected as HSA binders for conjugation with therapeutic proteins.
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Affiliation(s)
- Yi-Feng Shi
- Department of Biotechnology, School of Biological Engineering, Dalian Polytechnic University, Dalian, Liaoning Province, P. R. China
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Hussain W, Yang X, Ullah M, Wang H, Aziz A, Xu F, Asif M, Ullah MW, Wang S. Genetic engineering of bacteriophages: Key concepts, strategies, and applications. Biotechnol Adv 2023; 64:108116. [PMID: 36773707 DOI: 10.1016/j.biotechadv.2023.108116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Bacteriophages are the most abundant biological entity in the world and hold a tremendous amount of unexplored genetic information. Since their discovery, phages have drawn a great deal of attention from researchers despite their small size. The development of advanced strategies to modify their genomes and produce engineered phages with desired traits has opened new avenues for their applications. This review presents advanced strategies for developing engineered phages and their potential antibacterial applications in phage therapy, disruption of biofilm, delivery of antimicrobials, use of endolysin as an antibacterial agent, and altering the phage host range. Similarly, engineered phages find applications in eukaryotes as a shuttle for delivering genes and drugs to the targeted cells, and are used in the development of vaccines and facilitating tissue engineering. The use of phage display-based specific peptides for vaccine development, diagnostic tools, and targeted drug delivery is also discussed in this review. The engineered phage-mediated industrial food processing and biocontrol, advanced wastewater treatment, phage-based nano-medicines, and their use as a bio-recognition element for the detection of bacterial pathogens are also part of this review. The genetic engineering approaches hold great potential to accelerate translational phages and research. Overall, this review provides a deep understanding of the ingenious knowledge of phage engineering to move them beyond their innate ability for potential applications.
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Affiliation(s)
- Wajid Hussain
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaohan Yang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mati Ullah
- Department of Biotechnology, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huan Wang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ayesha Aziz
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fang Xu
- Huazhong University of Science and Technology Hospital, Wuhan 430074, China
| | - Muhammad Asif
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Shenqi Wang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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44
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Cho CH, Park CY, Chun HS, Park TJ, Park JP. Antibody-free and selective detection of okadaic acid using an affinity peptide-based indirect assay. Food Chem 2023; 422:136243. [PMID: 37141762 DOI: 10.1016/j.foodchem.2023.136243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
Okadaic acid (OA) is a type of marine biotoxin produced by some species of dinoflagellates in marine environments. Consumption of shellfish contaminated with OA can cause diarrhetic shellfish poisoning (DSP) in humans with symptoms that typically include abdominal pain, diarrhea and vomiting. In this study, we developed an affinity peptide-based direct competition enzyme-linked immunosorbent assay (dc-ELISA) for the detection of OA in real samples. The OA-specific peptide was successfully identified via M13 biopanning and a series of peptides were chemically synthesized and characterized their recognition activities. The dc-ELISA system showed good sensitivity and selectivity with a half-maximal inhibitory concentration (IC50) of 148.7 ng/mL and a limit of detection (LOD) of 5.41 ng/mL (equivalent, 21.52 ng/g). Moreover, the effectiveness of the developed dc-ELISA was validated using OA-spiked shellfish samples, and the developed dc-ELISA showed a high recovery rate. These results suggest that the affinity peptide-based dc-ELISA can be a promising tool for detecting OA in shellfish samples.
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Affiliation(s)
- Chae Hwan Cho
- Department of Food Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Chan Yeong Park
- Department of Chemistry, Institute of Interdisciplinary Convergence Research, Research Institute of Chem-Bio Diagnostic Technology, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Hyang Sook Chun
- Department of Food Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Tae Jung Park
- Department of Chemistry, Institute of Interdisciplinary Convergence Research, Research Institute of Chem-Bio Diagnostic Technology, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea.
| | - Jong Pil Park
- Department of Food Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea.
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Kim JH, Cho CH, Shin JH, Yang JC, Park TJ, Park J, Park JP. Highly sensitive and label-free detection of influenza H5N1 viral proteins using affinity peptide and porous BSA/MXene nanocomposite electrode. Anal Chim Acta 2023; 1251:341018. [PMID: 36925304 DOI: 10.1016/j.aca.2023.341018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 02/26/2023]
Abstract
Influenza viruses are known to cause pandemic flu through inter-human and animal-to-human transmissions. Neuraminidase (NA), which is a surface glycoprotein of both influenza A and B viruses, is a minor immunogenic determinant; however, it has been proposed as an ideal candidate for a real testing. We successfully identified an affinity peptide which is specific to the influenza H5N1 virus NA via phage display technique and observed initially its binding affinities using enzyme-linked immunosorbent assay (ELISA). In addition, four synthetic peptides were chemically synthesized to develop an affinity peptide-based electrochemical biosensing system. Among all peptides tested, INA BP2 was selected as a potential candidate and subjected to square-wave voltammetry (SWV) for evaluating their detection performance. To enhance analytical performance, a three-dimensional porous bovine serum albumin (BSA)-MXene (BSA/MXene) matrix was applied. The surface morphology of the BSA/MXene film-deposited electrode was analyzed using X-ray photoelectron spectroscopy (XPS), field-emission scanning electron microscopy (FE-SEM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Using SWV measurement, the BSA/MXene nanocomposite-based peptide sensor exhibited significant the dissociation constant (Kd = 9.34 ± 1.20 nM) and the limit of detection (LOD, 0.098 nM), resulting in good reproducibility, stability and recovery, even in the presence with spiked human plasma. These results demonstrate an alternative way of new bioanalytical sensing platform for developing more desirable sensitivity in other virus detection.
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Affiliation(s)
- Ji Hong Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chae Hwan Cho
- Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Jae Hwan Shin
- Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Jin Chul Yang
- Department of Polymer Science & Engineering, Kyungpook National University, 80 Daehak-ro, Daegu, 41566, Republic of Korea
| | - Tae Jung Park
- Department of Chemistry, Institute of Interdisciplinary Convergence Research, Research Institute of Chem-Bio Diagnostic Technology, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Jinyoung Park
- Department of Polymer Science & Engineering, Kyungpook National University, 80 Daehak-ro, Daegu, 41566, Republic of Korea.
| | - Jong Pil Park
- Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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Makky S, Abdelrahman F, Easwaran M, Safwat A, El-Shibiny A. Phages as delivery vehicles and phage display. Prog Mol Biol Transl Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Pung HS, Tye GJ, Leow CH, Ng WK, Lai NS. Generation of peptides using phage display technology for cancer diagnosis and molecular imaging. Mol Biol Rep 2023; 50:4653-4664. [PMID: 37014570 PMCID: PMC10072011 DOI: 10.1007/s11033-023-08380-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
Cancer is one of the leading causes of mortality worldwide; nearly 10 million people died from it in 2020. The high mortality rate results from the lack of effective screening approaches where early detection cannot be achieved, reducing the chance of early intervention to prevent cancer development. Non-invasive and deep-tissue imaging is useful in cancer diagnosis, contributing to a visual presentation of anatomy and physiology in a rapid and safe manner. Its sensitivity and specificity can be enhanced with the application of targeting ligands with the conjugation of imaging probes. Phage display is a powerful technology to identify antibody- or peptide-based ligands with effective binding specificity against their target receptor. Tumour-targeting peptides exhibit promising results in molecular imaging, but the application is limited to animals only. Modern nanotechnology facilitates the combination of peptides with various nanoparticles due to their superior characteristics, rendering novel strategies in designing more potent imaging probes for cancer diagnosis and targeting therapy. In the end, a myriad of peptide candidates that aimed for different cancers diagnosis and imaging in various forms of research were reviewed.
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Affiliation(s)
- Hai Shin Pung
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Woei Kean Ng
- Faculty of Medicine, AIMST University, Bedong, Kedah, 08100, Malaysia
| | - Ngit Shin Lai
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia.
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Skottrup PD, Ksiazek M, Potempa J. Phage display selection of human single domain antibodies towards karilysin, a metalloproteinase and secreted virulence factor from Tannerella forsythia. J Immunol Methods 2023;:113458. [PMID: 36921710 DOI: 10.1016/j.jim.2023.113458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 01/24/2023] [Accepted: 03/11/2023] [Indexed: 03/14/2023]
Abstract
Metalloproteases derived from microbial pathogens are important virulence factors contributing to evasion of antimicrobial mechanisms of the innate immune system. Karilysin is a metalloprotease recently discovered in the periodonto-pathogen Tanneralla forsythia and currently no monoclonal antibodies exist against karilysin, which is a gap in the molecular toolbox for structure-function studies of karilysin. In this study we have used phage display for fast selection of single domain antibodies (VHs) towards the karilysin catalytic domain (Kly18) using a human domain library based on a VH framework. Following five panning rounds, phage clones were sequenced, and three unique sequences were identified (termed Kly18-VHI-III). Initial screens identified Kly18-VHII-phage as capable of inhibiting Kly18 proteolytic activity. The free Kly18-VHII was expressed in the periplasmic space of BL21 E. coli using the pEt22b (+) vector and purified by IMAC and the inhibition capacity of purified Kly18-VHII was confirmed. The data presented in this study provides input to the molecular toolbox for the study of karilysin and Kly18-VHII could serve as a lead molecule for development of a karilysin-specific inhibitor.
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Kim SH, Yun HY, Jeong HJ. Generation of a novel antibody against BxPrx, a diagnostic marker of pine wilt disease. Mol Biol Rep 2023. [PMID: 36899277 DOI: 10.1007/s11033-023-08342-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/15/2023] [Indexed: 03/12/2023]
Abstract
BACKGROUND Bursaphelenchus xylophilus is a pathogenic nematode that causes pine wilt disease (PWD). To prevent the rapid spread of this pathogen, developing a method for rapid and accurate detection of B. xylophilus is required. METHODS AND RESULTS In this study, we produced a B. xylophilus peroxiredoxin (BxPrx), which is a protein that is overexpressed in B. xylophilus. Using recombinant BxPrx as an antigen, we generated and selected a novel antibody that binds to BxPrx via phage display and biopanning. We subcloned the anti-BxPrx single-chain variable fragment-encoding phagemid DNA to mammalian expression vector. We transfected the plasmid into mammalian cells and produced a highly sensitive recombinant antibody that enabled nanogram order detection of BxPrx. CONCLUSION The sequence of anti-BxPrx antibody as well as the rapid immunoassay system described here can be applied for rapid and accurate diagnosis of PWD.
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Valadan R, Dabiri M, Tehrani M, Hashemi Tabar G, Rafiei A. A cell-based subtractive panning strategy for selection of conformation-specific single-chain variable-fragment (scFv) against dimerization domain of EGFR. J Immunol Methods 2023; 515:113456. [PMID: 36898519 DOI: 10.1016/j.jim.2023.113456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023]
Abstract
BACKGROUND AND OBJECTIVE Overexpression of EGFR, a member of the ErbB receptor family, has been observed in several cancers and causes resistance to therapeutic antibodies, such as Herceptin. In this study, we produced a recombinant single-chain variable fragment (scFv) antibody against the EGFR dimerization domain. METHODS The recombinant scFv was generated using a cell-based subtractive panning strategy. Subtractive panning was performed on a genetically engineered, VERO/EGFR, cells as well as a triple-negative breast cancer, MDA-MB-468, cells. Phage cell-ELISA was used to monitor the binding of the selected scFvs to the dimerization domain of EGFR. Inhibition of EGFR and HER2 dimerization by the produced scFvs were finally evaluated using the dimerization inhibition test and the expression of apoptosis-related genes were measured using the quantitative RT-PCR. RESULTS PCR fingerprinting results showed a uniform digestion pattern following the third round of panning that confirmed the success of subtractive panning. Moreover, cell-ELISA validated the reactivity of the produced scFvs to EGFR following stimulation with EGF. Dimerization inhibition test showed the capacity of the scFvs to inhibit EGFR and HER2 dimerization. Investigation of apoptosis-related genes showed that treatment with the scFv antibody caused increased Bax and decreased Bcl2 expression. CONCLUSIONS Directed HER2 targeting was shown to be effective enough to block the functional domain of the cell receptor and its intracellular signaling pathway. The subtractive panning strategy used in this study could control the process of directed selection of specific antibodies against the dimerization domain of EGFR. Selected antibodies might then be functionally tested for antitumor effects in both in vitro and in vivo studies.
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Affiliation(s)
- Reza Valadan
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.; Molecular and Cell Biology Research Center (MCBRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mina Dabiri
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.; Molecular and Cell Biology Research Center (MCBRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohsen Tehrani
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.; Molecular and Cell Biology Research Center (MCBRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Gholamreza Hashemi Tabar
- Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran; Department of Pathobiology, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Alireza Rafiei
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.; Molecular and Cell Biology Research Center (MCBRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran..
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